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a/_sources/biodm/biodm.api.rst.txt b/_sources/biodm/biodm.api.rst.txt new file mode 100644 index 0000000..35a53c9 --- /dev/null +++ b/_sources/biodm/biodm.api.rst.txt @@ -0,0 +1,7 @@ +biodm.api module +================ + +.. automodule:: biodm.api + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.basics.k8scontroller.rst.txt b/_sources/biodm/biodm.basics.k8scontroller.rst.txt new file mode 100644 index 0000000..d1fbbb4 --- /dev/null +++ b/_sources/biodm/biodm.basics.k8scontroller.rst.txt @@ -0,0 +1,7 @@ +biodm.basics.k8scontroller module +================================= + +.. automodule:: biodm.basics.k8scontroller + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.basics.rootcontroller.rst.txt b/_sources/biodm/biodm.basics.rootcontroller.rst.txt new file mode 100644 index 0000000..b6b5354 --- /dev/null +++ b/_sources/biodm/biodm.basics.rootcontroller.rst.txt @@ -0,0 +1,7 @@ +biodm.basics.rootcontroller module +================================== + +.. automodule:: biodm.basics.rootcontroller + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.basics.rst.txt b/_sources/biodm/biodm.basics.rst.txt new file mode 100644 index 0000000..962da4e --- /dev/null +++ b/_sources/biodm/biodm.basics.rst.txt @@ -0,0 +1,19 @@ +biodm.basics package +==================== + +Submodules +---------- + +.. toctree:: + :maxdepth: 4 + + biodm.basics.k8scontroller + biodm.basics.rootcontroller + +Module contents +--------------- + +.. automodule:: biodm.basics + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.component.rst.txt b/_sources/biodm/biodm.component.rst.txt new file mode 100644 index 0000000..e2cde55 --- /dev/null +++ b/_sources/biodm/biodm.component.rst.txt @@ -0,0 +1,7 @@ +biodm.component module +====================== + +.. automodule:: biodm.component + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.components.controllers.admincontroller.rst.txt b/_sources/biodm/biodm.components.controllers.admincontroller.rst.txt new file mode 100644 index 0000000..ab0356c --- /dev/null +++ b/_sources/biodm/biodm.components.controllers.admincontroller.rst.txt @@ -0,0 +1,7 @@ +biodm.components.controllers.admincontroller module +=================================================== + +.. automodule:: biodm.components.controllers.admincontroller + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.components.controllers.controller.rst.txt b/_sources/biodm/biodm.components.controllers.controller.rst.txt new file mode 100644 index 0000000..fa9173e --- /dev/null +++ b/_sources/biodm/biodm.components.controllers.controller.rst.txt @@ -0,0 +1,7 @@ +biodm.components.controllers.controller module +============================================== + +.. automodule:: biodm.components.controllers.controller + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.components.controllers.resourcecontroller.rst.txt b/_sources/biodm/biodm.components.controllers.resourcecontroller.rst.txt new file mode 100644 index 0000000..cf4efdb --- /dev/null +++ b/_sources/biodm/biodm.components.controllers.resourcecontroller.rst.txt @@ -0,0 +1,7 @@ +biodm.components.controllers.resourcecontroller module +====================================================== + +.. automodule:: biodm.components.controllers.resourcecontroller + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.components.controllers.rst.txt b/_sources/biodm/biodm.components.controllers.rst.txt new file mode 100644 index 0000000..8708d3a --- /dev/null +++ b/_sources/biodm/biodm.components.controllers.rst.txt @@ -0,0 +1,21 @@ +biodm.components.controllers package +==================================== + +Submodules +---------- + +.. toctree:: + :maxdepth: 4 + + biodm.components.controllers.admincontroller + biodm.components.controllers.controller + biodm.components.controllers.resourcecontroller + biodm.components.controllers.s3controller + +Module contents +--------------- + +.. automodule:: biodm.components.controllers + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.components.controllers.s3controller.rst.txt b/_sources/biodm/biodm.components.controllers.s3controller.rst.txt new file mode 100644 index 0000000..1535989 --- /dev/null +++ b/_sources/biodm/biodm.components.controllers.s3controller.rst.txt @@ -0,0 +1,7 @@ +biodm.components.controllers.s3controller module +================================================ + +.. automodule:: biodm.components.controllers.s3controller + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.components.rst.txt b/_sources/biodm/biodm.components.rst.txt new file mode 100644 index 0000000..7402c2e --- /dev/null +++ b/_sources/biodm/biodm.components.rst.txt @@ -0,0 +1,27 @@ +biodm.components package +======================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + biodm.components.controllers + biodm.components.services + +Submodules +---------- + +.. toctree:: + :maxdepth: 4 + + biodm.components.table + +Module contents +--------------- + +.. automodule:: biodm.components + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.components.services.dbservice.rst.txt b/_sources/biodm/biodm.components.services.dbservice.rst.txt new file mode 100644 index 0000000..259f8d6 --- /dev/null +++ b/_sources/biodm/biodm.components.services.dbservice.rst.txt @@ -0,0 +1,7 @@ +biodm.components.services.dbservice module +========================================== + +.. automodule:: biodm.components.services.dbservice + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.components.services.k8service.rst.txt b/_sources/biodm/biodm.components.services.k8service.rst.txt new file mode 100644 index 0000000..b369418 --- /dev/null +++ b/_sources/biodm/biodm.components.services.k8service.rst.txt @@ -0,0 +1,7 @@ +biodm.components.services.k8service module +========================================== + +.. automodule:: biodm.components.services.k8service + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.components.services.kcservice.rst.txt b/_sources/biodm/biodm.components.services.kcservice.rst.txt new file mode 100644 index 0000000..c9dbc43 --- /dev/null +++ b/_sources/biodm/biodm.components.services.kcservice.rst.txt @@ -0,0 +1,7 @@ +biodm.components.services.kcservice module +========================================== + +.. automodule:: biodm.components.services.kcservice + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.components.services.rst.txt b/_sources/biodm/biodm.components.services.rst.txt new file mode 100644 index 0000000..4951f6d --- /dev/null +++ b/_sources/biodm/biodm.components.services.rst.txt @@ -0,0 +1,21 @@ +biodm.components.services package +================================= + +Submodules +---------- + +.. toctree:: + :maxdepth: 4 + + biodm.components.services.dbservice + biodm.components.services.k8service + biodm.components.services.kcservice + biodm.components.services.s3service + +Module contents +--------------- + +.. automodule:: biodm.components.services + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.components.services.s3service.rst.txt b/_sources/biodm/biodm.components.services.s3service.rst.txt new file mode 100644 index 0000000..af971e5 --- /dev/null +++ b/_sources/biodm/biodm.components.services.s3service.rst.txt @@ -0,0 +1,7 @@ +biodm.components.services.s3service module +========================================== + +.. automodule:: biodm.components.services.s3service + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.components.table.rst.txt b/_sources/biodm/biodm.components.table.rst.txt new file mode 100644 index 0000000..1b31acf --- /dev/null +++ b/_sources/biodm/biodm.components.table.rst.txt @@ -0,0 +1,7 @@ +biodm.components.table module +============================= + +.. automodule:: biodm.components.table + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.config.rst.txt b/_sources/biodm/biodm.config.rst.txt new file mode 100644 index 0000000..0e77756 --- /dev/null +++ b/_sources/biodm/biodm.config.rst.txt @@ -0,0 +1,7 @@ +biodm.config module +=================== + +.. automodule:: biodm.config + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.error.rst.txt b/_sources/biodm/biodm.error.rst.txt new file mode 100644 index 0000000..a03f9b1 --- /dev/null +++ b/_sources/biodm/biodm.error.rst.txt @@ -0,0 +1,7 @@ +biodm.error module +================== + +.. automodule:: biodm.error + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.exceptions.rst.txt b/_sources/biodm/biodm.exceptions.rst.txt new file mode 100644 index 0000000..e740dba --- /dev/null +++ b/_sources/biodm/biodm.exceptions.rst.txt @@ -0,0 +1,7 @@ +biodm.exceptions module +======================= + +.. automodule:: biodm.exceptions + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.managers.dbmanager.rst.txt b/_sources/biodm/biodm.managers.dbmanager.rst.txt new file mode 100644 index 0000000..35a74d6 --- /dev/null +++ b/_sources/biodm/biodm.managers.dbmanager.rst.txt @@ -0,0 +1,7 @@ +biodm.managers.dbmanager module +=============================== + +.. automodule:: biodm.managers.dbmanager + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.managers.k8smanager.rst.txt b/_sources/biodm/biodm.managers.k8smanager.rst.txt new file mode 100644 index 0000000..39f508d --- /dev/null +++ b/_sources/biodm/biodm.managers.k8smanager.rst.txt @@ -0,0 +1,7 @@ +biodm.managers.k8smanager module +================================ + +.. automodule:: biodm.managers.k8smanager + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.managers.kcmanager.rst.txt b/_sources/biodm/biodm.managers.kcmanager.rst.txt new file mode 100644 index 0000000..7a30fdc --- /dev/null +++ b/_sources/biodm/biodm.managers.kcmanager.rst.txt @@ -0,0 +1,7 @@ +biodm.managers.kcmanager module +=============================== + +.. automodule:: biodm.managers.kcmanager + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.managers.rst.txt b/_sources/biodm/biodm.managers.rst.txt new file mode 100644 index 0000000..4ef49a5 --- /dev/null +++ b/_sources/biodm/biodm.managers.rst.txt @@ -0,0 +1,21 @@ +biodm.managers package +====================== + +Submodules +---------- + +.. toctree:: + :maxdepth: 4 + + biodm.managers.dbmanager + biodm.managers.k8smanager + biodm.managers.kcmanager + biodm.managers.s3manager + +Module contents +--------------- + +.. automodule:: biodm.managers + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.managers.s3manager.rst.txt b/_sources/biodm/biodm.managers.s3manager.rst.txt new file mode 100644 index 0000000..c8e09d7 --- /dev/null +++ b/_sources/biodm/biodm.managers.s3manager.rst.txt @@ -0,0 +1,7 @@ +biodm.managers.s3manager module +=============================== + +.. automodule:: biodm.managers.s3manager + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.rst.txt b/_sources/biodm/biodm.rst.txt new file mode 100644 index 0000000..f6a86bf --- /dev/null +++ b/_sources/biodm/biodm.rst.txt @@ -0,0 +1,36 @@ +biodm package +============= + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + biodm.basics + biodm.components + biodm.managers + biodm.schemas + biodm.tables + biodm.utils + +Submodules +---------- + +.. toctree:: + :maxdepth: 4 + + biodm.api + biodm.component + biodm.config + biodm.error + biodm.exceptions + biodm.scope + +Module contents +--------------- + +.. automodule:: biodm + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.schemas.group.rst.txt b/_sources/biodm/biodm.schemas.group.rst.txt new file mode 100644 index 0000000..e9236d6 --- /dev/null +++ b/_sources/biodm/biodm.schemas.group.rst.txt @@ -0,0 +1,7 @@ +biodm.schemas.group module +========================== + +.. automodule:: biodm.schemas.group + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.schemas.k8sinstance.rst.txt b/_sources/biodm/biodm.schemas.k8sinstance.rst.txt new file mode 100644 index 0000000..0332a8c --- /dev/null +++ b/_sources/biodm/biodm.schemas.k8sinstance.rst.txt @@ -0,0 +1,7 @@ +biodm.schemas.k8sinstance module +================================ + +.. automodule:: biodm.schemas.k8sinstance + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.schemas.listgroup.rst.txt b/_sources/biodm/biodm.schemas.listgroup.rst.txt new file mode 100644 index 0000000..d1ff5c9 --- /dev/null +++ b/_sources/biodm/biodm.schemas.listgroup.rst.txt @@ -0,0 +1,7 @@ +biodm.schemas.listgroup module +============================== + +.. automodule:: biodm.schemas.listgroup + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.schemas.rst.txt b/_sources/biodm/biodm.schemas.rst.txt new file mode 100644 index 0000000..8275025 --- /dev/null +++ b/_sources/biodm/biodm.schemas.rst.txt @@ -0,0 +1,22 @@ +biodm.schemas package +===================== + +Submodules +---------- + +.. toctree:: + :maxdepth: 4 + + biodm.schemas.group + biodm.schemas.k8sinstance + biodm.schemas.listgroup + biodm.schemas.upload + biodm.schemas.user + +Module contents +--------------- + +.. automodule:: biodm.schemas + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.schemas.upload.rst.txt b/_sources/biodm/biodm.schemas.upload.rst.txt new file mode 100644 index 0000000..2610475 --- /dev/null +++ b/_sources/biodm/biodm.schemas.upload.rst.txt @@ -0,0 +1,7 @@ +biodm.schemas.upload module +=========================== + +.. automodule:: biodm.schemas.upload + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.schemas.user.rst.txt b/_sources/biodm/biodm.schemas.user.rst.txt new file mode 100644 index 0000000..9510367 --- /dev/null +++ b/_sources/biodm/biodm.schemas.user.rst.txt @@ -0,0 +1,7 @@ +biodm.schemas.user module +========================= + +.. automodule:: biodm.schemas.user + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.scope.rst.txt b/_sources/biodm/biodm.scope.rst.txt new file mode 100644 index 0000000..157d5cc --- /dev/null +++ b/_sources/biodm/biodm.scope.rst.txt @@ -0,0 +1,7 @@ +biodm.scope module +================== + +.. automodule:: biodm.scope + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.tables.asso.rst.txt b/_sources/biodm/biodm.tables.asso.rst.txt new file mode 100644 index 0000000..43bb069 --- /dev/null +++ b/_sources/biodm/biodm.tables.asso.rst.txt @@ -0,0 +1,7 @@ +biodm.tables.asso module +======================== + +.. automodule:: biodm.tables.asso + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.tables.group.rst.txt b/_sources/biodm/biodm.tables.group.rst.txt new file mode 100644 index 0000000..fae657d --- /dev/null +++ b/_sources/biodm/biodm.tables.group.rst.txt @@ -0,0 +1,7 @@ +biodm.tables.group module +========================= + +.. automodule:: biodm.tables.group + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.tables.history.rst.txt b/_sources/biodm/biodm.tables.history.rst.txt new file mode 100644 index 0000000..0a6ec55 --- /dev/null +++ b/_sources/biodm/biodm.tables.history.rst.txt @@ -0,0 +1,7 @@ +biodm.tables.history module +=========================== + +.. automodule:: biodm.tables.history + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.tables.k8sinstance.rst.txt b/_sources/biodm/biodm.tables.k8sinstance.rst.txt new file mode 100644 index 0000000..37ca361 --- /dev/null +++ b/_sources/biodm/biodm.tables.k8sinstance.rst.txt @@ -0,0 +1,7 @@ +biodm.tables.k8sinstance module +=============================== + +.. automodule:: biodm.tables.k8sinstance + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.tables.listgroup.rst.txt b/_sources/biodm/biodm.tables.listgroup.rst.txt new file mode 100644 index 0000000..d771fb4 --- /dev/null +++ b/_sources/biodm/biodm.tables.listgroup.rst.txt @@ -0,0 +1,7 @@ +biodm.tables.listgroup module +============================= + +.. automodule:: biodm.tables.listgroup + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.tables.rst.txt b/_sources/biodm/biodm.tables.rst.txt new file mode 100644 index 0000000..24d383d --- /dev/null +++ b/_sources/biodm/biodm.tables.rst.txt @@ -0,0 +1,25 @@ +biodm.tables package +==================== + +Submodules +---------- + +.. toctree:: + :maxdepth: 4 + + biodm.tables.asso + biodm.tables.group + biodm.tables.history + biodm.tables.k8sinstance + biodm.tables.listgroup + biodm.tables.upload + biodm.tables.upload_part + biodm.tables.user + +Module contents +--------------- + +.. automodule:: biodm.tables + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.tables.upload.rst.txt b/_sources/biodm/biodm.tables.upload.rst.txt new file mode 100644 index 0000000..eb8fa97 --- /dev/null +++ b/_sources/biodm/biodm.tables.upload.rst.txt @@ -0,0 +1,7 @@ +biodm.tables.upload module +========================== + +.. automodule:: biodm.tables.upload + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.tables.upload_part.rst.txt b/_sources/biodm/biodm.tables.upload_part.rst.txt new file mode 100644 index 0000000..83c99ce --- /dev/null +++ b/_sources/biodm/biodm.tables.upload_part.rst.txt @@ -0,0 +1,7 @@ +biodm.tables.upload\_part module +================================ + +.. automodule:: biodm.tables.upload_part + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.tables.user.rst.txt b/_sources/biodm/biodm.tables.user.rst.txt new file mode 100644 index 0000000..e042aa2 --- /dev/null +++ b/_sources/biodm/biodm.tables.user.rst.txt @@ -0,0 +1,7 @@ +biodm.tables.user module +======================== + +.. automodule:: biodm.tables.user + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.utils.rst.txt b/_sources/biodm/biodm.utils.rst.txt new file mode 100644 index 0000000..67232b4 --- /dev/null +++ b/_sources/biodm/biodm.utils.rst.txt @@ -0,0 +1,20 @@ +biodm.utils package +=================== + +Submodules +---------- + +.. toctree:: + :maxdepth: 4 + + biodm.utils.security + biodm.utils.sqla + biodm.utils.utils + +Module contents +--------------- + +.. automodule:: biodm.utils + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.utils.security.rst.txt b/_sources/biodm/biodm.utils.security.rst.txt new file mode 100644 index 0000000..2fbc26d --- /dev/null +++ b/_sources/biodm/biodm.utils.security.rst.txt @@ -0,0 +1,7 @@ +biodm.utils.security module +=========================== + +.. automodule:: biodm.utils.security + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.utils.sqla.rst.txt b/_sources/biodm/biodm.utils.sqla.rst.txt new file mode 100644 index 0000000..a76e8aa --- /dev/null +++ b/_sources/biodm/biodm.utils.sqla.rst.txt @@ -0,0 +1,7 @@ +biodm.utils.sqla module +======================= + +.. automodule:: biodm.utils.sqla + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/biodm.utils.utils.rst.txt b/_sources/biodm/biodm.utils.utils.rst.txt new file mode 100644 index 0000000..8b05ea8 --- /dev/null +++ b/_sources/biodm/biodm.utils.utils.rst.txt @@ -0,0 +1,7 @@ +biodm.utils.utils module +======================== + +.. automodule:: biodm.utils.utils + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/biodm/modules.rst.txt b/_sources/biodm/modules.rst.txt new file mode 100644 index 0000000..40b4b00 --- /dev/null +++ b/_sources/biodm/modules.rst.txt @@ -0,0 +1,7 @@ +API Reference +============= + +.. toctree:: + :maxdepth: 4 + + biodm diff --git a/_sources/developer_manual/advanced_use.rst.txt b/_sources/developer_manual/advanced_use.rst.txt new file mode 100644 index 0000000..5469c11 --- /dev/null +++ b/_sources/developer_manual/advanced_use.rst.txt @@ -0,0 +1,124 @@ +============ +Advanced Use +============ + +This section describes how to implement a server that goes beyond the standard functionalities +provided by ``BioDM``. + + +Custom resource +---------------- + +As previously explained, a resource is a ``Table``, ``Schema``, ``Controller`` triplet, internally +connected around a ``Service`` finally communicating with one or more ``Manager``. + + +Depending on the level of complexity brought in the custom feature you would like to implement, +you will have to fine tune, from one up to all, of those components together. + + +Following sections are assuming you are weaving a valid Table and Schema as explained in earlier +parts of the documentation. + + +A bit about Internals +~~~~~~~~~~~~~~~~~~~~~~ + + +Standard pipeline for an incoming request goes like this: + +.. code:: + + ->Server->Middlewares->Controller->Service(s)->Manager(s) + + +Controller is the ``BioDM`` component that manages a set of routes. In order to avoid most mistakes +with Controllers it is recommended to visit Starlette documentation. + +Bread and butter for resources are ``ResourceController`` and ``DatabaseService``. You may add a +feature by extending them. + + +Keycloack Groups: a case study +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +``/users`` and ``/groups`` are examples of custom resources. +Idea with them is to have a `synchronized copy` of those resources from keycloak. +When requestin + +Basic operations and routes stay the same, so the controller is not changing. Following is the code +snippet that manages group creation. + +Basic idea is to query +our keycloak server before creating a new group to ensure its existence and recover its keycloak +UUID that is necessary for some operations. Then populate it in the data dictionary that is finally +sent to ``DatabaseService`` (here the composite case) that will handle insert/update statement +building and execution. + + +.. code-block:: python + :caption: kcservice.py + + class KCService(CompositeEntityService): + """Abstract class for local keycloak entities.""" + @property + def kc(self) -> KeycloakManager: + """Return KCManager instance.""" + return self.app.kc + + @abstractmethod + async def read_or_create(self, data: Dict[str, Any], /) -> None: + """Try to read from DB, create on keycloak side if not present. + Populate 'id' - Keycloak UUID in string form - in data.""" + raise NotImplementedError + + + class KCGroupService(KCService): + @staticmethod + def kcpath(path) -> Path: + """Compute keycloak path from api path.""" + return Path("/" + path.replace("__", "/")) + + async def read_or_create(self, data: Dict[str, Any]) -> None: + """READ group from keycloak, create if missing. + + :param data: Group data + :type data: Dict[str, Any] + """ + path = self.kcpath(data['path']) + + group = await self.kc.get_group_by_path(str(path)) + if group: + data["id"] = group["id"] + return + + parent_id = None + if not path.parent.parts == ('/',): + parent = await self.kc.get_group_by_path(str(path.parent)) + if not parent: + raise ValueError("Input path does not match any parent group.") + parent_id = parent['id'] + + data['id'] = await self.kc.create_group(path.name, parent_id) + + async def write( + self, + data: List[Dict[str, Any]] | Dict[str, Any], + stmt_only: bool = False, + user_info: UserInfo | None = None, + **kwargs + ): + """Create entities on Keycloak Side before passing to parent class for DB.""" + # Check permissions + await self._check_permissions("write", user_info, data) + + # Create on keycloak side + for group in to_it(data): + # Group first. + await self.read_or_create(group) + # Then Users. + for user in group.get("users", []): + await User.svc.read_or_create(user, [group["path"]], [group["id"]],) + + # Send to DB + return await super().write(data, stmt_only=stmt_only, **kwargs) diff --git a/_sources/developer_manual/demo.rst.txt b/_sources/developer_manual/demo.rst.txt new file mode 100644 index 0000000..c92b933 --- /dev/null +++ b/_sources/developer_manual/demo.rst.txt @@ -0,0 +1,146 @@ +Minimal Demo +============ + +Say you or your organization needs to store ``Datasets``, each containing a set of ``File`` we will go +over the following minimal example. + +.. code-block:: python + :caption: demo.py + + import marshmallow as ma + from marshmallow import fields as mf + import sqlalchemy as sa + from sqlalchemy import orm as sao + from typing import List + import uvicorn + + import biodm as bd + from biodm.components.controllers import ResourceController, S3Controller + + + # Tables + class Dataset(bd.components.Versioned, bd.components.Base): + name : sao.Mapped[str] = sa.Column(sa.String(50), nullable=False) + description : sao.Mapped[str] = sa.Column(sa.String(500), nullable=False) + username_owner: sao.Mapped[int] = sa.Column(sa.ForeignKey("USER.username"), nullable=False) + owner : sao.Mapped["User"] = sao.relationship(foreign_keys=[username_owner]) + files : sao.Mapped[List["File"]] = sao.relationship(back_populates="dataset") + + class File(bd.components.S3File, bd.components.Base): + id = sa.Column(sa.Integer, primary_key=True) + id_dataset = sa.Column(sa.ForeignKey("DATASET.id"), nullable=False) + dataset: sao.Mapped["Dataset"] = sao.relationship(back_populates="files", single_parent=True, foreign_keys=[id_dataset]) + + # Schemas + class DatasetSchema(ma.Schema): + id = mf.Integer() + version = mf.Integer() + name = mf.String(required=True) + description = mf.String(required=False) + username_owner = mf.String(required=True, load_only=True) + owner = mf.Nested("UserSchema") + files = mf.List(mf.Nested("FileSchema")) + + class FileSchema(ma.Schema): + id = mf.Integer() + filename = mf.String(required=True) + extension = mf.String(required=True) + url = mf.String( dump_only=True) + ready = mf.Bool( dump_only=True) + id_dataset = mf.Integer(required=True, load_only=True) + dataset = mf.Nested("DatasetSchema") + + # Controllers + class DatasetController(ResourceController): + def __init__(self, app) -> None: + super().__init__(app=app) + + class FileController(S3Controller): + def __init__(self, app) -> None: + super().__init__(app=app) + + # Server + def main(): + return bd.Api(debug=True, controllers=[DatasetController, FileController],) + + if __name__ == "__main__": + uvicorn.run( + f"{__name__}:main", factory=True, + host=bd.config.SERVER_HOST, port=bd.config.SERVER_PORT, + loop="uvloop", log_level="debug", access_log=False + ) + + +And voilà, If your use case is very basic it is a simple as that. This tiny codebase +deploys a server with two new RESTful resources, accessible respectively at ``/files`` and +``/datasets``. + +Importantly ``/schema``, ``/files/schema``, ``/datasets/schema`` will let you, or an +``OpenAPISchema v3.0.0`` compliant tool, discover all possible routes. + +Moreover, it comes with two preset resources ``/users``, ``/groups`` that are required for +permission management down the road. + +All incoming Requests are logged in ``History`` table + +Let's examine some key points: + + +Naming convention +------------------ +Sticking to the simple naming convention introduced above for the three required components to +add a new respource lets ``BioDM`` easily infer their relationships from name lookup in registries. + + +- ``Table``: name of the resource in singular +- ``Schema``: same prefixed by Schema +- ``Controller``: same prefixed by controller + +.. note:: + + This is the Zen approach. You may however name those as you please and manually set relationships + in Controller's ``__init__`` method. + + +Base Resource +-------------- +For a resource that is not interacting with an external serivce, this is covered by pairing +``BioDM``'s ``SQLAlchemy`` Declarative ``Base`` and ``ResourceController`` components. + + +File management +---------------- +.. note:: + + At the moment, s3 protocol, using pre-signed url, only. + + +``S3File`` `base class` set on a table, populates it with a set of +``Column`` fields essential for the task. +All but ``ready`` flag may be seen on ``FileSchema``. + +``S3Controller`` will then populate ``upload_form`` field when creating a new resource at ``/files``. +This is a stringified form for direct upload on the storage bay. +Once the file is uploaded, readiness flag is set to true. +From that point on, urls to download the file can be obtained by visiting +``GET /files/{id}/download`` + + +Versioning +----------- +In the example above you may see that Dataset has no primary key. +It is because it inherits from ``Versioned`` that populate +``[id, version]`` as primary key. + +Versioned resources are read-only, eventual updates have to pass by +``PUT /datasets/{id}_{version}/release`` route that will produce a new resource, incrementing version. + +.. note:: + + Nothing prevents you from expanding further on that primary key in your table class. + +.. warning:: + + SQLite doesn't support autoincrement in the case of a composite primary key. + ``BioDM`` supports the canonical leading ``id`` case at the cost of an extra request to fetch + max id before inserting. Other configuration will yield errors. diff --git a/_sources/developer_manual/doc_endpoints.rst.txt b/_sources/developer_manual/doc_endpoints.rst.txt new file mode 100644 index 0000000..22957a8 --- /dev/null +++ b/_sources/developer_manual/doc_endpoints.rst.txt @@ -0,0 +1,84 @@ +Documenting endpoints +===================== + +``BioDM`` populates an ``OpenAPISchema v3.0.0`` compliant documentation for all endpoints via +`apispec `_. +In particular that allows for automated discovery via compatible tools such as ``swagger-ui``. + +It is functional but not very specific in its description. In case you would like to expand on it +we provide ``@overload_docstrings`` decorator, which works in combination with permissions +decorators. + +.. warning:: + + In case you're stacking up a permission decorator and this one, you should **always** put + ``@overload_docstring`` **first** as this creates a shell function calling the parent class + method for the sole purpose of specifying the docstring as they are read-only. + +.. code-block:: python + :caption: demo.py + + from biodm.utils.security import group_required, admin_required + + class DatasetController(bdc.ResourceController): + def __init__(self, app) -> None: + super().__init__(app=app) + + @group_required(['my_team']) + @overload_docstring + async def write(**kwargs): + """ + requestBody: + description: payload. + required: true + content: + application/json: + schema: DatasetSchema + responses: + 201: + description: Write Dataset resource. + content: + application/json: + schema: DatasetSchema + 204: + description: Empty Payload. + """ + ... + class TagController(ResourceController): + @overload_docstring + async def read(**kwargs): + """ + parameters: + - in: path + name: name + description: Tag name + responses: + 200: + description: Found matching Tag. + examples: | + {"name": "epidemiology"} + content: + application/json: + schema: TagSchema + 404: + description: Tag not found. + """ + ... + + +Docstrings Guide +----------------- + +Docstrings comply with apispec in order to provide a correct schema. +In particular you have to be precise with input parameters and marshmallow schema reference names. + +This is required in order to output specification in ``OpenAPISchema`` format, with link discovery +which enables support for ``swagger-ui`` and the rest of the ecosystem. + +.. note:: + + The core patches abstract method docstrings at runtime in order to generate that are left + undocumented. However, if you are using ``@overload_docstrings`` ensuring that it generates a + valid schema that works with the tools is up to you. + To obtain the full generated docstring you may get it from a ``Controller`` after start phase + using printing methods or a debug session. diff --git a/_sources/developer_manual/index.rst.txt b/_sources/developer_manual/index.rst.txt new file mode 100644 index 0000000..b6e48b6 --- /dev/null +++ b/_sources/developer_manual/index.rst.txt @@ -0,0 +1,81 @@ +.. _developer-manual: + +================ +Developer Manual +================ + +This section describes how to use ``biodm`` package in order to swiftly deploy a modular +data management API tailored to your needs. + +You also may consult ``src/example/`` toy project, which encapsulates more complex project needs. + +Following, we will go in detail about the toolkit and builtins. + + +Basics +------ + +At the core, Data Management means storing collections of files and their associated metadata. + +``BioDM`` is leveraging SQLAlchemy ORM Tables definitions + matching Marshmallow Schemas, specifying +metadata and relationships, to setup standard RESTful endpoints. + +Furthermore, it is providing a structure and toolkit in order to manage common Data Management problems +such as: s3 protocol remote file storage, group based permissions access (on both resources and +endpoints), resource versioning (coming up), cluster jobs and so on. + +Moreover, the modular and flexible architecture allows you to easily extend base features for +instance specific use cases. + + +Concepts +--------- +The main server class ``biodm.Api`` is a vessel for ``biodm.components.controllers.Controller`` +subinstances. + +Each Controller is independently responsible for exposing a set of routes, validating and serializing +`i/o` and send incomming Request data to a relevant ``biodm.component.ApiService`` subinstance. + +Services, are tied to a Table and calling each other in order to parse and adapt +input data. +All Services are ``biodm.components.services.DatabaseService`` subinstances as their +primary mission is to faithfully log activity and maintain data integrity. + + +Finally this internal representation is sent to a ``biodm.component.ApiManager``, each holding +primitives enabling communication with an external micro-service (i.e. DB, S3, Kubernetes, +...). + + +Configuration +-------------- +``BioDM`` extends `Starlette `_, +hence its Configuration system works by populating a ``.env`` file, preferably sitting in the same directory as the running script. + +We invite you to consult `config.py `_ +to discover all possible options. + +Functionalities depending on external micro-services are enabled if matching configuration options are provided. + +**e.g.