Merge pull request #294 from 4dn-dcic/smaht-ingestion-20231201

SMaHT ingestion work. Moved structured_data.py from smaht-portal to here. (Tests still in smaht-portal though for now).

CHANGELOG.rst

@@ -6,6 +6,12 @@ dcicutils
 Change Log
 ----------
 
+8.5.0
+=====
+* Moved structured_data.py from smaht-portal to here; new portal_utils and data_readers modules.
+* Strip sheet name in data_readers.Excel; respecte (ignore) hidden sheets.
+
+
 8.4.0
 =====
 * More work related to SMaHT ingestion (bundle/sheet_utils, data_readers, etc).

dcicutils/data_readers.py

@@ -2,27 +2,30 @@
 import csv
 import openpyxl
 from typing import Any, Generator, Iterator, List, Optional, Type, Tuple, Union
-from dcicutils.misc_