** Keycloak functionalities shall be activated, if and only if, defaultless config parameters prefixed by ``KC_`` are populated. +Otherwise, User/Group tables shall still be deployed. However, they shall not be synced against a keycloak server. + +You may have a look at ``compose.test.yml`` file to see how testing containers used in our `CI`, are deployed with partial configuration in order to test by parts. + + +BioDM toolkit Guide +-------------------- + +Following we have a tutorial in the form of a small demo server, that we will expand upon to +introduce the toolkit: + +.. toctree:: + :maxdepth: 2 + :caption: Manual: + + demo + s3conf + permissions + table_schema + doc_endpoints + advanced_use diff --git a/_sources/developer_manual/permissions.rst.txt b/_sources/developer_manual/permissions.rst.txt new file mode 100644 index 0000000..6d34aa7 --- /dev/null +++ b/_sources/developer_manual/permissions.rst.txt @@ -0,0 +1,115 @@ +Permissions +============ + +In order to protect your data, ``BioDM`` provides two structures of permissions. + +Those are requiring a keycloak service running and the following variables to +be provided in a ``.env`` file at the same level as your ``demo.py`` script. + +.. code-block:: shell + :caption: .env + + KC_HOST= + KC_REALM= + KC_PUBLIC_KEY= + KC_ADMIN= + KC_ADMIN_PASSWORD= + KC_CLIENT_ID= + KC_CLIENT_SECRET= + +Coarse: Static rule on a Controller endpoint +--------------------------------------------- + +``biodm.utils.security`` module contains three decorators that are meant to be used +on Controller endpoints in order to apply static permissions directly within the codebase. + + +* ``@token_required()`` + + * Protects the endpoint demanding incomming requests to by signed with a valid ``Keycloak JW Token`` + +* ``@group_required(groups=[gpath_1,... gpath_n])`` + + * Like token_required, plus assesses that requesting ``User`` is part of one of those ``Groups``. + +* ``@admin_required()`` + + * group_required special case, requesting ``User`` must be part of ``admin`` group. + + +On our example, this is how you could apply those on `DatasetController`: + +.. code-block:: python + :caption: demo.py + + from biodm.utils.security import group_required, admin_required + + class DatasetController(bdc.ResourceController): + def __init__(self, app) -> None: + super().__init__(app=app) + self.write = group_required(self.create, ['my_team']) + self.update = group_required(self.update, ['my_team']) + self.delete = admin_required(self.delete) + +Here we restricted the creation and updating of datasets to ``my_team``, deletion is ``admin`` +priviledge and reading data is left public. + + +.. _dev-user-permissions: + +Fine: Dynamic user owned permissions +------------------------------------- + +If your data management platform is intended to receive data from users, ``BioDM`` provide tools to +let them in control of permissions by providing them directly as the resource input data. + +``biodm.components.Permission`` class is designed as an extra SQLAlchemy table argument that let +you flag composition pattern (i.e. One-to-Many relationships) with the following permissions that +will be applied recursively for all children of that particular entity: + +- ``Read`` +- ``Write`` +- ``Download`` + +In our example: + +.. code-block:: python + :caption: demo.py + + from biodm.components import Permission + + + class Dataset(bd.components.Base): + id : sao.Mapped[int] = sa.Column(sa.Integer, primary_key=True) + ... + files : sao.Mapped[List["File"]] = sao.relationship(back_populates="dataset") + + __permissions__ = ( + Permission(files, write=True, read=False, download=True), + ) + +The latter enables ``File`` permissions at the ``Dataset`` level. + +In other words it lets you define for a top level resource who is allowed to interact +with a nested collection and its elements. + +.. note:: + + Those permissions will be taken into account when directly accessing ``/files`` API routes. + + +Strict composition +~~~~~~~~~~~~~~~~~~ + +Currently, ``BioDM`` assumes a strict composition pattern of resource for those permissions. +Which allow them to be taken into account while directly accessing children resource routes +like mentioned above. + +Unfortunately, that also means that distributing permissions from two, or more, parent level +resources is currently not tested and shall most likely result in soft-locking those resources. + +This may or may not be supported in a future version of the Core, depending on technical +feasibility. + +If you wish to achieve something in that vein, it is for now advised to create an identical +resource with a different name. diff --git a/_sources/developer_manual/s3conf.rst.txt b/_sources/developer_manual/s3conf.rst.txt new file mode 100644 index 0000000..b73786e --- /dev/null +++ b/_sources/developer_manual/s3conf.rst.txt @@ -0,0 +1,43 @@ +S3 Configuration +================== + +For file management this demo requires an ``s3`` compatible storage service. +To quickly deploy micro-services dependencies for testing purposes, refer to +:ref:`development-environment`. + +The following variables have to be provided. + +.. code-block:: shell + :caption: .env + + S3_ENDPOINT_URL= + S3_BUCKET_NAME= + S3_ACCESS_KEY_ID= + S3_SECRET_ACCESS_KEY= + + +File management +---------------- +To ensure bucket key uniqueness for uploaded files, the key gets prefixed by +``S3File.key_salt`` column. By default this is an ``uuid4``. + +In case you would like to have precise control over how your files are named on the bucket this +can be done by overloading ``key_salt`` with a ``hybrid_property`` in the following way. + +.. code-block:: python + :caption: demo.py + + from sqlalchemy.ext.hybrid import hybrid_property + + class File(bd.components.S3File, bd.components.Base): + class File() + ... + @hybrid_property + async def key_salt(self) -> str: + # Pop session, populated by S3Service just before asking for that attr. + session = self.__dict__.pop('session') + # Use session to fetch what you need. + await session.refresh(self, ['dataset']) + await session.refresh(self.dataset, ['project']) + # Build your custom prefix. + return f"{self.dataset.project.name}_{self.dataset.name}" diff --git a/_sources/developer_manual/table_schema.rst.txt b/_sources/developer_manual/table_schema.rst.txt new file mode 100644 index 0000000..bc810d7 --- /dev/null +++ b/_sources/developer_manual/table_schema.rst.txt @@ -0,0 +1,128 @@ +Tables and Schemas +============================ + +This section describes how ``BioDM`` is leveraging your ``Tables`` and ``Schemas`` in order to set +up resources. It contains some useful information for developers to design their own. + +It is recommended to visit the documentation of both ``SQLAlchemy`` and ``Marshmallow`` beforehand. +Moreover, our ``example`` project also provides plenty of inspiration for this task. + +Tables +------ + +In principle any valid ``SQLALchemy`` table is accepted by ``BioDM``. Yet, +depending how you configure it, it shall adopt varying behaviours. + +SQLAlchemy 2.0 ORM API is a really nice and convenient piece of technology. +However, it does not natively support trees of entities (nested dictionaries). + +To palliate this problem, ``BioDM`` does a pass of parsing on schema validation results under the +hood, using Tables as litterals in order to build the hirarchical tree of statements. +In a second pass, it inserts the whole tree in order, ensuring integrity. + + +Relationship specifics +~~~~~~~~~~~~~~~~~~~~~~ + +Statement building leverages tables ``relationships`` definitions, taking orientation into account. + +In particular, if a relationship is one-armed (pointing in one direction only), it will not +be possible to create a nested resource in the other direction. + + +Schemas +------- + +``Marshmallow`` also comes with some limitations, such as not being able to infer foreign key +population in respect to nested entities while ``de-serializing``. + +**E.g.** Given the following matching table and schema: + +.. code:: python + + class Dataset(Base): + id: Mapped[int] = mapped_column(Integer(), primary_key=True) + ... + id_project: Mapped[int] = mapped_column(ForeignKey("PROJECT.id"), nullable=False) + project: Mapped["Project"] = relationship(back_populates="datasets") + + class DatasetSchema(Schema): + id = Integer() + ... + id_project = Integer() + project = Nested('ProjectSchema') + +If you ``POST`` a new ``/datasets`` resource definition with a nested project. +Upon validating, ``id_project`` will not be populated, which ultimately is your +``NOT NULL FOREIGN KEY`` field. Hence SQL insert statement shall raise integrity errors. + +``Marshmallow`` is offering built-ins in the form of decorators that let you tag functions +attached to the ``Schema`` such as ``@pre_load`` which is a hook called before validation, +that lets you manually get data if you detect it present in the dict. + +This technique has two major disadvantages: + +* It is quite cumbersome and error prone for the developer, as for each relationship you may + have to set foreign keys on either side and is as many conditions checking what is + present in your input dict and whatnot. + +* This cannot take into account generated keys. In our example, we may be creating the + project as well. Hence it will not have an id yet, thus raise a ``ValidationError`` for the + dataset if we set ``required=True`` flag for ``id_project``. + + +To bypass those limitations, ``BioDM`` validates incoming data using ``Marshmallow``'s +``partial=True`` flag. Meaning that ``required`` keywords on fields are ignored and may be skipped +overall. At validation step we are checking the overall structure and type of fields. + +This yields a (List of) dictionary (of nested Dictionaries) that is sent down to a ``Service`` +for statement building and insertion. The Core will use knowledge of Table relationships to infer +this foreign key population and raise appropriate errors in case of truely incomplete input data. + +This ultimately allows for more flexibily on input such as sending a mixin of create/update of new +resources via ``POST``. + + +Nested flags policy +~~~~~~~~~~~~~~~~~~~ + +Serialization is following down ``Nested`` fields. In particular that means it is important to +limit the depth of data that is fetched, as it is easy to end up in infinite loops in case of +circular dependencies. + +**E.g.** + +.. code:: python + + class GroupSchema(Schema): + """Schema for Keycloak Groups. id field is purposefully left out as we manage it internally.""" + path = String(metadata={"description": "Group name chain separated by '__'"}) + ... + users = List(Nested('UserSchema', exclude=['groups'])) + children = List(Nested('GroupSchema', exclude=['children', 'parent'])) + parent = Nested('GroupSchema', exclude=['children', 'parent']) + + +In the example above, without those exclude flags, excluding references to nested Groups further +down Serialization would go into infinite recursion. + +Marshmallow provides other primitives: ``only``, ``load_only``, ``dump_only``, that can also be +used to do this restriction. + + +.. warning:: + + It is important to make sure that your dumping configuration does not impede a Schema's + loading capabilites of essential fields for creating a new resource. + + +For most cases, you may simply set fields identical to matching Table, using Marshmallow syntax. +Furthemore, Schemas are the "i/o surface" of your app. This is where you decide what gets +loaded and dumped for a specific resource. + +.. note:: + + Setting "metadata.description" like for path in our example example above, is used for + automatic apispec docstrings generation. + + diff --git a/_sources/getting_started.rst.txt b/_sources/getting_started.rst.txt new file mode 100644 index 0000000..0131646 --- /dev/null +++ b/_sources/getting_started.rst.txt @@ -0,0 +1,352 @@ +=============== +Getting Started +=============== + +Install +------- +* Recommended: :pep:`405` Create virtual environment + +.. code-block:: bash + + python3 -m venv venv + source venv/bin/activate/ + +.. warning:: + + using built in python tools such as ``venv`` and ``pip`` is preferred. + ``conda`` and co. package managers are currently untested. + +* Using pip and git + +.. code-block:: bash + + pip3 install git+https://github.com/bag-cnag/biodm + +* Install with kubernetes functionalities + +.. code-block:: bash + + pip3 install "biodm[kubernetes] @ git+https://github.com/bag-cnag/biodm" + +* Build from sources + +.. code-block:: bash + + git clone https://github.com/bag-cnag/biodm + cd biodm/ + pip3 install -r src/requirements/dev.txt + pip3 install . + + +Start Server +------------ + +E.g. for our ``example`` project. +Configuration is done through ``.env`` files, thus server has to be run from its immediate directory. +The one provided at ``src/example/.env`` is set on development environment values. + +.. code-block:: bash + + cd src/example/ + python3 app.py + +.. _development-environment: + +Development environment +----------------------- + +* Install in editable mode + +.. code-block:: bash + + pip3 install -r src/requirements/dev.txt + pip3 install -e . + +Quick dependency setup +~~~~~~~~~~~~~~~~~~~~~~ + +To start all service dependnencies at once and skip individual configuration you may use +the provided ``compose.yml``. Passing the flag --build it will also build for you an appropriate +keycloak image with your local certificates in order to serve ``https://`` requests. + +.. code-block:: bash + + docker compose up --build -d + +Default configuration parameters are set on fixed IPs declared in this ``compose.yml`` file. + +**optional - strongly recommended for keycloak -:** for testing convenience you +may add those lines to your host table. + +.. code-block:: bash + + sudo cat >> /etc/hosts <`_: + +.. code-block:: bash + + cd docker/ && \ + docker build . -t keycloak:22.0_local-certs \ + -f Dockerfile.keycloak-22.0_local-certs \ + --build-arg _KC_DB=postgres \ + --build-arg _KC_DB_USERNAME=postgres \ + --build-arg _KC_DB_PASSWORD=pass \ + --build-arg=_KC_HOSTNAME=keycloak.local \ + --build-arg _KC_DB_URL=jdbc:postgresql://10.10.0.5:5432/keycloak && \ + cd - + +Keycloak also needs a databse: + +.. code-block:: bash + + docker run --name kc-db -e POSTGRES_PASSWORD=pass -e POSTGRES_DB=keycloak -d postgres:16-bookworm + docker exec -u postgres biodm-pg createdb keycloak + + + +Then you may start keycloak itself: + +.. code-block:: bash + + docker run --name local_keycloak -e KEYCLOAK_USER=admin -e KEYCLOAK_PASSWORD=admin -p 8443:8080 keycloak:22.0.5_local-certs + + +.. rubric:: Configuration + +Once keycloak is running you need to configure a realm and a client for the app to log in. +Default values are: + +.. code-block:: shell + + KC_REALM="3TR" + KC_CLIENT_ID="submission_client" + +Once you've created the realm, create the client. Then + + * set `Access Type` to confidential + * set `Inplicit Flow Enabled` to `True`. + * Add Valid Redirect Uri: + + * **dev**: `http://*` and `https://*` + * **prod**: provide the url of the login callback `{SERVER_HOST}/syn_ack`. + +.. note:: + + Depending on your keycloak version or running instance `SERVER_HOST` may have to be appended with `/auth`. + +Then you should provide the server with the `SECRET` field located in the +`Credentials` tab, that appears **after** you changed access type and the realm public key +located at ``{KC_HOST}[auth/]realms/{KC_REALM}/``. + +To be able to serve as a gateway to administrate keycloak concepts, +the API also needs admin credentials: + +.. code-block:: shell + + KC_HOST={url} + KC_CLIENT_SECRET={secret} + KC_PUBLIC_KEY={public_key} + KC_ADMIN={admin_id} + KC_ADMIN_PASSWORD={admin_password} + + +* Minio + +.. code-block:: bash + + docker run -e MINIO_ROOT_USER=admin \ + -e MINIO_ROOT_PASSWORD=12345678 \ + -e MINIO_DEFAULT_BUCKETS=bucketdevel3tropal \ + -p 9000:9000 \ + -p 9001:9001 \ + bitnami/minio:2024-debian-12 + +Then visit the administration interface at `localhost:9001`, +generate a key and populate: + +.. code-block:: shell + + S3_ENDPOINT_URL={url} + S3_BUCKET_NAME={bucket_name} + S3_ACCESS_KEY_ID={access_key_id} + S3_SECRET_ACCESS_KEY={access_key} + +Documentation +------------- + +* pre-requisite: + +.. code-block:: bash + + pip3 install -r src/requirements/docs.txt + +Then you may use the following: + +.. code-block:: bash + + sphinx-apidoc --implicit-namespaces --separate -H "API Reference" -fo docs/biodm/ src/biodm "**/*tests*" + python3 -m sphinx -b html docs/ docs/build/html + + +Tests +----- + +Unit +~~~~ + +Unit tests are leveraging an in-memory sqlite database and not testing any feature requiring +deployement of an external service. + +* pre-requisite: + +.. code-block:: bash + + pip3 install -r src/requirements/dev.txt + + +* run tests + +Just like example, tests have to be run within their directory. + +.. code-block:: bash + + cd src/biodm/tests/ + pytest + cd - + +* coverage + +.. code-block:: bash + + cd src/biodm/tests/ + pytest --cov-report term --cov=../ + cd - + +* run in a VSCode debugpy session + +To run a unit test in a debugging session, you may create the following ``.vscode/launch.json`` +file at the root of this repository. The ``run and debug`` tab should now ofer an extra option. +If you installed sources in editable mode, that allows you to set breakpoints within +``BioDM`` codebase. + +.. code-block:: json + :caption: launch.json + + { + "version": "0.2.0", + "configurations": [ + { + "name": "PyTest: BioDM Unit tests", + "type": "debugpy", + "request": "launch", + "cwd": "${workspaceFolder}/src/tests/unit", + "subProcess": true, + "module": "pytest", + "python": "/path/to/myvenv/bin/python3", // Replace with your virtual environment + "args": [ + // "-k", "test_basics", // Optional: pick your tests + "-vv" + ], + "justMyCode": false, + }, + ] + } + + +Integration +~~~~~~~~~~~ + +Integration tests are leveraging ``docker compose`` and the development environment to simulate +external services allowing for end to end testing. It is effectively testing the app from +outside. + +Integration are split in silos according to their external service dependency: + +* Keycloak + +.. code-block:: bash + + docker compose -f compose.test.yml run --build test-keycloak-run + docker compose -f compose.test.yml down + +* S3 + +.. code-block:: bash + + docker compose -f compose.test.yml run --build test-s3-run + docker compose -f compose.test.yml down + +* run in a VSCode debugpy session + +**pre-requisite** development environment up + +For integration tests you need two sessions: server side (api) and client side (tests), you +may adjust the following configurations to your need. + +VSCode supports running both sessions at the same time from the ``run and debug`` tab. + +.. code-block:: json + :caption: launch.json + + { + "version": "0.2.0", + "configurations": [ + { + "name": "Python: BioDM Example API", + "type": "debugpy", + "request": "launch", + "cwd": "${workspaceFolder}/src/example/", + "program": "app.py", + "console": "integratedTerminal", + "python": "/path/to/myvenv/bin/python3", // Replace with your virtual environment + "justMyCode": false, + }, + { + "name": "PyTest: BioDM Integration tests", + "type": "debugpy", + "request": "launch", + "cwd": "${workspaceFolder}/src/tests/integration/kc|s3|k8", // pick one directory + "subProcess": true, + "module": "pytest", + "python": "/path/to/myvenv/bin/python3", // Replace with your virtual environment + "args": [ + // "-k", "some_test_name" // Optional: pick your tests + "-vv" + ], + "justMyCode": false, + "envFile": "${cwd}.env" + }, + ] + } diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt new file mode 100644 index 0000000..cba591b --- /dev/null +++ b/_sources/index.rst.txt @@ -0,0 +1,30 @@ +.. biodm documentation master file + +***************************************************** +BioDM: A fast and RESTful Data Management framework +***************************************************** + +.. mdinclude:: ../README.md + + +Welcome to biodm's documentation! +================================== + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + getting_started + developer_manual/index + user_manual + biodm/modules + licence + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/_sources/licence.rst.txt b/_sources/licence.rst.txt new file mode 100644 index 0000000..8f3cf1f --- /dev/null +++ b/_sources/licence.rst.txt @@ -0,0 +1,4 @@ +License +======= + +.. literalinclude:: ../LICENSE diff --git a/_sources/user_manual.rst.txt b/_sources/user_manual.rst.txt new file mode 100644 index 0000000..29c156e --- /dev/null +++ b/_sources/user_manual.rst.txt @@ -0,0 +1,371 @@ +.. _user-manual: + +=========== +User Manual +=========== + +This section describes how your Users may communicate with the API once it is deployed. + +The examples are demonstrating using ``curl``, but they are free to use any HTTP library out there. + +Integration tests located at ``src/tests/integration`` are also providing plenty of resources. + +Base routes +----------- + +* OpenAPI schema + +.. code-block:: bash + + curl ${SERVER_ENDPOINT}/schema + +Yields full API schema in JSON form. + +* Liveness endpoint + +.. code-block:: bash + + curl ${SERVER_ENDPOINT}/live + +Returns ``live`` with a ``200`` status code. + +* Login + +.. code-block:: bash + + curl ${SERVER_ENDPOINT}/login + +Returns a keycloak login url. +Visiting and authenticating there gives you an authentication ``JSON Web Token`` that you shall +provide in header to hit protected routes, see authenticated next. + +.. code-block:: bash + + curl ${SERVER_ENDPOINT}/login + +* Authenticated + +.. code-block:: bash + + export TOKEN=ey.... + curl -S "${SERVER_ENDPOINT}/authenticated"\ + -H "Authorization: Bearer ${TOKEN}" + +This routes checks token and returns requesting user info: `username`, `groups` and `projects`. + + +* Syn Ack + +This route is the callback login route located at ``${SERVER_ENDPOINT}/syn_ack`` +and it is not meant to be accessed directly. + + +Entity routes +------------- + +For each entity being managed by a ``ResourceController``, the following routes are supported. + +.. note:: + + * As per REST standard, each entity is accessible under a resource prefix which is the name of the entity in plural form. + * URLs end **without** trailing slashes + * In the case of a multi-indexed entity (**i.e.** composite primary key), ``{id}`` + refers to primary key elements separated by underscore symbol ``_``. + +* POST + +.. code-block:: bash + + curl -d ${JSON_OBJECT}\ + ${SERVER_ENDPOINT}/my_resources + +Supports submitting a resource and or a list of resource with nested resources. + +**Flexible write**: + +This endpoint works as a flexible write operation. It supports a mixin input of old and new data: + +- new data shall comply to resource Shema ruleset. + +- reference old data by setting (at least) primary key values in the dict. + + - Other fields will be applied as an update. + +* GET + +one + +.. code-block:: bash + + curl ${SERVER_ENDPOINT}/my_resources/{id} + +or all + +.. code-block:: bash + + curl ${SERVER_ENDPOINT}/my_resources + +* PUT + +Not available for versioned resources, see Versioning below. + +.. code-block:: bash + + curl -X PUT\ + -H "Content-Type: application/json"\ + -d ${UPDATED_JSON_OBJECT}\ + ${SERVER_ENDPOINT}/my_resources/{id} + +* DELETE + +.. code-block:: bash + + curl -X DELETE\ + ${SERVER_ENDPOINT}/my_resources/{id} + +Groups +~~~~~~ + +Group key is its ``path`` according to top level groups. Since ``/`` is a reserved route character +it is replaced by double underscore: ``__`` (with no prefix). + +**E.g**. ``parent__child__grandchild`` + + +Versioning +~~~~~~~~~~~ + +When a table is inheriting from ``Versioned`` e.g ``Dataset`` in our demo, associated controller +exposes an extra route: ``POST /my_versioned_resources/{id}_{version}/release``. + + +This triggers creation of a new row with a version increment. + +.. note:: + + ``PUT /release`` is the way of updating versioned resources. + The endpoint ``PUT /`` (a.k.a ``update``) will not be available for such resources, and + any attempt at updating by reference through ``POST /`` will raise an error. + + +**E.g.** + +.. code-block:: bash + + curl -X POST ${SERVER_ENDPOINT}/my_file_resources/{id}_{version}/release + +OR to pass in an update for the new version. + +.. code-block:: bash + + curl -d '{"name": "new_name"}' ${SERVER_ENDPOINT}/my_file_resources/{id}_{version}/release + +.. note:: + + In the case of a resource both ``Versioned`` and ``S3File``, ``POST /release`` will generate + a new upload form and set ready flag to false. + +Filtering +~~~~~~~~~ + +When requesting all resources under a prefix (i.e. ``GET /my_resources``) +it is possible to filter results by appending a QueryString starting with ``?`` +and followed by: + +* ``field=value`` pairs, separated by ``&`` + + * Use ``field=val1,val2,val3`` to ``OR`` between multiple values + * Use ``nested.field=val`` to select on a nested attribute field + * Use ``*`` in a string attribute for wildcards + +* ``field.op(value)`` + + * Currently only ``[lt, le, gt, ge]`` operators are supported for numerical values. + +**e.g.** + +.. note:: + + When querying with ``curl``, don't forget to escape ``&`` symbol or enclose the whole url in quotes, else your scripting language may intepret it as several commands. + + +Query a nested collection +~~~~~~~~~~~~~~~~~~~~~~~~~ + +Alternatively you may get a resource nested collection like this + +.. code-block:: bash + + curl ${SERVER_ENDPOINT}/my_resources/{id}/{collection} + +It also supports partial results. i.e. by appending ``?fields=f1,...,fn`` + + +File management +--------------- + +Files are stored leveraging an S3 bucket instance. Upload and Downloads are requested directly +there through `boto3 presigned-urls `_. + +* Upload + +On creating a new ``/file`` resource, it is required that you pass in the size in ``bytes`` that +you can obtain from its descriptor. + +The resource shall contain a nested dictionary called ``upload`` composed of ``parts``, +containing presigned form for direct file upload. + +Next we distinguish two cases: + +Small files +~~~~~~~~~~~ + +In the case of a `small` file, i.e. less than `100MB` there is a single ``part``, containing a +presigned ``POST`` and you may simply use the ``form`` to perform the upload. + +The following snippet demonstrates how to do this in `python`: + +.. code-block:: python + :caption: upload_small_file.py + + import requests + + # obtained from file['upload']['parts'][0]['form'] creation response + post = {'url': ..., 'fields': ...} + + file_path = "/path/to/my_file.ext" + file_name = "my_file.ext" + + with open(file_path, 'rb') as f: + files = {'file': (file_name, f)} + http_response = requests.post( + post['url'], + data=post['fields'], + files=files, + verify=True, + allow_redirects=True) + assert http_response.status_code == 201 + + +Upon completion, BioDM will be notified back via a callback, so the file is immediately available. + + +Large files +~~~~~~~~~~~ + +For large files, several parts will be present. Each allowing you to upload a chunk of +`size=100MB`, possibly less for the last one. + +For each part successfuly uploaded, the bucket will return you an ``ETag`` that you have to +keep track of and associate with the correct ``part_number``. + +Ultimately, the process has to be completed by submitting that mapping in order for the bucket +to aggregate all chunks into a file stored on the bucket. The bucket does not supports passing a +callback for a ``part_upload``. + +Similarely here is an example using ``python``: + +.. code-block:: python + :caption: upload_large_file.py + + import requests + + CHUNK_SIZE = 100*1024**2 # 100MB + parts_etags = [] + host: str = ... # Server instance endpoint + file_id = ... # obtained from file['id'] + upload_forms = [{'part_number': 1, 'form': ...}, ...] # obtained from file['upload']['parts'] + + # Upload file + with open(big_file_path, 'rb') as file: + for part in upload_forms: + part_data = file.read(CHUNK_SIZE) # Fetch one chunk. + response = requests.put( + part['form'], data=part_data, headers={'Content-Encoding': 'gzip'} + ) + assert response.status_code == 200 + + # Get etag and remove trailing quotes to not disturb subsequent (json) loading. + etag = response.headers.get('ETag', "").replace('"', '') + # Build mapping. + parts_etags.append({'PartNumber': part['part_number'], 'ETag': etag}) + + # Send completion notice with the mapping. + complete = requests.put( + f"{host}/files/{file_id}/complete_multipart", + data=json.dumps(parts_etags).encode('utf-8') + ) + assert complete.status_code == 201 + assert 'Completed.' in complete.text + + +.. note:: + + This example above is a quite naive approach. For very large files, you should make use of a + concurrency library (such as ``concurrent.futures`` or ``multiprocessing`` in ``python``) in + order to speed up that process, as parts can be uploaded in any order. + +* Download + +Calling ``GET /my_file_resources`` will only return associated metadata (and the upload form(s) +while it is still in prending state). + +To download a file use the following endpoint. + +.. code-block:: bash + + curl ${SERVER_ENDPOINT}/my_file_resources/{id}/download + +That will return a url to directly download the file via ``GET`` request. + +.. note:: + + Download urls are coming back with a redirect header, thus you may use + ``allow_redirects=True`` flag or equivalent when visiting this route to download in one go. + + +User permissions +---------------- + +When a Composition/One-to-Many relationship is flagged with permissions as described in +:ref:`dev-user-permissions` a new field ``perm_{relationship_name}`` is available for that resource. + +**E.g.** Dataset resource in our example, would have an extra field ``perm_files``. + +A Permission is holding a ListGroup object for each enabled verbs. +ListGroup being a route-less core table, allowing to manage lists of groups. + +**E.g.** In our example, CREATE/READ/DOWNLOAD are enabled, +hence a JSON representation of a dataset with its permissions looks like this, where leaving +"read" empty means it will only account for decorator permissions if provided and left public +otherwise. + +.. code-block:: json + + { + "name": "ds_test", + "owner": { + "username": "my_dataset_owner" + }, + "perm_files": { + "write": { + "groups": [ + {"name": "genomics_team"}, + {"name": "IT_team"}, + {"..."} + ] + }, + "download": { + "groups": [{"..."}] + } + } + } + + +.. note:: + + - Passing a top level group will allow all descending children group for that verb/resource tuple. + + - Permissions are taken into account if and only if keyclaok functionalities are enabled. + + - Without keycloak, no token exchange -> No way of getting back protected data. diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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+ }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/_static/basic.css b/_static/basic.css new file mode 100644 index 0000000..f316efc --- /dev/null +++ b/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; 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+ margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; 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+ float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; 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font-weight: bold } /* Literal.String.Escape */ +.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */ +.highlight .si { color: #A45A77; font-weight: bold } /* Literal.String.Interpol */ +.highlight .sx { color: #008000 } /* Literal.String.Other */ +.highlight .sr { color: #A45A77 } /* Literal.String.Regex */ +.highlight .s1 { color: #BA2121 } /* Literal.String.Single */ +.highlight .ss { color: #19177C } /* Literal.String.Symbol */ +.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #0000FF } /* Name.Function.Magic */ +.highlight .vc { color: #19177C } /* Name.Variable.Class */ +.highlight .vg { color: #19177C } /* Name.Variable.Global */ +.highlight .vi { color: #19177C } /* Name.Variable.Instance */ +.highlight .vm { color: #19177C } /* Name.Variable.Magic */ +.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/_static/searchtools.js b/_static/searchtools.js new file mode 100644 index 0000000..92da3f8 --- /dev/null +++ b/_static/searchtools.js @@ -0,0 +1,619 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlinks", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/biodm/biodm.api.html b/biodm/biodm.api.html new file mode 100644 index 0000000..262bc8c --- /dev/null +++ b/biodm/biodm.api.html @@ -0,0 +1,227 @@ + + + + + + + biodm.api module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.api module

+
+
+class Api(controllers: List[Type[Controller]] | None, instance: Dict[str, ModuleType] | None = None, debug: bool = False, test: bool = False, *args, **kwargs)
+

Bases: Starlette

+

Main Server class.

+
    +
  • Sets up and holds managers + OpenAPI schema generator

  • +
  • Instanciates CORE_CONTROLLERS and passed controllers +- Sets up routes

  • +
  • adds our middlewares

  • +
  • listens on events

  • +
+
+
+adopt_controllers(controllers: List[Type[Controller]]) List[Route]
+

Adopts controllers, and their associated routes.

+
+ +
+
+controllers: List[Controller] = []
+
+ +
+
+db: DatabaseManager
+
+ +
+
+deploy_managers() None
+

Conditionally deploy managers. Each manager connects to an external service. +Appart from the DB, managers are optional, with respect to config population.

+
+ +
+
+k8: K8sManager
+
+ +
+
+kc: KeycloakManager
+
+ +
+
+logger = <Logger biodm.api (WARNING)>
+
+ +
+
+async onstart() None
+
+ +
+
+s3: S3Manager
+
+ +
+
+property server_endpoint: str
+
+ +
+ +
+
+class HistoryMiddleware(app: Callable[[MutableMapping[str, Any], Callable[[], Awaitable[MutableMapping[str, Any]]], Callable[[MutableMapping[str, Any]], Awaitable[None]]], Awaitable[None]], server_host: str)
+

Bases: BaseHTTPMiddleware

+

Logins in authenticated user requests in History.

+
+
+async dispatch(request: Request, call_next: Callable) Any
+
+ +
+ +
+
+class TimeoutMiddleware(app: Callable[[MutableMapping[str, Any], Callable[[], Awaitable[MutableMapping[str, Any]]], Callable[[MutableMapping[str, Any]], Awaitable[None]]], Awaitable[None]], timeout: int = 30)
+

Bases: BaseHTTPMiddleware

+

Emit timeout signals.

+
+
+async dispatch(request: Request, call_next: Callable) Any
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.basics.html b/biodm/biodm.basics.html new file mode 100644 index 0000000..eb2871d --- /dev/null +++ b/biodm/biodm.basics.html @@ -0,0 +1,184 @@ + + + + + + + biodm.basics package — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.basics package

+
+

Submodules

+ +
+
+

Module contents

+
+
+class GroupController(app: Api, entity: str = '', table: Type[Base] | None = None, schema: Type[Schema] | None = None)
+

Bases: ResourceController

+

Group Controller.

+
+ +
+
+class UserController(app: Api, entity: str = '', table: Type[Base] | None = None, schema: Type[Schema] | None = None)
+

Bases: ResourceController

+

User Controller.

+
+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.basics.k8scontroller.html b/biodm/biodm.basics.k8scontroller.html new file mode 100644 index 0000000..7f63924 --- /dev/null +++ b/biodm/biodm.basics.k8scontroller.html @@ -0,0 +1,181 @@ + + + + + + + biodm.basics.k8scontroller module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.basics.k8scontroller module

+
+
+class K8sController(app)
+

Bases: ResourceController

+

Kubernetes Instances Controller.

+
+
+async create(request: Request) Response
+

Deploys K8s Instance.

+
+ +
+
+async instance_info(request: Request) Response
+

Instance info.

+
+ +
+
+property k8s
+
+ +
+
+async list_instances(request: Request) Response
+

List running K8s Instances.

+
+ +
+
+routes(schema: bool = False)
+

Routes for k8s instances management

+
+
Parameters:
+

schema (bool) – when called from schema generation, defaults to False

+
+
Return type:
+

starlette.routing.Mount

+
+
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.basics.rootcontroller.html b/biodm/biodm.basics.rootcontroller.html new file mode 100644 index 0000000..3ef233f --- /dev/null +++ b/biodm/biodm.basics.rootcontroller.html @@ -0,0 +1,198 @@ + + + + + + + biodm.basics.rootcontroller module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.basics.rootcontroller module

+
+
+class RootController(app: Api)
+

Bases: Controller

+

Bundles Routes located at the root of the app i.e. ‘/’.

+
+
+async authenticated(_, user_info: UserInfo)
+

Token verification endpoint.

+
+ +
+
+handshake()
+

Login handshake function.

+
+
Returns:
+

Syn_Ack url

+
+
Return type:
+

str

+
+
+
+ +
+
+async static live(_)
+

Liveness endpoint.

+
+ +
+
+async login(_)
+

Login endpoint.

+
+ +
+
+async openapi_schema(_)
+

Generates openapi schema.

+
+ +
+
+routes(**_)
+

Controller routes.

+
+ +
+
+async syn_ack(request)
+
+
Login callback function when the user logs in through the browser.

We get an authorization code that we redeem to keycloak for a token. +This way the client_secret remains hidden to the user.

+
+
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.component.html b/biodm/biodm.component.html new file mode 100644 index 0000000..56cdae8 --- /dev/null +++ b/biodm/biodm.component.html @@ -0,0 +1,207 @@ + + + + + + + biodm.component module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.component module

+
+
+class ApiComponent(app: Api)
+

Bases: object

+

Abstract API component, refrencing main server class and its loggger.

+
+
Parameters:
+

app (class:biodm.Api) – Reference to running server class.

+
+
+
+
+app: Api
+
+ +
+
+logger: logging.Logger
+
+ +
+ +
+
+class ApiManager(app: Api)
+

Bases: ApiComponent

+

Manager base class. +A manager represents an external service dependency. +It holds a connection object and relevant primitives for data state change.

+
+
+abstract property endpoint: str
+

External service endpoint.

+
+ +
+ +
+
+class ApiService(app: Api)
+

Bases: ApiComponent

+

Service base class. +A Service acts as a translation layer between a controller receiving a request +and managers executing data state change.

+
+
+abstract async delete(pk_val: List[Any], user_info: UserInfo | None = None, **kwargs: Dict[str, Any]) None
+
+ +
+
+abstract async filter(fields: List[str], params: Dict[str, str], stmt_only: bool = False, user_info: UserInfo | None = None, **kwargs: Dict[str, Any]) List[Base]
+
+ +
+
+abstract async read(pk_val: List[Any], fields: List[str], user_info: UserInfo | None = None, **kwargs: Dict[str, Any]) Base
+
+ +
+
+abstract async release(pk_val: List[Any], fields: List[str], update: Dict[str, Any], session: AsyncSession, user_info: UserInfo | None = None) Base
+
+ +
+
+abstract async write(data: Dict[str, Any] | List[Dict[str, Any]], stmt_only: bool = False, user_info: UserInfo | None = None, **kwargs: Dict[str, Any]) UpsertStmt | List[UpsertStmt] | Base | List[Base]
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.components.controllers.admincontroller.html b/biodm/biodm.components.controllers.admincontroller.html new file mode 100644 index 0000000..8b3113d --- /dev/null +++ b/biodm/biodm.components.controllers.admincontroller.html @@ -0,0 +1,152 @@ + + + + + + + biodm.components.controllers.admincontroller module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.components.controllers.admincontroller module

+
+
+class AdminController(*args, read_public=True, **kwargs)
+

Bases: ResourceController

+

Class for admin managed entities, i.e. KC User/Groups/Projects.

+
+
CRUD Behaviour:
    +
  • READ require an admin token based on read_public flag

  • +
  • CREATE/UPDATE/DELETE require an admin token

  • +
+
+
+
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.components.controllers.controller.html b/biodm/biodm.components.controllers.controller.html new file mode 100644 index 0000000..b9cd9ad --- /dev/null +++ b/biodm/biodm.components.controllers.controller.html @@ -0,0 +1,279 @@ + + + + + + + biodm.components.controllers.controller module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.components.controllers.controller module

+

Controller base class.

+
+
+class Controller(app: Api)
+

Bases: ApiComponent

+

Controller Base class: An APP Component exposing a set of routes mapped to method +endpoints including openapi schema generation for that given set.

+
+
+async openapi_schema(_)
+

Generates openapi schema for this controllers’ routes.

+
+
Relevant Documentation:
+
+
+
+ +
+
+abstract routes(**kwargs) List[Mount | Route] | List[Mount] | List[BaseRoute]
+

Controller routes.

+
+ +
+ +
+
+class EntityController(app: Api)
+

Bases: Controller

+
+
EntityController - A controller performing validation and serialization given a schema.

Also requires CRUD methods implementation for that entity.

+
+
+
+
Parameters:
+

schema (class:marshmallow.schema.Schema) – Entity schema class

+
+
+
+
+abstract async create(request: Request) Response
+
+ +
+
+abstract async delete(request: Request) Response
+
+ +
+
+abstract async filter(request: Request) Response
+
+ +
+
+abstract async read(request: Request) Response
+
+ +
+
+schema: Schema
+
+ +
+
+classmethod serialize(data: Dict[str, Any] | Base | List[Base], many: bool, only: Iterable[str] | None = None) str
+

Serialize SQLAlchemy statement execution result to json.

+
+
Parameters:
+
    +
  • data (dict, class:biodm.components.Base, List[class:biodm.components.Base]) – some request body

  • +
  • many (bool) – plurality flag, essential to marshmallow

  • +
  • only (Iterable[str]) – Set of fields to restrict serialization on, optional, defaults to None

  • +
+
+
+
+ +
+
+abstract async update(request: Request) Response
+
+ +
+
+classmethod validate(data: bytes, partial: bool = False) List[Dict[str, Any]] | Dict[str, Any]
+

Check incoming data against class schema and marshall to python dict.

+
+
Parameters:
+
    +
  • data (bytes) – some request body

  • +
  • partial (bool, defaults to False) – accept partial records

  • +
+
+
Returns:
+

Marshalled python dict and plurality flag.

+
+
Return type:
+

Tuple[(Any | List[Any] | Dict[str, Any] | None), bool]

+
+
+
+ +
+ +
+
+class HttpMethod(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)
+

Bases: Enum

+

HTTP Methods.

+
+
+DELETE = 'DELETE'
+
+ +
+
+GET = 'GET'
+
+ +
+
+PATCH = 'PATCH'
+
+ +
+
+POST = 'POST'
+
+ +
+
+PUT = 'PUT'
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.components.controllers.html b/biodm/biodm.components.controllers.html new file mode 100644 index 0000000..37b170e --- /dev/null +++ b/biodm/biodm.components.controllers.html @@ -0,0 +1,208 @@ + + + + + + + biodm.components.controllers package — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+ + +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.components.controllers.resourcecontroller.html b/biodm/biodm.components.controllers.resourcecontroller.html new file mode 100644 index 0000000..c559776 --- /dev/null +++ b/biodm/biodm.components.controllers.resourcecontroller.html @@ -0,0 +1,299 @@ + + + + + + + biodm.components.controllers.resourcecontroller module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.components.controllers.resourcecontroller module

+

Controller class for Tables acting as a Resource.

+
+
+class ResourceController(app: Api, entity: str = '', table: Type[Base] | None = None, schema: Type[Schema] | None = None)
+

Bases: EntityController

+

Class for controllers exposing routes constituting a ressource.

+

Implements and exposes routes under a prefix named as the resource pluralized +that act as a standard REST-to-CRUD interface.

+
+
Parameters:
+
    +
  • app (Api) – running server

  • +
  • entity (str, optional) – entity name, defaults to None, inferred if None

  • +
  • table (Base, optional) – entity table, defaults to None, inferred if None

  • +
  • schema (Schema, optional) – entity schema, defaults to None, inferred if None

  • +
+
+
+
+
+async create(request: Request) Response
+

CREATE.

+

Does “UPSERTS” behind the hood.

+
+
Parameters:
+

request (Request) – incomming request

+
+
Returns:
+

created object in JSON form

+
+
Return type:
+

Response

+
+
+
+ +
+
+async delete(request: Request) Response
+

Delete resource.

+
+
Parameters:
+

request (Request) – incomming request

+
+
Returns:
+

Deletion confirmation ‘Deleted.’

+
+
Return type:
+

Response

+
+
+
+ +
+
+async filter(request: Request) Response
+

Returns all resources, accepting a querystring filter.

+
+ +
+
+property prefix: str
+

Computes route path prefix from entity name.

+
+ +
+
+property qp_id: str
+

Return primary key in queryparam form.

+
+ +
+
+async read(request: Request) Response
+

Fetch associated entity matching id in the path.

+
+
Parameters:
+

request (Request) – incomming request

+
+
Returns:
+

JSON reprentation of the object

+
+
Return type:
+

Response

+
+
+
+ +
+
+async release(request: Request) Response
+

Releases a new version for a versioned resource.

+
+ +
+
+static replace_method_docstrings(method: str, doc: str)
+

Set a mirror function documented by input and calling parent class method.

+
+
Parameters:
+
    +
  • method (str) – method name

  • +
  • doc (str) – new documentation

  • +
+
+
+
+ +
+
+routes(**_) List[Mount | Route] | List[Mount] | List[BaseRoute]
+
+
Sets up standard RESTful endpoints.

child_routes: from children classes calling super().__init__().

+
+
+

Relevant doc: +- https://restfulapi.net/http-methods/

+
+ +
+
+async update(request: Request) Response
+

UPDATE. Essentially calling create, as it perorm upserts.

+
    +
  • Excluded of versioned resources routes.

  • +
+
+
Parameters:
+

request (Request) – incomming request

+
+
Returns:
+

updated object in JSON form

+
+
Return type:
+

Response

+
+
+
+ +
+ +
+
+overload_docstring(f: Callable)
+

Decorator to allow for docstring overloading.

+

To apply on a “c-like” preprocessor on controllers subclasses. +Targeted at the REST-to-CRUD mapped endpoints in order to do a per-entity schema documentation.

+

Necessary because docstring inheritance is managed a little bit weirdly +behind the hood in python and depending on the version the .__doc__ attribute of a +member function is not editable - Not the case as of python 3.11.2.

+

Relevant SO posts: +- https://stackoverflow.com/questions/38125271/extending-or-overwriting-a-docstring-when-composing-classes +- https://stackoverflow.com/questions/1782843/python-decorator-handling-docstrings +- https://stackoverflow.com/questions/13079299/dynamically-adding-methods-to-a-class

+
+
Parameters:
+

f (Callable) – The method we overload the docstrings of

+
+
+
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.components.controllers.s3controller.html b/biodm/biodm.components.controllers.s3controller.html new file mode 100644 index 0000000..fc3ba9c --- /dev/null +++ b/biodm/biodm.components.controllers.s3controller.html @@ -0,0 +1,190 @@ + + + + + + + biodm.components.controllers.s3controller module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.components.controllers.s3controller module

+
+
+class S3Controller(app, entity: str = '', table: type[Base] | None = None, schema: type[Schema] | None = None)
+

Bases: ResourceController

+

Controller for entities involving file management leveraging an S3Service.

+
+
+async complete_multipart(request: Request)
+

Unlike with a pre-signed POST, it is not possible to setup a callback for each part. +Client has to gather etags for each parts while uploading and sumbit them on this route +in order to complete a multipart upload.

+
+
Parameters:
+

request (Request) – incomming request

+
+
Returns:
+

Completion notice.

+
+
Return type:
+

Response

+
+
+
+ +
+
+async download(request: Request)
+

Returns boto3 presigned download URL with a redirect header.

+
+ +
+
+async post_success(request: Request)
+
+
Used as a callback in the s3 presigned upload urls that are emitted.

Uppon receival, update entity status in the DB.

+
+
+
+ +
+
+routes(**_) List[Mount | Route] | List[Mount] | List[BaseRoute]
+

Add an endpoint for successful file uploads and direct download.

+
+ +
+
+svc: S3Service
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.components.html b/biodm/biodm.components.html new file mode 100644 index 0000000..61a00fe --- /dev/null +++ b/biodm/biodm.components.html @@ -0,0 +1,255 @@ + + + + + + + biodm.components package — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.components package

+
+

Subpackages

+ +
+
+

Submodules

+ +
+
+

Module contents

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.components.services.dbservice.html b/biodm/biodm.components.services.dbservice.html new file mode 100644 index 0000000..63fa14f --- /dev/null +++ b/biodm/biodm.components.services.dbservice.html @@ -0,0 +1,310 @@ + + + + + + + biodm.components.services.dbservice module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.components.services.dbservice module

+

Database service: Translates requests data into SQLA statements and execute.

+
+
+class CompositeEntityService(app, table: Type[Base], *args, **kwargs)
+

Bases: UnaryEntityService

+

Handles the WRITE operation for composite entities.

+

SQLAlchemy doesn’t support creating ORM mapped objects with a hierarchical dict structure. +This class is implementing methods in order to parse and insert such data.

+
+
+property permission_relationships: Dict[str, Relationship]
+

Get permissions relationships by computing the difference of between instanciation time +and runtime, since those get populated later in Base.setup_permissions().

+
+ +
+
+async write(**kwargs) Base | List[Base] | UpsertStmt | List[UpsertStmt]
+

CREATE, Handle list and single case.

+
+ +
+ +
+
+class DatabaseService(app: Api)
+

Bases: ApiService

+

DB Service class: manages database transactions for entities. +This abstract class holds atomic database statement execution and utility functions plus +permission logic.

+
+
+async populate_ids_sqlite(**kwargs)
+

Handle SQLite autoincrement for composite primary key. +Which is a handy feature for a versioned entity. So we fetch the current max id in a +separate request and prepopulate the dicts. This is not the most performant, but sqlite +support is mostly for testing purposes.

+
+ +
+
+table: Type[Base]
+
+ +
+ +
+
+class UnaryEntityService(app, table: Type[Base], *args, **kwargs)
+

Bases: DatabaseService

+

Generic Database service class.

+

Called Unary. However, It effectively implements all methods except write for Composite +entities as their implementation is easy to make generic.

+
+
+async delete(pk_val, user_info: UserInfo | None = None, **kwargs) None
+

DELETE.

+
+ +
+
+async filter(fields: List[str], params: Dict[str, str], stmt_only: bool = False, user_info: UserInfo | None = None, **kwargs) List[Base]
+

READ rows filted on query parameters.

+
+ +
+
+gen_cond(pk_val: List[Any]) Any
+

Generates (pk_1 == pk_1.type.python_type(val_1)) & (pk_2 == …) …). +Without evaluating at runtime, so it can be plugged in a where condition.

+
+
Parameters:
+

pk_val (List[Any]) – Primary key values

+
+
Returns:
+

CNF Clause

+
+
Return type:
+

Any

+
+
+
+ +
+
+async getattr_in_session(**kwargs) List[Base]
+
+ +
+
+async read(pk_val: List[Any], fields: List[str], nested_attribute: str | None = None, user_info: UserInfo | None = None, **kwargs) Base
+

READ: fetch one ORM mapped object from value(s) of its primary key.

+
+
Parameters:
+
    +
  • pk_val (List[Any]) – entity primary key values in order

  • +
  • fields (List[str], optional) – fields to restrict the query on, defaults to None

  • +
  • user_info (UserInfo | None, optional) – userinfo, defaults to None

  • +
+
+
Returns:
+

SQLAlchemy ORM item

+
+
Return type:
+

Base

+
+
+
+ +
+
+async read_nested(**kwargs)
+

Read nested collection from an entity.

+
+ +
+
+async release(**kwargs) Base
+
+ +
+
+upsert(data: Dict[Any, str], futures: List[str] | None = None) Insert | Update
+
+
Generates an upsert (Insert + .on_conflict_do_x) depending on data population.

OR an explicit Update statement for partial data with full primary key.

+
+
+

This statement builder is by design taking a unit entity dict and +cannot check if partial data is complete in case this is coming from upper resources +in the hierarchical structure. +In that case statements are patched on the fly at insertion time at +CompositeEntityService._insert_composite().

+

In case of actually incomplete data, some upserts will fail, and raise it up to controller +which has the details about initial validation fail. +Ultimately, the goal is to offer support for a more flexible and tolerant mode of writing +data, use of it is optional.

+

Versioned resource: in the case of a versioned resource, passing a reference is allowed +BUT an update is not as updates shall go through /release route. +Statement will still be emited but simply discard the update.

+
+
Parameters:
+
    +
  • data (Dict[Any, str]) – validated data, unit - i.e. one single entity, no depth - dictionary

  • +
  • futures (List[str], optional) – Fields that will get populated at insertion time, defaults to none

  • +
+
+
Returns:
+

statement

+
+
Return type:
+

Insert | Update

+
+
+
+ +
+
+async write(data: Dict[str, Any] | List[Dict[str, Any]], stmt_only: Literal[True], user_info: UserInfo | None, **kwargs) UpsertStmt
+
+async write(data: Dict[str, Any] | List[Dict[str, Any]], stmt_only: Literal[False], user_info: UserInfo | None, **kwargs) Base | List[Base]
+
+
WRITE validated input data into the db.

Supports input list and a mixin of new and passed by reference inserted data.

+
+
+
    +
  • Does UPSERTS behind the hood, hence this method is also called by UPDATE

  • +
  • Perform permission check according to input data

  • +
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.components.services.html b/biodm/biodm.components.services.html new file mode 100644 index 0000000..f063819 --- /dev/null +++ b/biodm/biodm.components.services.html @@ -0,0 +1,216 @@ + + + + + + + biodm.components.services package — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+ + +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.components.services.k8service.html b/biodm/biodm.components.services.k8service.html new file mode 100644 index 0000000..e40ca69 --- /dev/null +++ b/biodm/biodm.components.services.k8service.html @@ -0,0 +1,156 @@ + + + + + + + biodm.components.services.k8service module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.components.services.k8service module

+
+
+class K8Service(app, table: Type[Base], *args, **kwargs)
+

Bases: CompositeEntityService

+

Manages kubernetes instances.

+
+
+k8s()
+
+ +
+
+async write(data: List[Dict[str, Any]] | Dict[str, Any], stmt_only: bool = False, user_info: UserInfo | None = None, **kwargs) Base | List[Base] | UpsertStmt | List[UpsertStmt]
+

Submits manifest to kubernetes cluster before inserting into DB.

+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.components.services.kcservice.html b/biodm/biodm.components.services.kcservice.html new file mode 100644 index 0000000..3ed8a0a --- /dev/null +++ b/biodm/biodm.components.services.kcservice.html @@ -0,0 +1,232 @@ + + + + + + + biodm.components.services.kcservice module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.components.services.kcservice module

+
+
+class KCGroupService(app, table: Type[Base], *args, **kwargs)
+

Bases: KCService

+
+
+async delete(pk_val: List[Any], user_info: UserInfo | None = None, **_) None
+

DELETE Group from DB then from Keycloak.

+
+ +
+
+static kcpath(path) Path
+

Compute keycloak path from api path.

+
+ +
+
+async read_or_create(data: Dict[str, Any]) None
+

READ group from keycloak, CREATE if missing.

+
+
Parameters:
+

data (Dict[str, Any]) – Group data

+
+
+
+ +
+
+async write(data: List[Dict[str, Any]] | Dict[str, Any], stmt_only: bool = False, user_info: UserInfo | None = None, **kwargs)
+

Create entities on Keycloak Side before passing to parent class for DB.

+
+ +
+ +
+
+class KCService(app, table: Type[Base], *args, **kwargs)
+

Bases: CompositeEntityService

+

Abstract class for local keycloak entities.

+
+
+kc()
+

Return KCManager instance.

+
+ +
+
+abstract async read_or_create(data: Dict[str, Any], /) None
+

Try to read from DB, create on keycloak side if not present. +Populate ‘id’ - Keycloak UUID in string form - in data.

+
+ +
+ +
+
+class KCUserService(app, table: Type[Base], *args, **kwargs)
+

Bases: KCService

+
+
+async delete(pk_val: List[Any], user_info: UserInfo | None = None, **_) None
+

DELETE User from DB then from keycloak.

+
+ +
+
+async read_or_create(data: Dict[str, Any], groups: List[str] | None = None, group_ids: List[str] | None = None) None
+

READ entry from Database, CREATE if missing.

+
+
Parameters:
+
    +
  • data (Dict[str, Any]) – Entry object representation

  • +
  • groups (List[str], optional) – User groups, defaults to None

  • +
  • group_ids (List[str], optional) – User groups ids, defaults to None

  • +
+
+
Returns:
+

User id

+
+
Return type:
+

str

+
+
+
+ +
+
+async write(data: Dict[str, Any] | List[Dict[str, Any]], stmt_only: bool = False, user_info: UserInfo | None = None, **kwargs)
+

CREATE entities on Keycloak, before inserting in DB.

+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.components.services.s3service.html b/biodm/biodm.components.services.s3service.html new file mode 100644 index 0000000..116860f --- /dev/null +++ b/biodm/biodm.components.services.s3service.html @@ -0,0 +1,195 @@ + + + + + + + biodm.components.services.s3service module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.components.services.s3service module

+
+
+class S3Service(app, table: Type[Base], *args, **kwargs)
+

Bases: CompositeEntityService

+

Class for automatic management of S3 bucket transactions for file resources.

+
+
+async complete_multipart(**kwargs)
+
+ +
+
+async download(**kwargs)
+
+ +
+
+async gen_key(item, session: AsyncSession)
+
+ +
+
+async gen_upload_form(file: S3File, session: AsyncSession)
+

Populates an Upload for a newly created file. Handling simple post and multipart_upload +cases.

+
+
Parameters:
+
    +
  • file (S3File) – New file

  • +
  • session (AsyncSession) – current session

  • +
+
+
+
+ +
+
+post_callback(item) str
+
+ +
+
+async post_success(**kwargs)
+
+ +
+
+async release(**kwargs) Base
+
+ +
+
+s3()
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.components.table.html b/biodm/biodm.components.table.html new file mode 100644 index 0000000..ed72bbb --- /dev/null +++ b/biodm/biodm.components.table.html @@ -0,0 +1,414 @@ + + + + + + + biodm.components.table module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.components.table module

+

SQLAlchemy tables convenience Parent classes: +- Declarative Base +- File entity +- Permission setup logic

+
+
+class Base(**kwargs: Any)
+

Bases: DeclarativeBase, AsyncAttrs

+

Base class for ORM declarative Tables.

+
+
Parameters:
+
    +
  • svc (DatabaseService) – Enable entity - service linkage

  • +
  • ctrl (ResourceController) – Enable entity - controller linkage -> Resources tables only

  • +
  • raw_permissions (Dict) – Stores rules for user defined permissions on hierarchical entities

  • +
  • permissions (Dict) – Stores processed permissions with hierarchical linkage.

  • +
+
+
+
+
+classmethod col(name: str)
+

Return columns object from name.

+
+ +
+
+classmethod colinfo(name: str) Tuple[Column, type]
+

Return column and associated python type for conditions.

+
+ +
+
+ctrl: ClassVar[Type[ResourceController]]
+
+ +
+
+classmethod has_default(name: str) bool
+

Flag if column has default value.

+
+ +
+
+classmethod is_autoincrement(name: str) bool
+

Flag if column is autoincrement.

+

Warning! This check is backend dependent and should be changed when supporting a new one. +E.g. Oracle backend will not react appropriately. +- https://groups.google.com/g/sqlalchemy/c/o5YQNH5UUko

+
+ +
+
+is_versioned = False
+
+ +
+
+metadata: ClassVar[MetaData] = MetaData()
+

Refers to the _schema.MetaData collection that will be used +for new _schema.Table objects.

+ +
+ +
+
+permissions: ClassVar[Dict[Any, Any]] = {}
+
+ +
+
+pk()
+

Return primary key names.

+
+ +
+
+raw_permissions: ClassVar[Dict[str, Tuple[Type[Self], Tuple[Permission]]]] = {}
+
+ +
+
+registry: ClassVar[_RegistryType] = <sqlalchemy.orm.decl_api.registry object>
+

Refers to the _orm.registry in use where new +_orm.Mapper objects will be associated.

+
+ +
+
+classmethod relationships()
+

Return table relationships.

+
+ +
+
+required()
+

Gets all required fields to create a new entry in this table.

+
+
Returns:
+

fields name list

+
+
Return type:
+

Set[str]

+
+
+
+ +
+
+classmethod setup_permissions(app)
+

After tables have been added to Base, and before you initialize DB +you shall call this method to factor in changes.

+
    +
  • +
    For each declared permission.
      +
    • +
      Creates an associative table
        +
      • +
        indexed by Parent table pk
          +
        • children hold parent id

        • +
        +
        +
        +
      • +
      +
      +
      +
    • +
    • +
      holds listgroup objects mapped to enabled verbs
        +
      • Set ref for Children controller

      • +
      +
      +
      +
    • +
    +
    +
    +
  • +
+

Has to be done after all tables have been declared.

+

Currently assumes straight composition: +i.e. You cannot flag an o2m with the same target in two different parent classes.

+
+ +
+
+svc: ClassVar[Type[DatabaseService]]
+
+ +
+
+classmethod target_table(name)
+

Return target table of a property.

+
+ +
+ +
+
+class Permission(field: Column, read: bool = False, write: bool = False, download: bool = False)
+

Bases: object

+

Holds permissions for a given entity’s attributes.

+
+
+download: bool = False
+
+ +
+
+property enabled_verbs: Set[str]
+
+ +
+
+field: Column
+
+ +
+
+fields = {'download', 'field', 'read', 'write'}
+
+ +
+
+read: bool = False
+
+ +
+
+write: bool = False
+
+ +
+ +
+
+class S3File
+

Bases: object

+

Class to use in order to have a file managed on S3 bucket associated to this table +Defaults internal fields that are expected by S3Service.

+
+
+dl_count = Column(None, Integer(), table=None, nullable=False, server_default=DefaultClause('0', for_update=False))
+
+ +
+
+emited_at = Column(None, TIMESTAMP(timezone=True), table=None, nullable=False, default=CallableColumnDefault(<function utcnow>))
+
+ +
+
+extension = Column(None, String(length=10), table=None, nullable=False)
+
+ +
+
+filename = Column(None, String(length=100), table=None, nullable=False)
+
+ +
+
+id_upload: Mapped[int] = <sqlalchemy.orm.properties.MappedColumn object>
+
+ +
+
+key_salt = Column(None, String(), table=None, nullable=False, default=CallableColumnDefault(<function S3File.<lambda>>))
+
+ +
+
+ready = Column(None, BOOLEAN(), table=None, nullable=False, server_default=DefaultClause('0', for_update=False))
+
+ +
+
+size = Column(None, Integer(), table=None, nullable=False)
+
+ +
+
+upload = <_RelationshipDeclared at 0x7f8c23b6fe30; no key>
+
+ +
+
+validated_at = Column(None, TIMESTAMP(timezone=True), table=None)
+
+ +
+ +
+
+class Versioned
+

Bases: object

+

Versioned entity parent class.

+
    +
  • Populates id/version primary_key fields

  • +
  • Enable release functionalities

  • +
+
+
+id = Column(None, Integer(), table=None, primary_key=True, nullable=False)
+
+ +
+
+version = Column(None, Integer(), table=None, primary_key=True, nullable=False, server_default=DefaultClause('1', for_update=False))
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.config.html b/biodm/biodm.config.html new file mode 100644 index 0000000..76220bf --- /dev/null +++ b/biodm/biodm.config.html @@ -0,0 +1,136 @@ + + + + + + + biodm.config module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.config module

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.error.html b/biodm/biodm.error.html new file mode 100644 index 0000000..f0acc3c --- /dev/null +++ b/biodm/biodm.error.html @@ -0,0 +1,155 @@ + + + + + + + biodm.error module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.error module

+
+
+class Error(status, detail=None)
+

Bases: object

+

Error class.

+
+
+property response
+
+ +
+ +
+
+async onerror(_, exc)
+

Error event handler.

+

Relevant documentation: https://restfulapi.net/http-status-codes/

+
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.exceptions.html b/biodm/biodm.exceptions.html new file mode 100644 index 0000000..f096360 --- /dev/null +++ b/biodm/biodm.exceptions.html @@ -0,0 +1,306 @@ + + + + + + + biodm.exceptions module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.exceptions module

+
+
+exception AsyncDBError
+

Bases: DBError

+

Raised when asyncpg fails.

+
+ +
+
+exception DBError
+

Bases: RuntimeError

+

Raised when DB related errors are catched.

+
+
+sa_error: Exception
+
+ +
+ +
+
+exception FailedCreate(detail: str)
+

Bases: RequestError

+

Could not create record.

+
+ +
+
+exception FailedDelete(detail: str)
+

Bases: RequestError

+

Raised when a delete operation is not successful.

+
+ +
+
+exception FailedRead(detail: str)
+

Bases: RequestError

+

Requested record doesn’t exist.

+
+ +
+
+exception FailedUpdate(detail: str)
+

Bases: RequestError

+

Raised when an update operation is not successful.

+
+ +
+
+exception FileNotUploadedError(detail: str)
+

Bases: RequestError

+

Raised when trying to download a file that has not been uploaded yet.

+
+ +
+
+exception ImplementionError
+

Bases: RuntimeError

+

Raised when a wrong use of components is detected.

+
+ +
+
+exception InvalidCollectionMethod(detail: str)
+

Bases: RequestError

+

Raised when a unit method is accesed as a collection.

+
+ +
+
+exception KeycloakUnavailableError
+

Bases: RuntimeError

+

Raised when Keycloak failed to initialize.

+
+ +
+
+exception ManifestError(detail: str)
+

Bases: RequestError

+

Raised when a request requiring a manifest id fails to find it in instance.

+
+ +
+
+exception MissingDB(detail: str)
+

Bases: RequestError

+

DB access attempted with no manager attached to the service.

+
+ +
+
+exception MissingService
+

Bases: RuntimeError

+

Raised when a controller expects a service that is not present.

+
+ +
+
+exception PartialIndex(detail: str)
+

Bases: RequestError

+

Raised when a method expecting entity primary key receives a partial index.

+
+ +
+
+exception PayloadEmptyError
+

Bases: RuntimeError

+

Raised when a route expecting a payload, is reached without one.

+
+ +
+
+exception PayloadJSONDecodingError
+

Bases: RuntimeError

+

Raised when payload data failed to be parsed in JSON format.

+
+ +
+
+exception PayloadValidationError
+

Bases: RuntimeError

+

Raised when input data can not be coerced into an entity.

+
+ +
+
+exception PostgresUnavailableError
+

Bases: RuntimeError

+

Raised when Postgres failed to initialize.

+
+ +
+
+exception RequestError(detail: str)
+

Bases: RuntimeError

+
+
+detail: str
+
+ +
+ +
+
+exception SchemaError
+

Bases: RuntimeError

+

Raised when faulty schema pattern is detected.

+
+ +
+
+exception TokenDecodingError(detail: str)
+

Bases: RequestError

+

Raised when token decoding failed.

+
+ +
+
+exception UnauthorizedError(detail: str)
+

Bases: RequestError

+

Raised when a request on a group restricted route is sent by an unauthorized user.

+
+ +
+
+exception UpdateVersionedError(detail: str)
+

Bases: RequestError

+

Raised when an attempt at updating a versioned resource is detected.

+
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.html b/biodm/biodm.html new file mode 100644 index 0000000..de59877 --- /dev/null +++ b/biodm/biodm.html @@ -0,0 +1,421 @@ + + + + + + + biodm package — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm package

+
+

Subpackages

+
+ +
+
+
+

Submodules

+ +
+
+

Module contents

+

BioDM framework.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.managers.dbmanager.html b/biodm/biodm.managers.dbmanager.html new file mode 100644 index 0000000..d23b7ce --- /dev/null +++ b/biodm/biodm.managers.dbmanager.html @@ -0,0 +1,189 @@ + + + + + + + biodm.managers.dbmanager module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.managers.dbmanager module

+
+
+class DatabaseManager(app: Api)
+

Bases: ApiManager

+

Manages DB side query execution.

+
+
+static async_database_url(url) str
+

Adds a matching async driver to a database url.

+
+ +
+
+property endpoint
+

External service endpoint.

+
+ +
+
+static in_session(db_exec: Callable) Callable
+
+
Decorator that ensures db_exec receives a session.

Session object is either passed as an argument (from nested obj creation) or a new context +manager is opened. This decorator guarantees exactly 1 session per request.

+
+
+

Also performs serialization within a sync session:

+
    +
  • Avoids errors in case serializing acceses a lazy attribute

  • +
  • All functions applying this decorator should pass down some **kwargs

  • +
+
+ +
+
+async init_db() None
+

Drop all tables and create them.

+
+ +
+
+session() AsyncGenerator[AsyncSession, None]
+

Opens and yields a new AsyncSession.

+
+ +
+
+static sqlite_declare_strrev(conn, _)
+

Custom string revese function for SQLite backend.

+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.managers.html b/biodm/biodm.managers.html new file mode 100644 index 0000000..e5a43ed --- /dev/null +++ b/biodm/biodm.managers.html @@ -0,0 +1,224 @@ + + + + + + + biodm.managers package — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.managers package

+
+

Submodules

+
+ +
+
+
+

Module contents

+

I/O with external services.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.managers.k8smanager.html b/biodm/biodm.managers.k8smanager.html new file mode 100644 index 0000000..b802238 --- /dev/null +++ b/biodm/biodm.managers.k8smanager.html @@ -0,0 +1,280 @@ + + + + + + + biodm.managers.k8smanager module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.managers.k8smanager module

+
+
+class K8sManager(app, host, cert, token, namespace)
+

Bases: ApiManager

+

Small util wrapper around kubernetes python client API.

+
+
Related config:

K8_HOST Address of the kubernetes cluster. +K8_TOKEN Token of the authorized serviceaccount. +K8_CERT Path to kubernetes cluster root certificate +K8_NAMESPACE Active namespace

+
+
+

The client exposes several APIs: +- https://github.com/kubernetes-client/python/blob/a6d44ff625b5e8d8ad380a70245d40fa3d5472b2/kubernetes/README.md?plain=1 +Each api has access to a subset of the ressources.

+
+
+property AppsV1Api: AppsV1Api
+

AppsV1 kubernetes api

+
+ +
+
+property CoreV1Api: CoreV1Api
+

CoreV1 kubernetes api

+
+ +
+
+property CustomObjectsApi: CustomObjectsApi
+

NetworkingV1 kubernetes api

+
+ +
+
+property NetworkingV1Api: NetworkingV1Api
+

NetworkingV1 kubernetes api

+
+ +
+
+authenticate(token, host, cert)
+

Set configuration with the credentials and certificate

+
+ +
+
+change_namespace(namespace: str)
+

Change active namespace

+
+ +
+
+create_custom_resource(manifest: dict) None
+

Create a custom resource.

+
+ +
+
+create_deployment(manifest: Dict[str, Any]) None
+

Create a deployment

+
+ +
+
+create_ingress(manifest: dict)
+

Create an ingress

+
+ +
+
+create_service(manifest: dict)
+

Create a service

+
+ +
+
+delete_custom_object(name: str, manifest: Dict[str, Any], group='cnag.eu', version='v1', plural='suis') Any
+
+ +
+
+property endpoint
+

External service endpoint.

+
+ +
+
+static get_custom_resource_params(manifest: dict) Tuple[str, str, str]
+
+ +
+
+static get_name_in_manifest(manifest: Dict[str, Any]) str
+

Try to find and return metadata.name field from a manifest

+
+ +
+
+list_custom_object(manifest: dict, label_selector) List[Any]
+
+ +
+
+list_deployments() list
+

List all deployments.

+
+ +
+
+list_pods()
+

List all pods.

+
+ +
+
+list_services_ports(**kwargs) list
+

List all service ports in use, support selectors.

+
+ +
+
+log(*args)
+

Conditional print

+
+ +
+
+read_deployment(name, **kwargs) list
+
+ +
+
+read_ingress(name) None
+
+ +
+
+read_service_status(name)
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.managers.kcmanager.html b/biodm/biodm.managers.kcmanager.html new file mode 100644 index 0000000..0237da4 --- /dev/null +++ b/biodm/biodm.managers.kcmanager.html @@ -0,0 +1,247 @@ + + + + + + + biodm.managers.kcmanager module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.managers.kcmanager module

+
+
+class KeycloakManager(app: Api, host: str, realm: str, public_key: str, admin: str, admin_password: str, client_id: str, client_secret: str, jwt_options: dict)
+

Bases: ApiManager

+

Manages a service account connection and an admin connection. +Use the first to authenticate tokens and the second to manage the realm.

+
+
+property admin
+

Admin connection.

+
+ +
+
+async auth_url(redirect_uri: str)
+

Authentication URL.

+
+ +
+
+async create_group(name: str, parent: str | None = None) str
+

Create group.

+
+ +
+
+async create_user(data: Dict[str, Any], groups: List[str] | None = None) str
+
+ +
+
+async decode_token(token: str)
+

Decode token.

+
+ +
+
+async delete_group(user_id: str)
+

Delete group with this id.

+
+ +
+
+async delete_user(user_id: str) None
+

Delete user with this id.

+
+ +
+
+property endpoint
+

External service endpoint.

+
+ +
+
+async get_group(id: str)
+
+ +
+
+async get_group_by_name(name: str)
+
+ +
+
+async get_group_by_path(path: str)
+
+ +
+
+async get_user_by_username(username: str)
+
+ +
+
+async get_user_groups(user_id: str)
+
+ +
+
+async group_user_add(user_id: str, group_id: str)
+

Add user with user_id to group with group_id.

+
+ +
+
+property openid
+

Service account connection.

+
+ +
+
+async redeem_code_for_token(code: str, redirect_uri: str)
+

Code for token.

+
+ +
+
+async update_group(group_id: str, data: Dict[str, Any])
+

Update group.

+
+ +
+
+async update_user(user_id: str, data: Dict[str, Any])
+

Update user.

+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.managers.s3manager.html b/biodm/biodm.managers.s3manager.html new file mode 100644 index 0000000..73df395 --- /dev/null +++ b/biodm/biodm.managers.s3manager.html @@ -0,0 +1,211 @@ + + + + + + + biodm.managers.s3manager module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.managers.s3manager module

+
+
+class S3Manager(app: Api, endpoint_url: str, bucket_name: str, access_key_id: str, secret_access_key: str, url_expiration: int, pending_expiration: int, region_name: str, file_size_limit: int)
+

Bases: ApiManager

+

Manages requests with an S3 storage instance.

+
+
+abort_multipart_upload(object_name, upload_id)
+
+ +
+
+complete_multipart_upload(object_name, upload_id, parts)
+
+ +
+
+create_multipart_upload(object_name) List[Any]
+

_summary_

+ +
+
Parameters:
+

object_name (_type_) – _description_

+
+
Raises:
+

e – _description_

+
+
Returns:
+

_description_

+
+
Return type:
+

List[Any]

+
+
+
+ +
+
+create_presigned_download_url(object_name: str) Any
+

Generate a presigned URL to share an S3 object

+
+
Parameters:
+

object_name (String) – Object Key

+
+
Returns:
+

Presigned URL as string.

+
+
+
+ +
+
+create_presigned_post(object_name, callback) Any
+

Generates a presigned url + form fiels to upload a given file on s3 bucket.

+

Relevant links: +- https://boto3.amazonaws.com/v1/documentation/api/latest/guide/s3-presigned-urls.html +- https://github.com/minio/minio/issues/19811#issue-2317920163

+
+ +
+
+create_upload_part(object_name, upload_id, part_number)
+
+ +
+
+property endpoint: str
+

External service endpoint.

+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.schemas.group.html b/biodm/biodm.schemas.group.html new file mode 100644 index 0000000..8fb6364 --- /dev/null +++ b/biodm/biodm.schemas.group.html @@ -0,0 +1,149 @@ + + + + + + + biodm.schemas.group module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.schemas.group module

+
+
+class GroupSchema(*, only: Sequence[str] | AbstractSet[str] | None = None, exclude: Sequence[str] | AbstractSet[str] = (), many: bool = False, context: dict | None = None, load_only: Sequence[str] | AbstractSet[str] = (), dump_only: Sequence[str] | AbstractSet[str] = (), partial: bool | Sequence[str] | AbstractSet[str] | None = None, unknown: str | None = None)
+

Bases: Schema

+

Schema for Keycloak Groups. id field is purposefully left out as we manage it internally.

+
+
+opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.schemas.html b/biodm/biodm.schemas.html new file mode 100644 index 0000000..157598b --- /dev/null +++ b/biodm/biodm.schemas.html @@ -0,0 +1,190 @@ + + + + + + + biodm.schemas package — Python documentation + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/biodm/biodm.schemas.k8sinstance.html b/biodm/biodm.schemas.k8sinstance.html new file mode 100644 index 0000000..2b9d8c8 --- /dev/null +++ b/biodm/biodm.schemas.k8sinstance.html @@ -0,0 +1,149 @@ + + + + + + + biodm.schemas.k8sinstance module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.schemas.k8sinstance module

+
+
+class K8sinstanceSchema(*, only: Sequence[str] | AbstractSet[str] | None = None, exclude: Sequence[str] | AbstractSet[str] = (), many: bool = False, context: dict | None = None, load_only: Sequence[str] | AbstractSet[str] = (), dump_only: Sequence[str] | AbstractSet[str] = (), partial: bool | Sequence[str] | AbstractSet[str] | None = None, unknown: str | None = None)
+

Bases: Schema

+

K8Instance Schema.

+
+
+opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.schemas.listgroup.html b/biodm/biodm.schemas.listgroup.html new file mode 100644 index 0000000..73484dc --- /dev/null +++ b/biodm/biodm.schemas.listgroup.html @@ -0,0 +1,148 @@ + + + + + + + biodm.schemas.listgroup module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.schemas.listgroup module

+
+
+class ListGroupSchema(*, only: Sequence[str] | AbstractSet[str] | None = None, exclude: Sequence[str] | AbstractSet[str] = (), many: bool = False, context: dict | None = None, load_only: Sequence[str] | AbstractSet[str] = (), dump_only: Sequence[str] | AbstractSet[str] = (), partial: bool | Sequence[str] | AbstractSet[str] | None = None, unknown: str | None = None)
+

Bases: Schema

+
+
+opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.schemas.upload.html b/biodm/biodm.schemas.upload.html new file mode 100644 index 0000000..2a76a9a --- /dev/null +++ b/biodm/biodm.schemas.upload.html @@ -0,0 +1,170 @@ + + + + + + + biodm.schemas.upload module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.schemas.upload module

+
+
+class PartsEtagSchema(*, only: Sequence[str] | AbstractSet[str] | None = None, exclude: Sequence[str] | AbstractSet[str] = (), many: bool = False, context: dict | None = None, load_only: Sequence[str] | AbstractSet[str] = (), dump_only: Sequence[str] | AbstractSet[str] = (), partial: bool | Sequence[str] | AbstractSet[str] | None = None, unknown: str | None = None)
+

Bases: Schema

+
+
+opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>
+
+ +
+ +
+
+class UploadPartSchema(*, only: Sequence[str] | AbstractSet[str] | None = None, exclude: Sequence[str] | AbstractSet[str] = (), many: bool = False, context: dict | None = None, load_only: Sequence[str] | AbstractSet[str] = (), dump_only: Sequence[str] | AbstractSet[str] = (), partial: bool | Sequence[str] | AbstractSet[str] | None = None, unknown: str | None = None)
+

Bases: Schema

+
+
+opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>
+
+ +
+ +
+
+class UploadSchema(*, only: Sequence[str] | AbstractSet[str] | None = None, exclude: Sequence[str] | AbstractSet[str] = (), many: bool = False, context: dict | None = None, load_only: Sequence[str] | AbstractSet[str] = (), dump_only: Sequence[str] | AbstractSet[str] = (), partial: bool | Sequence[str] | AbstractSet[str] | None = None, unknown: str | None = None)
+

Bases: Schema

+
+
+opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.schemas.user.html b/biodm/biodm.schemas.user.html new file mode 100644 index 0000000..32af5c2 --- /dev/null +++ b/biodm/biodm.schemas.user.html @@ -0,0 +1,149 @@ + + + + + + + biodm.schemas.user module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.schemas.user module

+
+
+class UserSchema(*, only: Sequence[str] | AbstractSet[str] | None = None, exclude: Sequence[str] | AbstractSet[str] = (), many: bool = False, context: dict | None = None, load_only: Sequence[str] | AbstractSet[str] = (), dump_only: Sequence[str] | AbstractSet[str] = (), partial: bool | Sequence[str] | AbstractSet[str] | None = None, unknown: str | None = None)
+

Bases: Schema

+

Schema for Keycloak Users. id field is purposefully left out as we manage it internally.

+
+
+opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.scope.html b/biodm/biodm.scope.html new file mode 100644 index 0000000..ed04293 --- /dev/null +++ b/biodm/biodm.scope.html @@ -0,0 +1,158 @@ + + + + + + + biodm.scope module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.scope module

+
+
+class Scope(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)
+

Bases: Flag

+

Runtime Feature Flag.

+
+
+DEBUG = 1
+
+ +
+
+PROD = 0
+
+ +
+
+TEST = 2
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.tables.asso.html b/biodm/biodm.tables.asso.html new file mode 100644 index 0000000..c90d064 --- /dev/null +++ b/biodm/biodm.tables.asso.html @@ -0,0 +1,137 @@ + + + + + + + biodm.tables.asso module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.tables.asso module

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.tables.group.html b/biodm/biodm.tables.group.html new file mode 100644 index 0000000..5db2f37 --- /dev/null +++ b/biodm/biodm.tables.group.html @@ -0,0 +1,179 @@ + + + + + + + biodm.tables.group module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.tables.group module

+
+
+class Group(**kwargs)
+

Bases: Base

+

Group table.

+
+
+children
+
+ +
+
+id: Mapped[str]
+
+ +
+
+n_members: Mapped[int]
+
+ +
+
+parent
+
+ +
+
+path: Mapped[str]
+
+ +
+
+path_parent
+
+ +
+
+users: Mapped[List[User]]
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.tables.history.html b/biodm/biodm.tables.history.html new file mode 100644 index 0000000..acb2a41 --- /dev/null +++ b/biodm/biodm.tables.history.html @@ -0,0 +1,169 @@ + + + + + + + biodm.tables.history module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.tables.history module

+
+
+class History(**kwargs)
+

Bases: Base

+

History table.

+
+
+content
+
+ +
+
+endpoint
+
+ +
+
+method
+
+ +
+
+timestamp
+
+ +
+
+username_user: Mapped[str]
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.tables.html b/biodm/biodm.tables.html new file mode 100644 index 0000000..9e5707c --- /dev/null +++ b/biodm/biodm.tables.html @@ -0,0 +1,223 @@ + + + + + + + biodm.tables package — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ + +
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.tables.k8sinstance.html b/biodm/biodm.tables.k8sinstance.html new file mode 100644 index 0000000..788456d --- /dev/null +++ b/biodm/biodm.tables.k8sinstance.html @@ -0,0 +1,174 @@ + + + + + + + biodm.tables.k8sinstance module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.tables.k8sinstance module

+
+
+class K8sInstance(**kwargs)
+

Bases: Base

+

K8Instance table.

+
+
+emited_at
+
+ +
+
+expiring_at
+
+ +
+
+id: Mapped[UUID]
+
+ +
+
+manifest
+
+ +
+
+namespace
+
+ +
+
+username_user
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.tables.listgroup.html b/biodm/biodm.tables.listgroup.html new file mode 100644 index 0000000..0caec26 --- /dev/null +++ b/biodm/biodm.tables.listgroup.html @@ -0,0 +1,154 @@ + + + + + + + biodm.tables.listgroup module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.tables.listgroup module

+
+
+class ListGroup(**kwargs)
+

Bases: Base

+

ListGroup table.

+
+
+groups: Mapped[List[Group]]
+
+ +
+
+id
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.tables.upload.html b/biodm/biodm.tables.upload.html new file mode 100644 index 0000000..dbfdaa6 --- /dev/null +++ b/biodm/biodm.tables.upload.html @@ -0,0 +1,158 @@ + + + + + + + biodm.tables.upload module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.tables.upload module

+
+
+class Upload(**kwargs)
+

Bases: Base

+
+
+id: Mapped[int]
+
+ +
+
+parts: Mapped[List[UploadPart]]
+
+ +
+
+s3_uploadId: Mapped[str]
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.tables.upload_part.html b/biodm/biodm.tables.upload_part.html new file mode 100644 index 0000000..4088165 --- /dev/null +++ b/biodm/biodm.tables.upload_part.html @@ -0,0 +1,163 @@ + + + + + + + biodm.tables.upload_part module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.tables.upload_part module

+
+
+class UploadPart(**kwargs)
+

Bases: Base

+
+
+form: Mapped[str]
+
+ +
+
+id_upload: Mapped[int]
+
+ +
+
+part_number: Mapped[int]
+
+ +
+
+upload: Mapped[Upload]
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.tables.user.html b/biodm/biodm.tables.user.html new file mode 100644 index 0000000..eaccd96 --- /dev/null +++ b/biodm/biodm.tables.user.html @@ -0,0 +1,174 @@ + + + + + + + biodm.tables.user module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.tables.user module

+
+
+class User(**kwargs)
+

Bases: Base

+

User table -> Not locally storing passwords.

+
+
+email
+
+ +
+
+first_name
+
+ +
+
+groups: Mapped[List[Group]]
+
+ +
+
+id: Mapped[str]
+
+ +
+
+last_name
+
+ +
+
+username
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.utils.html b/biodm/biodm.utils.html new file mode 100644 index 0000000..abba7cb --- /dev/null +++ b/biodm/biodm.utils.html @@ -0,0 +1,204 @@ + + + + + + + biodm.utils package — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+ + +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.utils.security.html b/biodm/biodm.utils.security.html new file mode 100644 index 0000000..dbf0d29 --- /dev/null +++ b/biodm/biodm.utils.security.html @@ -0,0 +1,296 @@ + + + + + + + biodm.utils.security module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.utils.security module

+

Security convenience functions.

+
+
+class UserInfo(*args, **kwargs)
+

Bases: aobject

+

Hold user info for a given request.

+

If the request contains an authentication header, self.info shall return User Info, else None

+
+
+class KeycloakManager(app: Api, host: str, realm: str, public_key: str, admin: str, admin_password: str, client_id: str, client_secret: str, jwt_options: dict)
+

Bases: ApiManager

+

Manages a service account connection and an admin connection. +Use the first to authenticate tokens and the second to manage the realm.

+
+
+property admin
+

Admin connection.

+
+ +
+
+async auth_url(redirect_uri: str)
+

Authentication URL.

+
+ +
+
+async create_group(name: str, parent: str | None = None) str
+

Create group.

+
+ +
+
+async create_user(data: Dict[str, Any], groups: List[str] | None = None) str
+
+ +
+
+async decode_token(token: str)
+

Decode token.

+
+ +
+
+async delete_group(user_id: str)
+

Delete group with this id.

+
+ +
+
+async delete_user(user_id: str) None
+

Delete user with this id.

+
+ +
+
+property endpoint
+

External service endpoint.

+
+ +
+
+async get_group(id: str)
+
+ +
+
+async get_group_by_name(name: str)
+
+ +
+
+async get_group_by_path(path: str)
+
+ +
+
+async get_user_by_username(username: str)
+
+ +
+
+async get_user_groups(user_id: str)
+
+ +
+
+async group_user_add(user_id: str, group_id: str)
+

Add user with user_id to group with group_id.

+
+ +
+
+property openid
+

Service account connection.

+
+ +
+
+async redeem_code_for_token(code: str, redirect_uri: str)
+

Code for token.

+
+ +
+
+async update_group(group_id: str, data: Dict[str, Any])
+

Update group.

+
+ +
+
+async update_user(user_id: str, data: Dict[str, Any])
+

Update user.

+
+ +
+ +
+
+static auth_header(request) str | None
+

Check and return token from headers if present else returns None.

+
+ +
+
+async decode_token(token: str) Tuple[str, List, List]
+

Decode token.

+
+ +
+
+property info: Tuple[str, List, List] | None
+
+ +
+
+kc: KeycloakManager
+
+ +
+ +
+
+admin_required(f)
+

group_required special case for admin group.

+
+ +
+
+group_required(f, groups: List)
+

Decorator for function expecting groups: decorates a controller CRUD function.

+
+ +
+
+login_required(f)
+

Docorator for function expecting header ‘Authorization: Bearer <token>’

+
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.utils.sqla.html b/biodm/biodm.utils.sqla.html new file mode 100644 index 0000000..8da73cb --- /dev/null +++ b/biodm/biodm.utils.sqla.html @@ -0,0 +1,168 @@ + + + + + + + biodm.utils.sqla module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.utils.sqla module

+
+
+class CompositeInsert(item: Insert, nested: Dict[str, Insert | Self | Tuple[Insert | Self]], delayed: Dict[str, Insert | Self | Tuple[Insert | Self]])
+

Bases: object

+

Class to hold composite entities statements before insertion.

+
+
Parameters:
+
    +
  • item (Insert) – Parent item insert statement

  • +
  • nested (Dict[str, Insert | CompositeInsert | List[Insert] | List[CompositeInsert]]) – Nested items insert statement indexed by attribute name

  • +
  • delayed (Dict[str, Insert | CompositeInsert | List[Insert] | List[CompositeInsert]]) – Nested list of items insert statements indexed by attribute name

  • +
+
+
+
+
+delayed: Dict[str, Insert | Self | Tuple[Insert | Self]]
+
+ +
+
+item: Insert
+
+ +
+
+nested: Dict[str, Insert | Self | Tuple[Insert | Self]]
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/biodm.utils.utils.html b/biodm/biodm.utils.utils.html new file mode 100644 index 0000000..e5f3973 --- /dev/null +++ b/biodm/biodm.utils.utils.html @@ -0,0 +1,228 @@ + + + + + + + biodm.utils.utils module — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

biodm.utils.utils module

+

Utils.

+
+
+class aobject(*args, **kwargs)
+

Bases: object

+

Inheriting this class allows you to define an async __init__. +Syntax sugar allowing you to create objects like this await MyClass(params).

+

Courtesy of: https://stackoverflow.com/a/45364670/6847689

+
+ +
+
+class classproperty(method: Callable[[...], _T])
+

Bases: Generic[_T]

+

Descriptor combining @classmethod and @property behaviours for python v3.11+. +note: only implements the getter.

+

Coutesy of: https://stackoverflow.com/a/76378416/6847689

+
+ +
+
+coalesce_dicts(ls: List[Dict[_T, _U]]) Dict[_T, _U]
+

Assembles multiple dicts into one. +- Overlapping keys: override value in order.

+
+ +
+
+json_bytes(d: Dict[Any, Any]) bytes
+

Encodes python Dict as utf-8 bytes.

+
+ +
+
+json_response(data: Any, status_code: int) Response
+

Formats a Response object and set application/json header.

+
+ +
+
+partition(ls: List[_T], cond: Callable[[_T], bool], excl_na: bool = True) Tuple[List[_T], List[_T]]
+

Partition a list into two based on condition. +Return list of values checking condition. +If excl_na, values whose truth value is False will be evicted from both lists.

+
+
Parameters:
+
    +
  • ls (list) – input list

  • +
  • cond (Callable[[_T], bool]) – Condition

  • +
  • excl_na – Exclude empty flag

  • +
+
+
Returns:
+

Lists of elements separated around condition

+
+
Return type:
+

List[_T], List[_T]

+
+
+
+ +
+
+to_it(x: _T | Tuple[_T, ...] | List[_T]) Tuple[_T, ...] | List[_T]
+

Return identity list/tuple or pack atomic value in an iterable tuple.

+
+ +
+
+touch(fname: str) None
+

Python version of the unix shell touch function.

+
+ +
+
+unevalled_all(ls: Iterator[Any]) Any
+

Build (ls[0] and ls[1] … ls[n]) but does not evaluate like all() does.

+
+ +
+
+unevalled_or(ls: Iterator[Any]) Any
+

Build (ls[0] or ls[1] … ls[n]) but does not evaluate like or() does.

+
+ +
+
+utcnow() datetime
+

Support for python==3.10 and below.

+
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/biodm/modules.html b/biodm/modules.html new file mode 100644 index 0000000..b53602d --- /dev/null +++ b/biodm/modules.html @@ -0,0 +1,214 @@ + + + + + + + API Reference — Python documentation + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/developer_manual/advanced_use.html b/developer_manual/advanced_use.html new file mode 100644 index 0000000..f29422d --- /dev/null +++ b/developer_manual/advanced_use.html @@ -0,0 +1,239 @@ + + + + + + + Advanced Use — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Advanced Use

+

This section describes how to implement a server that goes beyond the standard functionalities +provided by BioDM.

+
+

Custom resource

+

As previously explained, a resource is a Table, Schema, Controller triplet, internally +connected around a Service finally communicating with one or more Manager.

+

Depending on the level of complexity brought in the custom feature you would like to implement, +you will have to fine tune, from one up to all, of those components together.

+

Following sections are assuming you are weaving a valid Table and Schema as explained in earlier +parts of the documentation.

+
+

A bit about Internals

+

Standard pipeline for an incoming request goes like this:

+
->Server->Middlewares->Controller->Service(s)->Manager(s)
+
+
+

Controller is the BioDM component that manages a set of routes. In order to avoid most mistakes +with Controllers it is recommended to visit Starlette documentation.

+

Bread and butter for resources are ResourceController and DatabaseService. You may add a +feature by extending them.

+
+
+

Keycloack Groups: a case study

+

/users and /groups are examples of custom resources. +Idea with them is to have a synchronized copy of those resources from keycloak. +When requestin

+

Basic operations and routes stay the same, so the controller is not changing. Following is the code +snippet that manages group creation.

+

Basic idea is to query +our keycloak server before creating a new group to ensure its existence and recover its keycloak +UUID that is necessary for some operations. Then populate it in the data dictionary that is finally +sent to DatabaseService (here the composite case) that will handle insert/update statement +building and execution.

+
+
kcservice.py
+
class KCService(CompositeEntityService):
+    """Abstract class for local keycloak entities."""
+    @property
+    def kc(self) -> KeycloakManager:
+        """Return KCManager instance."""
+        return self.app.kc
+
+    @abstractmethod
+    async def read_or_create(self, data: Dict[str, Any], /) -> None:
+        """Try to read from DB, create on keycloak side if not present.
+        Populate 'id' - Keycloak UUID in string form - in data."""
+        raise NotImplementedError
+
+
+class KCGroupService(KCService):
+    @staticmethod
+    def kcpath(path) -> Path:
+        """Compute keycloak path from api path."""
+        return Path("/" + path.replace("__", "/"))
+
+    async def read_or_create(self, data: Dict[str, Any]) -> None:
+        """READ group from keycloak, create if missing.
+
+        :param data: Group data
+        :type data: Dict[str, Any]
+        """
+        path = self.kcpath(data['path'])
+
+        group = await self.kc.get_group_by_path(str(path))
+        if group:
+            data["id"] = group["id"]
+            return
+
+        parent_id = None
+        if not path.parent.parts == ('/',):
+            parent = await self.kc.get_group_by_path(str(path.parent))
+            if not parent:
+                raise ValueError("Input path does not match any parent group.")
+            parent_id = parent['id']
+
+        data['id'] = await self.kc.create_group(path.name, parent_id)
+
+    async def write(
+        self,
+        data: List[Dict[str, Any]] | Dict[str, Any],
+        stmt_only: bool = False,
+        user_info: UserInfo | None = None,
+        **kwargs
+    ):
+        """Create entities on Keycloak Side before passing to parent class for DB."""
+        # Check permissions
+        await self._check_permissions("write", user_info, data)
+
+        # Create on keycloak side
+        for group in to_it(data):
+            # Group first.
+            await self.read_or_create(group)
+            # Then Users.
+            for user in group.get("users", []):
+                await User.svc.read_or_create(user, [group["path"]], [group["id"]],)
+
+        # Send to DB
+        return await super().write(data, stmt_only=stmt_only, **kwargs)
+
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/developer_manual/demo.html b/developer_manual/demo.html new file mode 100644 index 0000000..48b91ae --- /dev/null +++ b/developer_manual/demo.html @@ -0,0 +1,270 @@ + + + + + + + Minimal Demo — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Minimal Demo

+

Say you or your organization needs to store Datasets, each containing a set of File we will go +over the following minimal example.

+
+
demo.py
+
import marshmallow as ma
+from marshmallow import fields as mf
+import sqlalchemy as sa
+from sqlalchemy import orm as sao
+from typing import List
+import uvicorn
+
+import biodm as bd
+from biodm.components.controllers import ResourceController, S3Controller
+
+
+# Tables
+class Dataset(bd.components.Versioned, bd.components.Base):
+    name          : sao.Mapped[str]          = sa.Column(sa.String(50),                   nullable=False)
+    description   : sao.Mapped[str]          = sa.Column(sa.String(500),                  nullable=False)
+    username_owner: sao.Mapped[int]          = sa.Column(sa.ForeignKey("USER.username"),  nullable=False)
+    owner         : sao.Mapped["User"]       = sao.relationship(foreign_keys=[username_owner])
+    files         : sao.Mapped[List["File"]] = sao.relationship(back_populates="dataset")
+
+class File(bd.components.S3File, bd.components.Base):
+    id                         = sa.Column(sa.Integer,                    primary_key=True)
+    id_dataset                 = sa.Column(sa.ForeignKey("DATASET.id"),   nullable=False)
+    dataset: sao.Mapped["Dataset"] = sao.relationship(back_populates="files", single_parent=True, foreign_keys=[id_dataset])
+
+# Schemas
+class DatasetSchema(ma.Schema):
+    id             = mf.Integer()
+    version        = mf.Integer()
+    name           = mf.String(required=True)
+    description    = mf.String(required=False)
+    username_owner = mf.String(required=True, load_only=True)
+    owner          = mf.Nested("UserSchema")
+    files          = mf.List(mf.Nested("FileSchema"))
+
+class FileSchema(ma.Schema):
+    id             = mf.Integer()
+    filename       = mf.String(required=True)
+    extension      = mf.String(required=True)
+    url            = mf.String(                 dump_only=True)
+    ready          = mf.Bool(                   dump_only=True)
+    id_dataset     = mf.Integer(required=True,  load_only=True)
+    dataset        = mf.Nested("DatasetSchema")
+
+# Controllers
+class DatasetController(ResourceController):
+    def __init__(self, app) -> None:
+        super().__init__(app=app)
+
+class FileController(S3Controller):
+    def __init__(self, app) -> None:
+        super().__init__(app=app)
+
+# Server
+def main():
+    return bd.Api(debug=True, controllers=[DatasetController, FileController],)
+
+if __name__ == "__main__":
+    uvicorn.run(
+        f"{__name__}:main", factory=True,
+        host=bd.config.SERVER_HOST, port=bd.config.SERVER_PORT,
+        loop="uvloop", log_level="debug", access_log=False
+    )
+
+
+
+

And voilà, If your use case is very basic it is a simple as that. This tiny codebase +deploys a server with two new RESTful resources, accessible respectively at /files and +/datasets.

+

Importantly /schema, /files/schema, /datasets/schema will let you, or an +OpenAPISchema v3.0.0 compliant tool, discover all possible routes.

+

Moreover, it comes with two preset resources /users, /groups that are required for +permission management down the road.

+

All incoming Requests are logged in History table

+

Let’s examine some key points:

+
+

Naming convention

+

Sticking to the simple naming convention introduced above for the three required components to +add a new respource lets BioDM easily infer their relationships from name lookup in registries.

+
    +
  • Table: name of the resource in singular

  • +
  • Schema: same prefixed by Schema

  • +
  • Controller: same prefixed by controller

  • +
+
+

Note

+

This is the Zen approach. You may however name those as you please and manually set relationships +in Controller’s __init__ method.

+
+
+
+

Base Resource

+

For a resource that is not interacting with an external serivce, this is covered by pairing +BioDM’s SQLAlchemy Declarative Base and ResourceController components.

+
+
+

File management

+
+

Note

+

At the moment, s3 protocol, using pre-signed url, only.

+
+

S3File base class set on a table, populates it with a set of +Column fields essential for the task. +All but ready flag may be seen on FileSchema.

+

S3Controller will then populate upload_form field when creating a new resource at /files. +This is a stringified form for direct upload on the storage bay. +Once the file is uploaded, readiness flag is set to true. +From that point on, urls to download the file can be obtained by visiting +GET /files/{id}/download

+
+
+

Versioning

+

In the example above you may see that Dataset has no primary key. +It is because it inherits from Versioned that populate +[id, version] as primary key.

+

Versioned resources are read-only, eventual updates have to pass by +PUT /datasets/{id}_{version}/release route that will produce a new resource, incrementing version.

+
+

Note

+

Nothing prevents you from expanding further on that primary key in your table class.

+
+
+

Warning

+

SQLite doesn’t support autoincrement in the case of a composite primary key. +BioDM supports the canonical leading id case at the cost of an extra request to fetch +max id before inserting. Other configuration will yield errors.

+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/developer_manual/doc_endpoints.html b/developer_manual/doc_endpoints.html new file mode 100644 index 0000000..35d1392 --- /dev/null +++ b/developer_manual/doc_endpoints.html @@ -0,0 +1,214 @@ + + + + + + + Documenting endpoints — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Documenting endpoints

+

BioDM populates an OpenAPISchema v3.0.0 compliant documentation for all endpoints via +apispec. +In particular that allows for automated discovery via compatible tools such as swagger-ui.

+

It is functional but not very specific in its description. In case you would like to expand on it +we provide @overload_docstrings decorator, which works in combination with permissions +decorators.

+
+

Warning

+

In case you’re stacking up a permission decorator and this one, you should always put +@overload_docstring first as this creates a shell function calling the parent class +method for the sole purpose of specifying the docstring as they are read-only.

+
+
+
demo.py
+
from biodm.utils.security import group_required, admin_required
+
+class DatasetController(bdc.ResourceController):
+    def __init__(self, app) -> None:
+        super().__init__(app=app)
+
+    @group_required(['my_team'])
+    @overload_docstring
+    async def write(**kwargs):
+        """
+        requestBody:
+            description: payload.
+            required: true
+            content:
+                application/json:
+                    schema: DatasetSchema
+        responses:
+        201:
+            description: Write Dataset resource.
+            content:
+                application/json:
+                    schema: DatasetSchema
+        204:
+            description: Empty Payload.
+        """
+    ...
+    class TagController(ResourceController):
+        @overload_docstring
+        async def read(**kwargs):
+            """
+            parameters:
+            - in: path
+              name: name
+              description: Tag name
+            responses:
+              200:
+                description: Found matching Tag.
+                examples: |
+                  {"name": "epidemiology"}
+                content:
+                  application/json:
+                    schema: TagSchema
+              404:
+                description: Tag not found.
+            """
+    ...
+
+
+
+
+

Docstrings Guide

+

Docstrings comply with apispec in order to provide a correct schema. +In particular you have to be precise with input parameters and marshmallow schema reference names.

+

This is required in order to output specification in OpenAPISchema format, with link discovery +which enables support for swagger-ui and the rest of the ecosystem.

+
+

Note

+

The core patches abstract method docstrings at runtime in order to generate that are left +undocumented. However, if you are using @overload_docstrings ensuring that it generates a +valid schema that works with the tools is up to you. +To obtain the full generated docstring you may get it from a Controller after start phase +using printing methods or a debug session.

+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/developer_manual/index.html b/developer_manual/index.html new file mode 100644 index 0000000..00a65c5 --- /dev/null +++ b/developer_manual/index.html @@ -0,0 +1,211 @@ + + + + + + + Developer Manual — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Developer Manual

+

This section describes how to use biodm package in order to swiftly deploy a modular +data management API tailored to your needs.

+

You also may consult src/example/ toy project, which encapsulates more complex project needs.

+

Following, we will go in detail about the toolkit and builtins.

+
+

Basics

+

At the core, Data Management means storing collections of files and their associated metadata.

+

BioDM is leveraging SQLAlchemy ORM Tables definitions + matching Marshmallow Schemas, specifying +metadata and relationships, to setup standard RESTful endpoints.

+

Furthermore, it is providing a structure and toolkit in order to manage common Data Management problems +such as: s3 protocol remote file storage, group based permissions access (on both resources and +endpoints), resource versioning (coming up), cluster jobs and so on.

+

Moreover, the modular and flexible architecture allows you to easily extend base features for +instance specific use cases.

+
+
+

Concepts

+

The main server class biodm.Api is a vessel for biodm.components.controllers.Controller +subinstances.

+

Each Controller is independently responsible for exposing a set of routes, validating and serializing +i/o and send incomming Request data to a relevant biodm.component.ApiService subinstance.

+

Services, are tied to a Table and calling each other in order to parse and adapt +input data. +All Services are biodm.components.services.DatabaseService subinstances as their +primary mission is to faithfully log activity and maintain data integrity.

+

Finally this internal representation is sent to a biodm.component.ApiManager, each holding +primitives enabling communication with an external micro-service (i.e. DB, S3, Kubernetes, +…).

+
+
+

Configuration

+

BioDM extends Starlette, +hence its Configuration system works by populating a .env file, preferably sitting in the same directory as the running script.

+

We invite you to consult config.py +to discover all possible options.

+

Functionalities depending on external micro-services are enabled if matching configuration options are provided.

+

e.g. Keycloak functionalities shall be activated, if and only if, defaultless config parameters prefixed by KC_ are populated. +Otherwise, User/Group tables shall still be deployed. However, they shall not be synced against a keycloak server.

+

You may have a look at compose.test.yml file to see how testing containers used in our CI, are deployed with partial configuration in order to test by parts.

+
+
+

BioDM toolkit Guide

+

Following we have a tutorial in the form of a small demo server, that we will expand upon to +introduce the toolkit:

+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/developer_manual/permissions.html b/developer_manual/permissions.html new file mode 100644 index 0000000..fdd62f1 --- /dev/null +++ b/developer_manual/permissions.html @@ -0,0 +1,239 @@ + + + + + + + Permissions — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Permissions

+

In order to protect your data, BioDM provides two structures of permissions.

+

Those are requiring a keycloak service running and the following variables to +be provided in a .env file at the same level as your demo.py script.

+
+
.env
+
KC_HOST=
+KC_REALM=
+KC_PUBLIC_KEY=
+KC_ADMIN=
+KC_ADMIN_PASSWORD=
+KC_CLIENT_ID=
+KC_CLIENT_SECRET=
+
+
+
+
+

Coarse: Static rule on a Controller endpoint

+

biodm.utils.security module contains three decorators that are meant to be used +on Controller endpoints in order to apply static permissions directly within the codebase.

+
    +
  • @token_required()

    +
      +
    • Protects the endpoint demanding incomming requests to by signed with a valid Keycloak JW Token

    • +
    +
  • +
  • @group_required(groups=[gpath_1,... gpath_n])

    +
      +
    • Like token_required, plus assesses that requesting User is part of one of those Groups.

    • +
    +
  • +
  • @admin_required()

    +
      +
    • group_required special case, requesting User must be part of admin group.

    • +
    +
  • +
+

On our example, this is how you could apply those on DatasetController:

+
+
demo.py
+
from biodm.utils.security import group_required, admin_required
+
+class DatasetController(bdc.ResourceController):
+    def __init__(self, app) -> None:
+        super().__init__(app=app)
+        self.write = group_required(self.create, ['my_team'])
+        self.update = group_required(self.update, ['my_team'])
+        self.delete = admin_required(self.delete)
+
+
+
+

Here we restricted the creation and updating of datasets to my_team, deletion is admin +priviledge and reading data is left public.

+
+
+

Fine: Dynamic user owned permissions

+

If your data management platform is intended to receive data from users, BioDM provide tools to +let them in control of permissions by providing them directly as the resource input data.

+

biodm.components.Permission class is designed as an extra SQLAlchemy table argument that let +you flag composition pattern (i.e. One-to-Many relationships) with the following permissions that +will be applied recursively for all children of that particular entity:

+
    +
  • Read

  • +
  • Write

  • +
  • Download

  • +
+

In our example:

+
+
demo.py
+
from biodm.components import Permission
+
+
+class Dataset(bd.components.Base):
+    id            : sao.Mapped[int]          = sa.Column(sa.Integer, primary_key=True)
+    ...
+    files         : sao.Mapped[List["File"]] = sao.relationship(back_populates="dataset")
+
+    __permissions__ = (
+        Permission(files, write=True, read=False, download=True),
+    )
+
+
+
+

The latter enables File permissions at the Dataset level.

+

In other words it lets you define for a top level resource who is allowed to interact +with a nested collection and its elements.

+
+

Note

+

Those permissions will be taken into account when directly accessing /files API routes.

+
+
+

Strict composition

+

Currently, BioDM assumes a strict composition pattern of resource for those permissions. +Which allow them to be taken into account while directly accessing children resource routes +like mentioned above.

+

Unfortunately, that also means that distributing permissions from two, or more, parent level +resources is currently not tested and shall most likely result in soft-locking those resources.

+

This may or may not be supported in a future version of the Core, depending on technical +feasibility.

+

If you wish to achieve something in that vein, it is for now advised to create an identical +resource with a different name.

+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/developer_manual/s3conf.html b/developer_manual/s3conf.html new file mode 100644 index 0000000..4558cc8 --- /dev/null +++ b/developer_manual/s3conf.html @@ -0,0 +1,175 @@ + + + + + + + S3 Configuration — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

S3 Configuration

+

For file management this demo requires an s3 compatible storage service. +To quickly deploy micro-services dependencies for testing purposes, refer to +Development environment.

+

The following variables have to be provided.

+
+
.env
+
S3_ENDPOINT_URL=
+S3_BUCKET_NAME=
+S3_ACCESS_KEY_ID=
+S3_SECRET_ACCESS_KEY=
+
+
+
+
+

File management

+

To ensure bucket key uniqueness for uploaded files, the key gets prefixed by +S3File.key_salt column. By default this is an uuid4.

+

In case you would like to have precise control over how your files are named on the bucket this +can be done by overloading key_salt with a hybrid_property in the following way.

+
+
demo.py
+
from sqlalchemy.ext.hybrid import hybrid_property
+
+class File(bd.components.S3File, bd.components.Base):
+    class File()
+        ...
+        @hybrid_property
+        async def key_salt(self) -> str:
+            # Pop session, populated by S3Service just before asking for that attr.
+            session = self.__dict__.pop('session')
+            # Use session to fetch what you need.
+            await session.refresh(self, ['dataset'])
+            await session.refresh(self.dataset, ['project'])
+            # Build your custom prefix.
+            return f"{self.dataset.project.name}_{self.dataset.name}"
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/developer_manual/table_schema.html b/developer_manual/table_schema.html new file mode 100644 index 0000000..d3aa7c8 --- /dev/null +++ b/developer_manual/table_schema.html @@ -0,0 +1,232 @@ + + + + + + + Tables and Schemas — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Tables and Schemas

+

This section describes how BioDM is leveraging your Tables and Schemas in order to set +up resources. It contains some useful information for developers to design their own.

+

It is recommended to visit the documentation of both SQLAlchemy and Marshmallow beforehand. +Moreover, our example project also provides plenty of inspiration for this task.

+
+

Tables

+

In principle any valid SQLALchemy table is accepted by BioDM. Yet, +depending how you configure it, it shall adopt varying behaviours.

+

SQLAlchemy 2.0 ORM API is a really nice and convenient piece of technology. +However, it does not natively support trees of entities (nested dictionaries).

+

To palliate this problem, BioDM does a pass of parsing on schema validation results under the +hood, using Tables as litterals in order to build the hirarchical tree of statements. +In a second pass, it inserts the whole tree in order, ensuring integrity.

+
+

Relationship specifics

+

Statement building leverages tables relationships definitions, taking orientation into account.

+

In particular, if a relationship is one-armed (pointing in one direction only), it will not +be possible to create a nested resource in the other direction.

+
+
+
+

Schemas

+

Marshmallow also comes with some limitations, such as not being able to infer foreign key +population in respect to nested entities while de-serializing.

+

E.g. Given the following matching table and schema:

+
class Dataset(Base):
+    id:          Mapped[int]   = mapped_column(Integer(), primary_key=True)
+    ...
+    id_project:  Mapped[int]   = mapped_column(ForeignKey("PROJECT.id"), nullable=False)
+    project: Mapped["Project"] = relationship(back_populates="datasets")
+
+class DatasetSchema(Schema):
+    id = Integer()
+    ...
+    id_project = Integer()
+    project = Nested('ProjectSchema')
+
+
+

If you POST a new /datasets resource definition with a nested project. +Upon validating, id_project will not be populated, which ultimately is your +NOT NULL FOREIGN KEY field. Hence SQL insert statement shall raise integrity errors.

+

Marshmallow is offering built-ins in the form of decorators that let you tag functions +attached to the Schema such as @pre_load which is a hook called before validation, +that lets you manually get data if you detect it present in the dict.

+

This technique has two major disadvantages:

+
    +
  • It is quite cumbersome and error prone for the developer, as for each relationship you may +have to set foreign keys on either side and is as many conditions checking what is +present in your input dict and whatnot.

  • +
  • This cannot take into account generated keys. In our example, we may be creating the +project as well. Hence it will not have an id yet, thus raise a ValidationError for the +dataset if we set required=True flag for id_project.

  • +
+

To bypass those limitations, BioDM validates incoming data using Marshmallow’s +partial=True flag. Meaning that required keywords on fields are ignored and may be skipped +overall. At validation step we are checking the overall structure and type of fields.

+

This yields a (List of) dictionary (of nested Dictionaries) that is sent down to a Service +for statement building and insertion. The Core will use knowledge of Table relationships to infer +this foreign key population and raise appropriate errors in case of truely incomplete input data.

+

This ultimately allows for more flexibily on input such as sending a mixin of create/update of new +resources via POST.

+
+

Nested flags policy

+

Serialization is following down Nested fields. In particular that means it is important to +limit the depth of data that is fetched, as it is easy to end up in infinite loops in case of +circular dependencies.

+

E.g.

+
class GroupSchema(Schema):
+    """Schema for Keycloak Groups. id field is purposefully left out as we manage it internally."""
+    path = String(metadata={"description": "Group name chain separated by '__'"})
+    ...
+    users = List(Nested('UserSchema', exclude=['groups']))
+    children = List(Nested('GroupSchema', exclude=['children', 'parent']))
+    parent = Nested('GroupSchema', exclude=['children', 'parent'])
+
+
+

In the example above, without those exclude flags, excluding references to nested Groups further +down Serialization would go into infinite recursion.

+

Marshmallow provides other primitives: only, load_only, dump_only, that can also be +used to do this restriction.

+
+

Warning

+

It is important to make sure that your dumping configuration does not impede a Schema’s +loading capabilites of essential fields for creating a new resource.

+
+

For most cases, you may simply set fields identical to matching Table, using Marshmallow syntax. +Furthemore, Schemas are the “i/o surface” of your app. This is where you decide what gets +loaded and dumped for a specific resource.

+
+

Note

+

Setting “metadata.description” like for path in our example example above, is used for +automatic apispec docstrings generation.

+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/genindex.html b/genindex.html new file mode 100644 index 0000000..072aa5d --- /dev/null +++ b/genindex.html @@ -0,0 +1,1509 @@ + + + + + + Index — Python documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
  • + +
  • +
  • +
+
+
+
+
+ + +

Index

+ +
+ A + | B + | C + | D + | E + | F + | G + | H + | I + | J + | K + | L + | M + | N + | O + | P + | Q + | R + | S + | T + | U + | V + | W + +
+

A

+ + + +
+ +

B

+ + + +
    +
  • Base (class in biodm.components.table) +
  • +
  • + biodm + +
  • +
  • + biodm.api + +
  • +
  • + biodm.basics + +
  • +
  • + biodm.basics.k8scontroller + +
  • +
  • + biodm.basics.rootcontroller + +
  • +
  • + biodm.component + +
  • +
  • + biodm.components + +
  • +
  • + biodm.components.controllers + +
  • +
  • + biodm.components.controllers.admincontroller + +
  • +
  • + biodm.components.controllers.controller + +
  • +
  • + biodm.components.controllers.resourcecontroller + +
  • +
  • + biodm.components.controllers.s3controller + +
  • +
  • + biodm.components.services + +
  • +
  • + biodm.components.services.dbservice + +
  • +
  • + biodm.components.services.k8service + +
  • +
  • + biodm.components.services.kcservice + +
  • +
  • + biodm.components.services.s3service + +
  • +
  • + biodm.components.table + +
  • +
  • + biodm.config + +
  • +
  • + biodm.error + +
  • +
  • + biodm.exceptions + +
  • +
  • + biodm.managers + +
  • +
  • + biodm.managers.dbmanager + +
  • +
    +
  • + biodm.managers.k8smanager + +
  • +
  • + biodm.managers.kcmanager + +
  • +
  • + biodm.managers.s3manager + +
  • +
  • + biodm.schemas + +
  • +
  • + biodm.schemas.group + +
  • +
  • + biodm.schemas.k8sinstance + +
  • +
  • + biodm.schemas.listgroup + +
  • +
  • + biodm.schemas.upload + +
  • +
  • + biodm.schemas.user + +
  • +
  • + biodm.scope + +
  • +
  • + biodm.tables + +
  • +
  • + biodm.tables.asso + +
  • +
  • + biodm.tables.group + +
  • +
  • + biodm.tables.history + +
  • +
  • + biodm.tables.k8sinstance + +
  • +
  • + biodm.tables.listgroup + +
  • +
  • + biodm.tables.upload + +
  • +
  • + biodm.tables.upload_part + +
  • +
  • + biodm.tables.user + +
  • +
  • + biodm.utils + +
  • +
  • + biodm.utils.security + +
  • +
  • + biodm.utils.sqla + +
  • +
  • + biodm.utils.utils + +
  • +
+ +

C

+ + + +
+ +

D

+ + + +
+ +

E

+ + + +
+ +

F

+ + + +
+ +

G

+ + + +
+ +

H

+ + + +
+ +

I

+ + + +
+ +

J

+ + + +
+ +

K

+ + + +
+ +

L

+ + + +
+ +

M

+ + +
+ +

N

+ + + +
+ +

O

+ + + +
+ +

P

+ + + +
+ +

Q

+ + +
+ +

R

+ + + +
+ +

S

+ + + +
+ +

T

+ + + +
+ +

U

+ + + +
+ +

V

+ + + +
+ +

W

+ + +
+ + + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/getting_started.html b/getting_started.html new file mode 100644 index 0000000..c75c822 --- /dev/null +++ b/getting_started.html @@ -0,0 +1,444 @@ + + + + + + + Getting Started — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Getting Started

+
+

Install

+
    +
  • Recommended: PEP 405 Create virtual environment

  • +
+
python3 -m venv venv
+source venv/bin/activate/
+
+
+
+

Warning

+

using built in python tools such as venv and pip is preferred. +conda and co. package managers are currently untested.

+
+
    +
  • Using pip and git

  • +
+
pip3 install git+https://github.com/bag-cnag/biodm
+
+
+
    +
  • Install with kubernetes functionalities

  • +
+
pip3 install "biodm[kubernetes] @ git+https://github.com/bag-cnag/biodm"
+
+
+
    +
  • Build from sources

  • +
+
git clone https://github.com/bag-cnag/biodm
+cd biodm/
+pip3 install -r src/requirements/dev.txt
+pip3 install .
+
+
+
+
+

Start Server

+

E.g. for our example project. +Configuration is done through .env files, thus server has to be run from its immediate directory. +The one provided at src/example/.env is set on development environment values.

+
cd src/example/
+python3 app.py
+
+
+
+
+

Development environment

+
    +
  • Install in editable mode

  • +
+
pip3 install -r src/requirements/dev.txt
+pip3 install -e .
+
+
+
+

Quick dependency setup

+

To start all service dependnencies at once and skip individual configuration you may use +the provided compose.yml. Passing the flag –build it will also build for you an appropriate +keycloak image with your local certificates in order to serve https:// requests.

+
docker compose up --build -d
+
+
+

Default configuration parameters are set on fixed IPs declared in this compose.yml file.

+

optional - strongly recommended for keycloak -: for testing convenience you +may add those lines to your host table.

+
sudo cat >> /etc/hosts <<EOF
+# biodm-dev
+10.10.0.2       postgres.local
+10.10.0.3       keycloak.local
+10.10.0.4       s3bucket.local
+EOF
+
+
+

It might be a pre-requisite for keycloak as it is quite strict with security protocols. +Definitely something to try if you cannot reach admin UI or your app is unable to fetch any data.

+

Swagger-UI This compose file also bundles a Swagger-UI set to discover API routes. +It is available at http://localhost:9080

+

Optional: - To personalize defaults, see Individual configuration below. +- Keycloak comes with a default 3TR realm and appropriate client that has user/group rights. +- MinIO launches with admin credentials, that are used as ACCESS_KEY.

+
+
+

Individual configuration

+
    +
  • Database

  • +
+
docker run --name api-db -e POSTGRES_PASSWORD=pass -d postgres:16-bookworm
+docker exec -u postgres api-db createdb biodm
+
+
+
    +
  • Keycloak

  • +
+

First you need to build the image yourself according to the documentation:

+
cd docker/ && \
+docker build . -t keycloak:22.0_local-certs \
+               -f Dockerfile.keycloak-22.0_local-certs \
+               --build-arg _KC_DB=postgres \
+               --build-arg _KC_DB_USERNAME=postgres \
+               --build-arg _KC_DB_PASSWORD=pass \
+               --build-arg=_KC_HOSTNAME=keycloak.local \
+               --build-arg _KC_DB_URL=jdbc:postgresql://10.10.0.5:5432/keycloak && \
+cd -
+
+
+

Keycloak also needs a databse:

+
docker run --name kc-db -e POSTGRES_PASSWORD=pass -e POSTGRES_DB=keycloak -d postgres:16-bookworm
+docker exec -u postgres biodm-pg createdb keycloak
+
+
+

Then you may start keycloak itself:

+
docker run --name local_keycloak -e KEYCLOAK_USER=admin -e KEYCLOAK_PASSWORD=admin -p 8443:8080 keycloak:22.0.5_local-certs
+
+
+

Configuration

+

Once keycloak is running you need to configure a realm and a client for the app to log in. +Default values are:

+
KC_REALM="3TR"
+KC_CLIENT_ID="submission_client"
+
+
+

Once you’ve created the realm, create the client. Then

+
+
    +
  • set Access Type to confidential

  • +
  • set Inplicit Flow Enabled to True.

  • +
  • Add Valid Redirect Uri:

    +
      +
    • dev: http://* and https://*

    • +
    • prod: provide the url of the login callback {SERVER_HOST}/syn_ack.

    • +
    +
  • +
+
+
+

Note

+

Depending on your keycloak version or running instance SERVER_HOST may have to be appended with /auth.

+
+

Then you should provide the server with the SECRET field located in the +Credentials tab, that appears after you changed access type and the realm public key +located at {KC_HOST}[auth/]realms/{KC_REALM}/.

+

To be able to serve as a gateway to administrate keycloak concepts, +the API also needs admin credentials:

+
KC_HOST={url}
+KC_CLIENT_SECRET={secret}
+KC_PUBLIC_KEY={public_key}
+KC_ADMIN={admin_id}
+KC_ADMIN_PASSWORD={admin_password}
+
+
+
    +
  • Minio

  • +
+
docker run -e MINIO_ROOT_USER=admin \
+        -e MINIO_ROOT_PASSWORD=12345678 \
+        -e MINIO_DEFAULT_BUCKETS=bucketdevel3tropal \
+        -p 9000:9000 \
+        -p 9001:9001 \
+        bitnami/minio:2024-debian-12
+
+
+

Then visit the administration interface at localhost:9001, +generate a key and populate:

+
S3_ENDPOINT_URL={url}
+S3_BUCKET_NAME={bucket_name}
+S3_ACCESS_KEY_ID={access_key_id}
+S3_SECRET_ACCESS_KEY={access_key}
+
+
+
+
+
+

Documentation

+
    +
  • pre-requisite:

  • +
+
pip3 install -r src/requirements/docs.txt
+
+
+

Then you may use the following:

+
sphinx-apidoc --implicit-namespaces --separate -H "API Reference" -fo docs/biodm/ src/biodm "**/*tests*"
+python3 -m sphinx -b html docs/ docs/build/html
+
+
+
+
+

Tests

+
+

Unit

+

Unit tests are leveraging an in-memory sqlite database and not testing any feature requiring +deployement of an external service.

+
    +
  • pre-requisite:

  • +
+
pip3 install -r src/requirements/dev.txt
+
+
+
    +
  • run tests

  • +
+

Just like example, tests have to be run within their directory.

+
cd src/biodm/tests/
+pytest
+cd -
+
+
+
    +
  • coverage

  • +
+
cd src/biodm/tests/
+pytest --cov-report term --cov=../
+cd -
+
+
+
    +
  • run in a VSCode debugpy session

  • +
+

To run a unit test in a debugging session, you may create the following .vscode/launch.json +file at the root of this repository. The run and debug tab should now ofer an extra option. +If you installed sources in editable mode, that allows you to set breakpoints within +BioDM codebase.

+
+
launch.json
+
{
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "PyTest: BioDM Unit tests",
+            "type": "debugpy",
+            "request": "launch",
+            "cwd": "${workspaceFolder}/src/tests/unit",
+            "subProcess": true,
+            "module": "pytest",
+            "python": "/path/to/myvenv/bin/python3", // Replace with your virtual environment
+            "args": [
+                // "-k", "test_basics", // Optional: pick your tests
+                "-vv"
+            ],
+            "justMyCode": false,
+        },
+    ]
+}
+
+
+
+
+
+

Integration

+

Integration tests are leveraging docker compose and the development environment to simulate +external services allowing for end to end testing. It is effectively testing the app from +outside.

+

Integration are split in silos according to their external service dependency:

+
    +
  • Keycloak

  • +
+
docker compose -f compose.test.yml run --build test-keycloak-run
+docker compose -f compose.test.yml down
+
+
+
    +
  • S3

  • +
+
docker compose -f compose.test.yml run --build test-s3-run
+docker compose -f compose.test.yml down
+
+
+
    +
  • run in a VSCode debugpy session

  • +
+

pre-requisite development environment up

+

For integration tests you need two sessions: server side (api) and client side (tests), you +may adjust the following configurations to your need.

+

VSCode supports running both sessions at the same time from the run and debug tab.

+
+
launch.json
+
{
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: BioDM Example API",
+            "type": "debugpy",
+            "request": "launch",
+            "cwd": "${workspaceFolder}/src/example/",
+            "program": "app.py",
+            "console": "integratedTerminal",
+            "python": "/path/to/myvenv/bin/python3", // Replace with your virtual environment
+            "justMyCode": false,
+        },
+        {
+            "name": "PyTest: BioDM Integration tests",
+            "type": "debugpy",
+            "request": "launch",
+            "cwd": "${workspaceFolder}/src/tests/integration/kc|s3|k8", // pick one directory
+            "subProcess": true,
+            "module": "pytest",
+            "python": "/path/to/myvenv/bin/python3", // Replace with your virtual environment
+            "args": [
+                // "-k", "some_test_name" // Optional: pick your tests
+                "-vv"
+            ],
+            "justMyCode": false,
+            "envFile": "${cwd}.env"
+        },
+    ]
+}
+
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 0000000..152869f --- /dev/null +++ b/index.html @@ -0,0 +1,237 @@ + + + + + + + BioDM: A fast and RESTful Data Management framework — Python documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

BioDM: A fast and RESTful Data Management framework

+
+

BioDM: A fast and RESTful Data Management framework

+

logo


+

Introduction Presentation: https://www.overleaf.com/read/wxpdnptnkpsy

+

Source Code: https://github.com/bag-cnag/biodm

+

Documentation: https://bag-cnag.github.io/biodm/

+
+

BioDM is a fast, modular, stateless and asynchronous REST API framework with the following core features:

+
    +
  • Provide standard HTTP REST-to-CRUD endpoints from developper provided entity definitions:

    +
      +
    • `SQLAlchemy <https://github.com/sqlalchemy/sqlalchemy/>`_ tables

    • +
    • `marshmallow <https://github.com/marshmallow-code/marshmallow>`_ schemas

    • +
    +
  • +
  • Inter-operate services ecosystem:

    +
      +
    • Permissions leveraging Keycloak

    • +
    • Storage leveraging S3 protocol

    • +
    • Jobs & Visualization leveraging Kubernetes cluster

    • +
    +
  • +
+

-> Act as an API gateway and log relevant data.

+
    +
  • Also sets up essentials:

    +
      +
    • Liveness endpoint

    • +
    • Login and token retrieval system

    • +
    • OpenAPI schema generation through apispec

    • +
    +
  • +
+
+

Quickstart

+
+

Install

+
pip3 install git+https://github.com/bag-cnag/biodm
+
+
+
+
+

Run app

+

To run the API you will also need an ASGI server, i.e. uvicorn+uvloop by default:

+
pip3 install uvicorn uvloop
+
+
+

OR

+
pip3 install -r src/requirements/dev.txt
+
+
+

Then you may run our example after populating src/example/.env with your desired configuration:

+
cd src/example/
+python3 src/example/app.py
+
+
+

Alternatively, if your goal is simply to run example locally +you may use the following command beforehand in order to deploy the development stack:

+
docker compose -f compose.yml up --build -d
+
+
+

This stack comes with an interactive swagger-ui visitable at http://localhost:9080/ +once the server is running.

+
+
+
+

About

+

Developed at CNAG

+
+
+

Contributing

+

No contributing policy yet. However, issues and pull requests are welcome.

+
+
+

Licence

+

GNU/AGPLv3

+
+
+
+

Welcome to biodm’s documentation!

+ +
+
+

Indices and tables

+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/licence.html b/licence.html new file mode 100644 index 0000000..5c55998 --- /dev/null +++ b/licence.html @@ -0,0 +1,792 @@ + + + + + + + License — Python documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

License

+
                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
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+author or copyright holder as a result of your choosing to follow a
+later version.
+
+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
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+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<https://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/objects.inv b/objects.inv new file mode 100644 index 0000000..45c9543 Binary files /dev/null and b/objects.inv differ diff --git a/py-modindex.html b/py-modindex.html new file mode 100644 index 0000000..81b0498 --- /dev/null +++ b/py-modindex.html @@ -0,0 +1,354 @@ + + + + + + Python Module Index — Python documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
  • + +
  • +
  • +
+
+
+
+
+ + +

Python Module Index

+ +
+ b +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
 
+ b
+ biodm +
    + biodm.api +
    + biodm.basics +
    + biodm.basics.k8scontroller +
    + biodm.basics.rootcontroller +
    + biodm.component +
    + biodm.components +
    + biodm.components.controllers +
    + biodm.components.controllers.admincontroller +
    + biodm.components.controllers.controller +
    + biodm.components.controllers.resourcecontroller +
    + biodm.components.controllers.s3controller +
    + biodm.components.services +
    + biodm.components.services.dbservice +
    + biodm.components.services.k8service +
    + biodm.components.services.kcservice +
    + biodm.components.services.s3service +
    + biodm.components.table +
    + biodm.config +
    + biodm.error +
    + biodm.exceptions +
    + biodm.managers +
    + biodm.managers.dbmanager +
    + biodm.managers.k8smanager +
    + biodm.managers.kcmanager +
    + biodm.managers.s3manager +
    + biodm.schemas +
    + biodm.schemas.group +
    + biodm.schemas.k8sinstance +
    + biodm.schemas.listgroup +
    + biodm.schemas.upload +
    + biodm.schemas.user +
    + biodm.scope +
    + biodm.tables +
    + biodm.tables.asso +
    + biodm.tables.group +
    + biodm.tables.history +
    + biodm.tables.k8sinstance +
    + biodm.tables.listgroup +
    + biodm.tables.upload +
    + biodm.tables.upload_part +
    + biodm.tables.user +
    + biodm.utils +
    + biodm.utils.security +
    + biodm.utils.sqla +
    + biodm.utils.utils +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/search.html b/search.html new file mode 100644 index 0000000..d66db3b --- /dev/null +++ b/search.html @@ -0,0 +1,129 @@ + + + + + + Search — Python documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
  • + +
  • +
  • +
+
+
+
+
+ + + + +
+ +
+ +
+
+ +
+
+
+
+ + + + + + + + + \ No newline at end of file diff --git a/searchindex.js b/searchindex.js new file mode 100644 index 0000000..404732c --- /dev/null +++ b/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"A bit about Internals": [[47, "a-bit-about-internals"]], "API Reference": [[46, "api-reference"]], "About": [[55, "about"]], "Advanced Use": [[47, "advanced-use"]], "Base Resource": [[48, "base-resource"]], "Base routes": [[57, "base-routes"]], "Basics": [[50, "basics"]], "BioDM toolkit Guide": [[50, "biodm-toolkit-guide"]], "BioDM: A fast and RESTful Data Management framework": [[55, "biodm-a-fast-and-restful-data-management-framework"], [55, "id1"]], "Coarse: Static rule on a Controller endpoint": [[51, "coarse-static-rule-on-a-controller-endpoint"]], "Concepts": [[50, "concepts"]], "Configuration": [[50, "configuration"]], "Contents:": [[55, null]], "Contributing": [[55, "contributing"]], "Custom resource": [[47, "custom-resource"]], "Developer Manual": [[50, "developer-manual"]], "Development environment": [[54, "development-environment"]], "Docstrings Guide": [[49, "docstrings-guide"]], "Documentation": [[54, "id2"]], "Documenting endpoints": [[49, "documenting-endpoints"]], "Entity routes": [[57, "entity-routes"]], "File management": [[48, "file-management"], [52, "file-management"], [57, "file-management"]], "Filtering": [[57, "filtering"]], "Fine: Dynamic user owned permissions": [[51, "fine-dynamic-user-owned-permissions"]], "Getting Started": [[54, "getting-started"]], "Groups": [[57, "groups"]], "Indices and tables": [[55, "indices-and-tables"]], "Individual configuration": [[54, "individual-configuration"]], "Install": [[54, "install"], [55, "install"]], "Integration": [[54, "integration"]], "Keycloack Groups: a case study": [[47, "keycloack-groups-a-case-study"]], "Large files": [[57, "large-files"]], "Licence": [[55, "licence"]], "License": [[56, "license"]], "Manual:": [[50, null]], "Minimal Demo": [[48, "minimal-demo"]], "Module contents": [[0, "module-biodm"], [2, "module-biodm.basics"], [6, "module-biodm.components"], [7, "module-biodm.components.controllers"], [12, "module-biodm.components.services"], [21, "module-biodm.managers"], [26, "module-biodm.schemas"], [33, "module-biodm.tables"], [42, "module-biodm.utils"]], "Naming convention": [[48, "naming-convention"]], "Nested flags policy": [[53, "nested-flags-policy"]], "Permissions": [[51, "permissions"]], "Query a nested collection": [[57, "query-a-nested-collection"]], "Quick dependency setup": [[54, "quick-dependency-setup"]], "Quickstart": [[55, "quickstart"]], "Relationship specifics": [[53, "relationship-specifics"]], "Run app": [[55, "run-app"]], "S3 Configuration": [[52, "s3-configuration"]], "Schemas": [[53, "schemas"]], "Small files": [[57, "small-files"]], "Start Server": [[54, "start-server"]], "Strict composition": [[51, "strict-composition"]], "Submodules": [[0, "submodules"], [2, "submodules"], [6, "submodules"], [7, "submodules"], [12, "submodules"], [21, "submodules"], [26, "submodules"], [33, "submodules"], [42, "submodules"]], "Subpackages": [[0, "subpackages"], [6, "subpackages"]], "Tables": [[53, "tables"]], "Tables and Schemas": [[53, "tables-and-schemas"]], "Tests": [[54, "tests"]], "Unit": [[54, "unit"]], "User Manual": [[57, "user-manual"]], "User permissions": [[57, "user-permissions"]], "Versioning": [[48, "versioning"], [57, "versioning"]], "Welcome to biodm\u2019s documentation!": [[55, "welcome-to-biodm-s-documentation"]], "biodm package": [[0, "biodm-package"]], "biodm.api module": [[1, "module-biodm.api"]], "biodm.basics package": [[2, "biodm-basics-package"]], "biodm.basics.k8scontroller module": [[3, "module-biodm.basics.k8scontroller"]], "biodm.basics.rootcontroller module": [[4, "module-biodm.basics.rootcontroller"]], "biodm.component module": [[5, "module-biodm.component"]], "biodm.components package": [[6, "biodm-components-package"]], "biodm.components.controllers package": [[7, "biodm-components-controllers-package"]], "biodm.components.controllers.admincontroller module": [[8, "module-biodm.components.controllers.admincontroller"]], "biodm.components.controllers.controller module": [[9, "module-biodm.components.controllers.controller"]], "biodm.components.controllers.resourcecontroller module": [[10, "module-biodm.components.controllers.resourcecontroller"]], "biodm.components.controllers.s3controller module": [[11, "module-biodm.components.controllers.s3controller"]], "biodm.components.services package": [[12, "biodm-components-services-package"]], "biodm.components.services.dbservice module": [[13, "module-biodm.components.services.dbservice"]], "biodm.components.services.k8service module": [[14, "module-biodm.components.services.k8service"]], "biodm.components.services.kcservice module": [[15, "module-biodm.components.services.kcservice"]], "biodm.components.services.s3service module": [[16, "module-biodm.components.services.s3service"]], "biodm.components.table module": [[17, "module-biodm.components.table"]], "biodm.config module": [[18, "module-biodm.config"]], "biodm.error module": [[19, "module-biodm.error"]], "biodm.exceptions module": [[20, "module-biodm.exceptions"]], "biodm.managers package": [[21, "biodm-managers-package"]], "biodm.managers.dbmanager module": [[22, "module-biodm.managers.dbmanager"]], "biodm.managers.k8smanager module": [[23, "module-biodm.managers.k8smanager"]], "biodm.managers.kcmanager module": [[24, "module-biodm.managers.kcmanager"]], "biodm.managers.s3manager module": [[25, "module-biodm.managers.s3manager"]], "biodm.schemas package": [[26, "biodm-schemas-package"]], "biodm.schemas.group module": [[27, "module-biodm.schemas.group"]], "biodm.schemas.k8sinstance module": [[28, "module-biodm.schemas.k8sinstance"]], "biodm.schemas.listgroup module": [[29, "module-biodm.schemas.listgroup"]], "biodm.schemas.upload module": [[30, "module-biodm.schemas.upload"]], "biodm.schemas.user module": 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"module-biodm.managers", false]], "biodm.managers.dbmanager": [[22, "module-biodm.managers.dbmanager", false]], "biodm.managers.k8smanager": [[23, "module-biodm.managers.k8smanager", false]], "biodm.managers.kcmanager": [[24, "module-biodm.managers.kcmanager", false]], "biodm.managers.s3manager": [[25, "module-biodm.managers.s3manager", false]], "biodm.schemas": [[26, "module-biodm.schemas", false]], "biodm.schemas.group": [[27, "module-biodm.schemas.group", false]], "biodm.schemas.k8sinstance": [[28, "module-biodm.schemas.k8sinstance", false]], "biodm.schemas.listgroup": [[29, "module-biodm.schemas.listgroup", false]], "biodm.schemas.upload": [[30, "module-biodm.schemas.upload", false]], "biodm.schemas.user": [[31, "module-biodm.schemas.user", false]], "biodm.scope": [[32, "module-biodm.scope", false]], "biodm.tables": [[33, "module-biodm.tables", false]], "biodm.tables.asso": [[34, "module-biodm.tables.asso", false]], "biodm.tables.group": [[35, "module-biodm.tables.group", false]], 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biodm.components.controllers.controller)": [[9, "biodm.components.controllers.controller.Controller", false]], "controllers (api attribute)": [[1, "biodm.api.Api.controllers", false]], "corev1api (k8smanager property)": [[23, "biodm.managers.k8smanager.K8sManager.CoreV1Api", false]], "create() (entitycontroller method)": [[9, "biodm.components.controllers.controller.EntityController.create", false]], "create() (k8scontroller method)": [[3, "biodm.basics.k8scontroller.K8sController.create", false]], "create() (resourcecontroller method)": [[10, "biodm.components.controllers.resourcecontroller.ResourceController.create", false]], "create_custom_resource() (k8smanager method)": [[23, "biodm.managers.k8smanager.K8sManager.create_custom_resource", false]], "create_deployment() (k8smanager method)": [[23, "biodm.managers.k8smanager.K8sManager.create_deployment", false]], "create_group() (keycloakmanager method)": [[24, "biodm.managers.kcmanager.KeycloakManager.create_group", false]], 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method)": [[43, "biodm.utils.security.UserInfo.KeycloakManager.create_user", false]], "ctrl (base attribute)": [[17, "biodm.components.table.Base.ctrl", false]], "customobjectsapi (k8smanager property)": [[23, "biodm.managers.k8smanager.K8sManager.CustomObjectsApi", false]], "databasemanager (class in biodm.managers.dbmanager)": [[22, "biodm.managers.dbmanager.DatabaseManager", false]], "databaseservice (class in biodm.components.services.dbservice)": [[13, "biodm.components.services.dbservice.DatabaseService", false]], "db (api attribute)": [[1, "biodm.api.Api.db", false]], "dberror": [[20, "biodm.exceptions.DBError", false]], "debug (scope attribute)": [[32, "biodm.scope.Scope.DEBUG", false]], "decode_token() (keycloakmanager method)": [[24, "biodm.managers.kcmanager.KeycloakManager.decode_token", false]], "decode_token() (userinfo method)": [[43, "biodm.utils.security.UserInfo.decode_token", false]], "decode_token() (userinfo.keycloakmanager method)": [[43, "biodm.utils.security.UserInfo.KeycloakManager.decode_token", false]], "delayed (compositeinsert attribute)": [[44, "biodm.utils.sqla.CompositeInsert.delayed", false]], "delete (httpmethod attribute)": [[9, "biodm.components.controllers.controller.HttpMethod.DELETE", false]], "delete() (apiservice method)": [[5, "biodm.component.ApiService.delete", false]], "delete() (entitycontroller method)": [[9, "biodm.components.controllers.controller.EntityController.delete", false]], "delete() (kcgroupservice method)": [[15, "biodm.components.services.kcservice.KCGroupService.delete", false]], "delete() (kcuserservice method)": [[15, "biodm.components.services.kcservice.KCUserService.delete", false]], "delete() (resourcecontroller method)": [[10, "biodm.components.controllers.resourcecontroller.ResourceController.delete", false]], "delete() (unaryentityservice method)": [[13, "biodm.components.services.dbservice.UnaryEntityService.delete", false]], "delete_custom_object() (k8smanager method)": [[23, "biodm.managers.k8smanager.K8sManager.delete_custom_object", false]], "delete_group() (keycloakmanager method)": [[24, "biodm.managers.kcmanager.KeycloakManager.delete_group", false]], "delete_group() (userinfo.keycloakmanager method)": [[43, "biodm.utils.security.UserInfo.KeycloakManager.delete_group", false]], "delete_user() (keycloakmanager method)": [[24, "biodm.managers.kcmanager.KeycloakManager.delete_user", false]], "delete_user() (userinfo.keycloakmanager method)": [[43, "biodm.utils.security.UserInfo.KeycloakManager.delete_user", false]], "deploy_managers() (api method)": [[1, "biodm.api.Api.deploy_managers", false]], "detail (requesterror attribute)": [[20, "biodm.exceptions.RequestError.detail", false]], "dispatch() (historymiddleware method)": [[1, "biodm.api.HistoryMiddleware.dispatch", false]], "dispatch() (timeoutmiddleware method)": [[1, "biodm.api.TimeoutMiddleware.dispatch", false]], "dl_count (s3file attribute)": [[17, "biodm.components.table.S3File.dl_count", false]], "download (permission attribute)": [[17, "biodm.components.table.Permission.download", false]], "download() (s3controller method)": [[11, "biodm.components.controllers.s3controller.S3Controller.download", false]], "download() (s3service method)": [[16, "biodm.components.services.s3service.S3Service.download", false]], "email (user attribute)": [[41, "biodm.tables.user.User.email", false]], "emited_at (k8sinstance attribute)": [[37, "biodm.tables.k8sinstance.K8sInstance.emited_at", false]], "emited_at (s3file attribute)": [[17, "biodm.components.table.S3File.emited_at", false]], "enabled_verbs (permission property)": [[17, "biodm.components.table.Permission.enabled_verbs", false]], "endpoint (apimanager property)": [[5, "biodm.component.ApiManager.endpoint", false]], "endpoint (databasemanager property)": [[22, "biodm.managers.dbmanager.DatabaseManager.endpoint", false]], "endpoint (history attribute)": [[36, "biodm.tables.history.History.endpoint", false]], "endpoint 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false]], "failedupdate": [[20, "biodm.exceptions.FailedUpdate", false]], "field (permission attribute)": [[17, "biodm.components.table.Permission.field", false]], "fields (permission attribute)": [[17, "biodm.components.table.Permission.fields", false]], "filename (s3file attribute)": [[17, "biodm.components.table.S3File.filename", false]], "filenotuploadederror": [[20, "biodm.exceptions.FileNotUploadedError", false]], "filter() (apiservice method)": [[5, "biodm.component.ApiService.filter", false]], "filter() (entitycontroller method)": [[9, "biodm.components.controllers.controller.EntityController.filter", false]], "filter() (resourcecontroller method)": [[10, "biodm.components.controllers.resourcecontroller.ResourceController.filter", false]], "filter() (unaryentityservice method)": [[13, "biodm.components.services.dbservice.UnaryEntityService.filter", false]], "first_name (user attribute)": [[41, "biodm.tables.user.User.first_name", false]], "form (uploadpart attribute)": [[40, "biodm.tables.upload_part.UploadPart.form", false]], "gen_cond() (unaryentityservice method)": [[13, "biodm.components.services.dbservice.UnaryEntityService.gen_cond", false]], "gen_key() (s3service method)": [[16, "biodm.components.services.s3service.S3Service.gen_key", false]], "gen_upload_form() (s3service method)": [[16, "biodm.components.services.s3service.S3Service.gen_upload_form", false]], "get (httpmethod attribute)": [[9, "biodm.components.controllers.controller.HttpMethod.GET", false]], "get_custom_resource_params() (k8smanager static method)": [[23, "biodm.managers.k8smanager.K8sManager.get_custom_resource_params", false]], "get_group() (keycloakmanager method)": [[24, "biodm.managers.kcmanager.KeycloakManager.get_group", false]], "get_group() (userinfo.keycloakmanager method)": [[43, "biodm.utils.security.UserInfo.KeycloakManager.get_group", false]], "get_group_by_name() (keycloakmanager method)": [[24, "biodm.managers.kcmanager.KeycloakManager.get_group_by_name", false]], "get_group_by_name() (userinfo.keycloakmanager method)": [[43, "biodm.utils.security.UserInfo.KeycloakManager.get_group_by_name", false]], "get_group_by_path() (keycloakmanager method)": [[24, "biodm.managers.kcmanager.KeycloakManager.get_group_by_path", false]], "get_group_by_path() (userinfo.keycloakmanager method)": [[43, "biodm.utils.security.UserInfo.KeycloakManager.get_group_by_path", false]], "get_name_in_manifest() (k8smanager static method)": [[23, "biodm.managers.k8smanager.K8sManager.get_name_in_manifest", false]], "get_user_by_username() (keycloakmanager method)": [[24, "biodm.managers.kcmanager.KeycloakManager.get_user_by_username", false]], "get_user_by_username() (userinfo.keycloakmanager method)": [[43, "biodm.utils.security.UserInfo.KeycloakManager.get_user_by_username", false]], "get_user_groups() (keycloakmanager method)": [[24, "biodm.managers.kcmanager.KeycloakManager.get_user_groups", false]], "get_user_groups() (userinfo.keycloakmanager method)": [[43, "biodm.utils.security.UserInfo.KeycloakManager.get_user_groups", false]], "getattr_in_session() (unaryentityservice method)": [[13, "biodm.components.services.dbservice.UnaryEntityService.getattr_in_session", false]], "group (class in biodm.tables.group)": [[35, "biodm.tables.group.Group", false]], "group_required() (in module biodm.utils.security)": [[43, "biodm.utils.security.group_required", false]], "group_user_add() (keycloakmanager method)": [[24, "biodm.managers.kcmanager.KeycloakManager.group_user_add", false]], "group_user_add() (userinfo.keycloakmanager method)": [[43, "biodm.utils.security.UserInfo.KeycloakManager.group_user_add", false]], "groupcontroller (class in biodm.basics)": [[2, "biodm.basics.GroupController", false]], "groups (listgroup attribute)": [[38, "biodm.tables.listgroup.ListGroup.groups", false]], "groups (user attribute)": [[41, "biodm.tables.user.User.groups", false]], "groupschema (class in biodm.schemas.group)": [[27, "biodm.schemas.group.GroupSchema", false]], "handshake() (rootcontroller method)": [[4, "biodm.basics.rootcontroller.RootController.handshake", false]], "has_default() (base class method)": [[17, "biodm.components.table.Base.has_default", false]], "history (class in biodm.tables.history)": [[36, "biodm.tables.history.History", false]], "historymiddleware (class in biodm.api)": [[1, "biodm.api.HistoryMiddleware", false]], "httpmethod (class in biodm.components.controllers.controller)": [[9, "biodm.components.controllers.controller.HttpMethod", false]], "id (group attribute)": [[35, "biodm.tables.group.Group.id", false]], "id (k8sinstance attribute)": [[37, "biodm.tables.k8sinstance.K8sInstance.id", false]], "id (listgroup attribute)": [[38, "biodm.tables.listgroup.ListGroup.id", false]], "id (upload attribute)": [[39, "biodm.tables.upload.Upload.id", false]], "id (user attribute)": [[41, "biodm.tables.user.User.id", false]], "id (versioned attribute)": [[17, "biodm.components.table.Versioned.id", false]], "id_upload (s3file attribute)": [[17, "biodm.components.table.S3File.id_upload", false]], "id_upload (uploadpart attribute)": [[40, "biodm.tables.upload_part.UploadPart.id_upload", false]], "implementionerror": [[20, "biodm.exceptions.ImplementionError", false]], "in_session() (databasemanager static method)": [[22, "biodm.managers.dbmanager.DatabaseManager.in_session", false]], "info (userinfo property)": [[43, "biodm.utils.security.UserInfo.info", false]], "init_db() (databasemanager method)": [[22, "biodm.managers.dbmanager.DatabaseManager.init_db", false]], "instance_info() (k8scontroller method)": [[3, "biodm.basics.k8scontroller.K8sController.instance_info", false]], "invalidcollectionmethod": [[20, "biodm.exceptions.InvalidCollectionMethod", false]], "is_autoincrement() (base class method)": [[17, "biodm.components.table.Base.is_autoincrement", false]], "is_versioned (base attribute)": [[17, "biodm.components.table.Base.is_versioned", false]], "item (compositeinsert attribute)": [[44, "biodm.utils.sqla.CompositeInsert.item", false]], "json_bytes() (in module biodm.utils.utils)": [[45, "biodm.utils.utils.json_bytes", false]], "json_response() (in module biodm.utils.utils)": [[45, "biodm.utils.utils.json_response", false]], "k8 (api attribute)": [[1, "biodm.api.Api.k8", false]], "k8s (k8scontroller property)": [[3, "biodm.basics.k8scontroller.K8sController.k8s", false]], "k8s() (k8service method)": [[14, "biodm.components.services.k8service.K8Service.k8s", false]], "k8scontroller (class in biodm.basics.k8scontroller)": [[3, "biodm.basics.k8scontroller.K8sController", false]], "k8service (class in biodm.components.services.k8service)": [[14, "biodm.components.services.k8service.K8Service", false]], "k8sinstance (class in biodm.tables.k8sinstance)": [[37, "biodm.tables.k8sinstance.K8sInstance", false]], "k8sinstanceschema (class in biodm.schemas.k8sinstance)": [[28, "biodm.schemas.k8sinstance.K8sinstanceSchema", false]], "k8smanager (class in biodm.managers.k8smanager)": [[23, "biodm.managers.k8smanager.K8sManager", false]], "kc (api attribute)": [[1, "biodm.api.Api.kc", false]], "kc (userinfo attribute)": [[43, "biodm.utils.security.UserInfo.kc", false]], "kc() (kcservice method)": [[15, "biodm.components.services.kcservice.KCService.kc", false]], "kcgroupservice (class in biodm.components.services.kcservice)": [[15, "biodm.components.services.kcservice.KCGroupService", false]], "kcpath() (kcgroupservice static method)": [[15, "biodm.components.services.kcservice.KCGroupService.kcpath", false]], "kcservice (class in biodm.components.services.kcservice)": [[15, "biodm.components.services.kcservice.KCService", false]], "kcuserservice (class in biodm.components.services.kcservice)": [[15, "biodm.components.services.kcservice.KCUserService", false]], "key_salt (s3file attribute)": [[17, "biodm.components.table.S3File.key_salt", false]], "keycloakmanager (class in biodm.managers.kcmanager)": [[24, "biodm.managers.kcmanager.KeycloakManager", false]], "keycloakunavailableerror": [[20, "biodm.exceptions.KeycloakUnavailableError", false]], "last_name (user attribute)": [[41, "biodm.tables.user.User.last_name", false]], "list_custom_object() (k8smanager method)": [[23, "biodm.managers.k8smanager.K8sManager.list_custom_object", false]], "list_deployments() (k8smanager method)": [[23, "biodm.managers.k8smanager.K8sManager.list_deployments", false]], "list_instances() (k8scontroller method)": [[3, "biodm.basics.k8scontroller.K8sController.list_instances", false]], "list_pods() (k8smanager method)": [[23, "biodm.managers.k8smanager.K8sManager.list_pods", false]], "list_services_ports() (k8smanager method)": [[23, "biodm.managers.k8smanager.K8sManager.list_services_ports", false]], "listgroup (class in biodm.tables.listgroup)": [[38, "biodm.tables.listgroup.ListGroup", false]], "listgroupschema (class in biodm.schemas.listgroup)": [[29, "biodm.schemas.listgroup.ListGroupSchema", false]], "live() (rootcontroller static method)": [[4, "biodm.basics.rootcontroller.RootController.live", false]], "log() (k8smanager method)": [[23, "biodm.managers.k8smanager.K8sManager.log", false]], "logger (api attribute)": [[1, "biodm.api.Api.logger", false]], "logger (apicomponent attribute)": [[5, "biodm.component.ApiComponent.logger", false]], "login() (rootcontroller method)": [[4, "biodm.basics.rootcontroller.RootController.login", false]], "login_required() (in module biodm.utils.security)": [[43, "biodm.utils.security.login_required", false]], "manifest (k8sinstance attribute)": [[37, "biodm.tables.k8sinstance.K8sInstance.manifest", false]], "manifesterror": [[20, "biodm.exceptions.ManifestError", false]], "metadata (base attribute)": [[17, "biodm.components.table.Base.metadata", false]], "method (history attribute)": [[36, "biodm.tables.history.History.method", false]], "missingdb": [[20, "biodm.exceptions.MissingDB", false]], "missingservice": [[20, 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"swiftli": 50, "symbol": 57, "syn": 57, "syn_ack": [2, 4, 54, 57], "sync": [22, 50], "synchron": 47, "syntax": [45, 53], "system": [50, 55, 56], "systemat": 56, "t": [13, 20, 48, 54, 57], "tab": 54, "tabl": [0, 2, 6, 10, 11, 12, 13, 14, 15, 16, 22, 46, 47, 48, 50, 51, 54, 57], "tag": [49, 53], "tagcontrol": 49, "tagschema": 49, "tailor": 50, "take": [13, 53, 56], "taken": [51, 57], "tangibl": 56, "target": [10, 17], "target_t": [6, 17], "task": [48, 53], "technic": 51, "techniqu": 53, "technolog": 56, "technologi": 53, "tell": 56, "term": [54, 56], "termin": 56, "test": [0, 1, 13, 32, 50, 51, 52, 55, 57], "test_bas": 54, "text": 57, "than": [56, 57], "thei": [49, 50, 56, 57], "them": [11, 22, 47, 51, 56], "therefor": 56, "thi": [4, 9, 11, 13, 17, 22, 24, 43, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57], "thing": 56, "third": 56, "those": [13, 47, 48, 51, 53, 54, 56], "though": 56, "thread": 25, "threaten": 56, "three": [48, 51, 56], "through": [4, 13, 54, 55, 56, 57], "thu": [53, 54, 56, 57], "ti": 50, "time": [13, 54, 56], "timeout": 1, "timeoutmiddlewar": [0, 1, 46], "timestamp": [17, 33, 36], "timezon": 17, "tini": 48, "to_it": [0, 42, 45, 47], "togeth": 47, "toi": 50, "token": [4, 8, 20, 23, 24, 43, 51, 55, 57], "token_requir": 51, "tokendecodingerror": [0, 20, 46], "toler": 13, "too": 56, "tool": [48, 49, 51, 54, 56], "toolkit": 55, "top": [51, 57], "touch": [0, 42, 45], "track": 57, "trade": 56, "trademark": 56, "trail": 57, "transact": [13, 16, 56], "transfer": 56, "translat": [5, 12, 13], "transmiss": 56, "treat": 56, "treati": 56, "tree": 53, "trigger": 57, "triplet": 47, "true": [8, 13, 17, 45, 48, 49, 51, 53, 54, 57], "trueli": 53, "truth": 45, "try": [15, 20, 23, 47, 54], "tune": 47, "tupl": [9, 17, 23, 43, 44, 45, 57], "tutori": 50, "two": [17, 45, 48, 51, 53, 54, 56, 57], "txt": [54, 55], "type": [1, 2, 3, 4, 9, 10, 11, 13, 14, 15, 16, 17, 25, 32, 45, 47, 48, 53, 54, 56, 57], "typic": 56, "u": 54, "ui": [49, 54, 55], "ultim": [13, 53, 57], "unabl": 54, "unaccept": 56, "unari": 13, "unaryentityservic": [6, 12, 13], "unauthor": 20, "unauthorizederror": [0, 20, 46], "under": [10, 53, 56, 57], "underscor": 57, "undocu": 49, "unevalled_al": [0, 42, 45], "unevalled_or": [0, 42, 45], "unfortun": 51, "uniqu": 52, "unit": [13, 20], "unix": 45, "unknown": [27, 28, 29, 30, 31], "unless": 56, "unlik": 11, "unlimit": 56, "unmodifi": 56, "unnecessari": 56, "unpack": 56, "untest": 54, "until": 56, "up": [1, 10, 13, 47, 49, 50, 53, 54, 55, 57], "updat": [5, 7, 8, 9, 10, 11, 13, 20, 24, 43, 47, 48, 51, 53, 56, 57], "update_group": [21, 24, 42, 43], "update_us": [21, 24, 42, 43], "updated_json_object": 57, "updateversionederror": [0, 20, 46], "upload": [0, 6, 11, 16, 17, 20, 25, 26, 33, 40, 48, 52, 57], "upload_form": [48, 57], "upload_id": 25, "upload_large_fil": 57, "upload_part": [0, 33], "upload_small_fil": 57, "uploadpart": [0, 33, 39, 40], "uploadpartschema": [0, 26, 30], "uploadschema": [0, 26, 30], "upon": [50, 53, 57], "upper": 13, "uppon": 11, "upsert": [10, 12, 13], "upsertstmt": [5, 13, 14], "uri": 54, "url": [4, 11, 22, 24, 25, 43, 48, 54, 57], "url_expir": 25, "us": [11, 13, 17, 20, 23, 24, 43, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57], "user": [0, 1, 2, 4, 8, 15, 17, 20, 24, 26, 33, 35, 43, 47, 48, 50, 53, 54, 55, 56], "user_id": [24, 43], "user_info": [4, 5, 13, 14, 15, 47], "usercontrol": [0, 2], "userinfo": [0, 4, 5, 13, 14, 15, 42, 43, 47], "usernam": [24, 33, 41, 43, 48, 57], "username_own": 48, "username_us": [33, 36, 37], "userschema": [0, 26, 31, 48, 53], "utcnow": [0, 17, 42, 45], "utf": [45, 57], "util": [0, 13, 23, 46, 49, 51], "uuid": [15, 37, 47], "uuid4": 52, "uvicorn": [48, 55], "uvloop": [48, 55], "v1": [23, 25], "v3": [45, 48, 49], "val": 57, "val1": 57, "val2": 57, "val3": 57, "val_1": 13, "valid": [7, 9, 13, 47, 49, 50, 51, 53, 54, 56], "validated_at": [6, 17], "validationerror": 53, "valu": [9, 13, 17, 32, 45, 54, 57], "valueerror": 47, "vari": 53, "variabl": [51, 52], "ve": 54, "vein": 51, "venv": 54, "verb": [17, 57], "verbatim": 56, "veri": [48, 49, 57], "verif": 4, "verifi": 57, "version": [0, 6, 10, 13, 17, 20, 23, 45, 50, 51, 54, 56], "vessel": 50, "via": [49, 53, 57], "view": 56, "violat": 56, "virtual": 54, "visibl": 56, "visit": [47, 48, 53, 54, 55, 57], "visual": 55, "void": 56, "voil\u00e0": 48, "volum": 56, "vscode": 54, "vsgump": 25, "vv": 54, "w": 56, "wa": 56, "wai": [4, 52, 56, 57], "waiv": 56, "waiver": 56, "want": 56, "warn": [1, 17], "warranti": 56, "we": [4, 10, 13, 27, 31, 48, 49, 50, 51, 53, 56, 57], "weav": 47, "web": 57, "weirdli": 10, "welcom": 56, "well": [53, 56], "were": 56, "what": [52, 53, 56], "whatev": 56, "whatnot": 53, "when": [3, 4, 10, 17, 20, 47, 48, 51, 56, 57], "where": [13, 17, 53, 56, 57], "whether": 56, "which": [13, 49, 50, 51, 53, 56, 57], "while": [11, 51, 53, 57], "who": [51, 56], "whole": [53, 56, 57], "whom": 56, "whose": [45, 56], "why": 56, "wide": 56, "wildcard": 57, "window": 56, "wipo": 56, "wish": [51, 56], "within": [22, 51, 54, 56], "without": [13, 20, 53, 56, 57], "word": 51, "work": [49, 50, 56, 57], "workspacefold": 54, "worldwid": 56, "would": [47, 49, 52, 53, 56, 57], "wrapper": 23, "write": [0, 5, 6, 12, 13, 14, 15, 17, 47, 49, 51, 56, 57], "written": 56, "wrong": 20, "www": [9, 55, 56], "wxpdnptnkpsy": 55, "x": [45, 57], "year": 56, "yet": [20, 53, 55], "yield": [22, 48, 53, 57], "yml": [50, 54, 55], "you": [17, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57], "your": [48, 50, 51, 52, 53, 54, 55, 56, 57], "yourself": [54, 56], "zen": 48}, "titles": ["biodm package", "biodm.api module", "biodm.basics package", "biodm.basics.k8scontroller module", "biodm.basics.rootcontroller module", "biodm.component module", "biodm.components package", "biodm.components.controllers package", "biodm.components.controllers.admincontroller module", "biodm.components.controllers.controller module", "biodm.components.controllers.resourcecontroller module", "biodm.components.controllers.s3controller module", "biodm.components.services package", "biodm.components.services.dbservice module", "biodm.components.services.k8service module", "biodm.components.services.kcservice module", "biodm.components.services.s3service module", "biodm.components.table module", "biodm.config module", "biodm.error module", "biodm.exceptions module", "biodm.managers package", "biodm.managers.dbmanager module", "biodm.managers.k8smanager module", "biodm.managers.kcmanager module", "biodm.managers.s3manager module", "biodm.schemas package", "biodm.schemas.group module", "biodm.schemas.k8sinstance module", "biodm.schemas.listgroup module", "biodm.schemas.upload module", "biodm.schemas.user module", "biodm.scope module", "biodm.tables package", "biodm.tables.asso module", "biodm.tables.group module", "biodm.tables.history module", "biodm.tables.k8sinstance module", "biodm.tables.listgroup module", "biodm.tables.upload module", "biodm.tables.upload_part module", "biodm.tables.user module", "biodm.utils package", "biodm.utils.security module", "biodm.utils.sqla module", "biodm.utils.utils module", "API Reference", "Advanced Use", "Minimal Demo", "Documenting endpoints", "Developer Manual", "Permissions", "S3 Configuration", "Tables and Schemas", "Getting Started", "BioDM: A fast and RESTful Data Management framework", "License", "User Manual"], "titleterms": {"": 55, "A": [47, 55], "about": [47, 55], "admincontrol": 8, "advanc": 47, "api": [1, 46], "app": 55, "asso": 34, "base": [48, 57], "basic": [2, 3, 4, 50], "biodm": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 55], "bit": 47, "case": 47, "coars": 51, "collect": 57, "compon": [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17], "composit": 51, "concept": 50, "config": 18, "configur": [50, 52, 54], "content": [0, 2, 6, 7, 12, 21, 26, 33, 42, 55], "contribut": 55, "control": [7, 8, 9, 10, 11, 51], "convent": 48, "custom": 47, "data": 55, "dbmanag": 22, "dbservic": 13, "demo": 48, "depend": 54, "develop": [50, 54], "docstr": 49, "document": [49, 54, 55], "dynam": 51, "endpoint": [49, 51], "entiti": 57, "environ": 54, "error": 19, "except": 20, "fast": 55, "file": [48, 52, 57], "filter": 57, "fine": 51, "flag": 53, "framework": 55, "get": 54, "group": [27, 35, 47, 57], "guid": [49, 50], "histori": 36, "indic": 55, "individu": 54, "instal": [54, 55], "integr": 54, "intern": 47, "k8scontrol": 3, "k8servic": 14, "k8sinstanc": [28, 37], "k8smanag": 23, "kcmanag": 24, "kcservic": 15, "keycloack": 47, "larg": 57, "licenc": 55, "licens": 56, "listgroup": [29, 38], "manag": [21, 22, 23, 24, 25, 48, 52, 55, 57], "manual": [50, 57], "minim": 48, "modul": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "name": 48, "nest": [53, 57], "own": 51, "packag": [0, 2, 6, 7, 12, 21, 26, 33, 42], "permiss": [51, 57], "polici": 53, "queri": 57, "quick": 54, "quickstart": 55, "refer": 46, "relationship": 53, "resourc": [47, 48], "resourcecontrol": 10, "rest": 55, "rootcontrol": 4, "rout": 57, "rule": 51, "run": 55, "s3": 52, "s3control": 11, "s3manag": 25, "s3servic": 16, "schema": [26, 27, 28, 29, 30, 31, 53], "scope": 32, "secur": 43, "server": 54, "servic": [12, 13, 14, 15, 16], "setup": 54, "small": 57, "specif": 53, "sqla": 44, "start": 54, "static": 51, "strict": 51, "studi": 47, "submodul": [0, 2, 6, 7, 12, 21, 26, 33, 42], "subpackag": [0, 6], "tabl": [17, 33, 34, 35, 36, 37, 38, 39, 40, 41, 53, 55], "test": 54, "toolkit": 50, "unit": 54, "upload": [30, 39], "upload_part": 40, "us": 47, "user": [31, 41, 51, 57], "util": [42, 43, 44, 45], "version": [48, 57], "welcom": 55}}) \ No newline at end of file diff --git a/user_manual.html b/user_manual.html new file mode 100644 index 0000000..101a1a6 --- /dev/null +++ b/user_manual.html @@ -0,0 +1,454 @@ + + + + + + + User Manual — Python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

User Manual

+

This section describes how your Users may communicate with the API once it is deployed.

+

The examples are demonstrating using curl, but they are free to use any HTTP library out there.

+

Integration tests located at src/tests/integration are also providing plenty of resources.

+
+

Base routes

+
    +
  • OpenAPI schema

  • +
+
curl ${SERVER_ENDPOINT}/schema
+
+
+

Yields full API schema in JSON form.

+
    +
  • Liveness endpoint

  • +
+
curl ${SERVER_ENDPOINT}/live
+
+
+

Returns live with a 200 status code.

+
    +
  • Login

  • +
+
curl ${SERVER_ENDPOINT}/login
+
+
+

Returns a keycloak login url. +Visiting and authenticating there gives you an authentication JSON Web Token that you shall +provide in header to hit protected routes, see authenticated next.

+
curl ${SERVER_ENDPOINT}/login
+
+
+
    +
  • Authenticated

  • +
+
export TOKEN=ey....
+curl -S "${SERVER_ENDPOINT}/authenticated"\
+     -H "Authorization: Bearer ${TOKEN}"
+
+
+

This routes checks token and returns requesting user info: username, groups and projects.

+
    +
  • Syn Ack

  • +
+

This route is the callback login route located at ${SERVER_ENDPOINT}/syn_ack +and it is not meant to be accessed directly.

+
+
+

Entity routes

+

For each entity being managed by a ResourceController, the following routes are supported.

+
+

Note

+
    +
  • As per REST standard, each entity is accessible under a resource prefix which is the name of the entity in plural form.

  • +
  • URLs end without trailing slashes

  • +
  • In the case of a multi-indexed entity (i.e. composite primary key), {id} +refers to primary key elements separated by underscore symbol _.

  • +
+
+
    +
  • POST

  • +
+
curl -d ${JSON_OBJECT}\
+     ${SERVER_ENDPOINT}/my_resources
+
+
+

Supports submitting a resource and or a list of resource with nested resources.

+

Flexible write:

+

This endpoint works as a flexible write operation. It supports a mixin input of old and new data:

+
    +
  • new data shall comply to resource Shema ruleset.

  • +
  • reference old data by setting (at least) primary key values in the dict.

    +
      +
    • Other fields will be applied as an update.

    • +
    +
  • +
+
    +
  • GET

  • +
+

one

+
curl ${SERVER_ENDPOINT}/my_resources/{id}
+
+
+

or all

+
curl ${SERVER_ENDPOINT}/my_resources
+
+
+
    +
  • PUT

  • +
+

Not available for versioned resources, see Versioning below.

+
curl -X PUT\
+     -H "Content-Type: application/json"\
+     -d ${UPDATED_JSON_OBJECT}\
+     ${SERVER_ENDPOINT}/my_resources/{id}
+
+
+
    +
  • DELETE

  • +
+
curl -X DELETE\
+     ${SERVER_ENDPOINT}/my_resources/{id}
+
+
+
+

Groups

+

Group key is its path according to top level groups. Since / is a reserved route character +it is replaced by double underscore: __ (with no prefix).

+

E.g. parent__child__grandchild

+
+
+

Versioning

+

When a table is inheriting from Versioned e.g Dataset in our demo, associated controller +exposes an extra route: POST /my_versioned_resources/{id}_{version}/release.

+

This triggers creation of a new row with a version increment.

+
+

Note

+

PUT /release is the way of updating versioned resources. +The endpoint PUT / (a.k.a update) will not be available for such resources, and +any attempt at updating by reference through POST / will raise an error.

+
+

E.g.

+
curl -X POST ${SERVER_ENDPOINT}/my_file_resources/{id}_{version}/release
+
+
+

OR to pass in an update for the new version.

+
curl -d '{"name": "new_name"}' ${SERVER_ENDPOINT}/my_file_resources/{id}_{version}/release
+
+
+
+

Note

+

In the case of a resource both Versioned and S3File, POST /release will generate +a new upload form and set ready flag to false.

+
+
+
+

Filtering

+

When requesting all resources under a prefix (i.e. GET /my_resources) +it is possible to filter results by appending a QueryString starting with ? +and followed by:

+
    +
  • field=value pairs, separated by &

    +
      +
    • Use field=val1,val2,val3 to OR between multiple values

    • +
    • Use nested.field=val to select on a nested attribute field

    • +
    • Use * in a string attribute for wildcards

    • +
    +
  • +
  • field.op(value)

    +
      +
    • Currently only [lt, le, gt, ge] operators are supported for numerical values.

    • +
    +
  • +
+

e.g.

+
+

Note

+

When querying with curl, don’t forget to escape & symbol or enclose the whole url in quotes, else your scripting language may intepret it as several commands.

+
+
+
+

Query a nested collection

+

Alternatively you may get a resource nested collection like this

+
curl ${SERVER_ENDPOINT}/my_resources/{id}/{collection}
+
+
+

It also supports partial results. i.e. by appending ?fields=f1,...,fn

+
+
+
+

File management

+

Files are stored leveraging an S3 bucket instance. Upload and Downloads are requested directly +there through boto3 presigned-urls.

+
    +
  • Upload

  • +
+

On creating a new /file resource, it is required that you pass in the size in bytes that +you can obtain from its descriptor.

+

The resource shall contain a nested dictionary called upload composed of parts, +containing presigned form for direct file upload.

+

Next we distinguish two cases:

+
+

Small files

+

In the case of a small file, i.e. less than 100MB there is a single part, containing a +presigned POST and you may simply use the form to perform the upload.

+

The following snippet demonstrates how to do this in python:

+
+
upload_small_file.py
+
import requests
+
+# obtained from file['upload']['parts'][0]['form'] creation response
+post = {'url': ..., 'fields': ...}
+
+file_path = "/path/to/my_file.ext"
+file_name = "my_file.ext"
+
+with open(file_path, 'rb') as f:
+    files = {'file': (file_name, f)}
+    http_response = requests.post(
+        post['url'],
+        data=post['fields'],
+        files=files,
+        verify=True,
+        allow_redirects=True)
+    assert http_response.status_code == 201
+
+
+
+

Upon completion, BioDM will be notified back via a callback, so the file is immediately available.

+
+
+

Large files

+

For large files, several parts will be present. Each allowing you to upload a chunk of +size=100MB, possibly less for the last one.

+

For each part successfuly uploaded, the bucket will return you an ETag that you have to +keep track of and associate with the correct part_number.

+

Ultimately, the process has to be completed by submitting that mapping in order for the bucket +to aggregate all chunks into a file stored on the bucket. The bucket does not supports passing a +callback for a part_upload.

+

Similarely here is an example using python:

+
+
upload_large_file.py
+
import requests
+
+CHUNK_SIZE = 100*1024**2 # 100MB
+parts_etags = []
+host: str = ... # Server instance endpoint
+file_id = ... # obtained from file['id']
+upload_forms = [{'part_number': 1, 'form': ...}, ...] # obtained from file['upload']['parts']
+
+# Upload file
+with open(big_file_path, 'rb') as file:
+    for part in upload_forms:
+        part_data = file.read(CHUNK_SIZE) # Fetch one chunk.
+        response = requests.put(
+            part['form'], data=part_data, headers={'Content-Encoding': 'gzip'}
+        )
+        assert response.status_code == 200
+
+        # Get etag and remove trailing quotes to not disturb subsequent (json) loading.
+        etag = response.headers.get('ETag', "").replace('"', '')
+        # Build mapping.
+        parts_etags.append({'PartNumber': part['part_number'], 'ETag': etag})
+
+# Send completion notice with the mapping.
+complete = requests.put(
+    f"{host}/files/{file_id}/complete_multipart",
+    data=json.dumps(parts_etags).encode('utf-8')
+)
+assert complete.status_code == 201
+assert 'Completed.' in complete.text
+
+
+
+
+

Note

+

This example above is a quite naive approach. For very large files, you should make use of a +concurrency library (such as concurrent.futures or multiprocessing in python) in +order to speed up that process, as parts can be uploaded in any order.

+
+
    +
  • Download

  • +
+

Calling GET /my_file_resources will only return associated metadata (and the upload form(s) +while it is still in prending state).

+

To download a file use the following endpoint.

+
curl ${SERVER_ENDPOINT}/my_file_resources/{id}/download
+
+
+

That will return a url to directly download the file via GET request.

+
+

Note

+

Download urls are coming back with a redirect header, thus you may use +allow_redirects=True flag or equivalent when visiting this route to download in one go.

+
+
+
+
+

User permissions

+

When a Composition/One-to-Many relationship is flagged with permissions as described in +Fine: Dynamic user owned permissions a new field perm_{relationship_name} is available for that resource.

+

E.g. Dataset resource in our example, would have an extra field perm_files.

+

A Permission is holding a ListGroup object for each enabled verbs. +ListGroup being a route-less core table, allowing to manage lists of groups.

+

E.g. In our example, CREATE/READ/DOWNLOAD are enabled, +hence a JSON representation of a dataset with its permissions looks like this, where leaving +“read” empty means it will only account for decorator permissions if provided and left public +otherwise.

+
{
+    "name": "ds_test",
+    "owner": {
+        "username": "my_dataset_owner"
+    },
+    "perm_files": {
+        "write": {
+            "groups": [
+                {"name": "genomics_team"},
+                {"name": "IT_team"},
+                {"..."}
+            ]
+        },
+        "download": {
+            "groups": [{"..."}]
+        }
+    }
+}
+
+
+
+

Note

+
    +
  • Passing a top level group will allow all descending children group for that verb/resource tuple.

  • +
  • Permissions are taken into account if and only if keyclaok functionalities are enabled.

    +
      +
    • Without keycloak, no token exchange -> No way of getting back protected data.

    • +
    +
  • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file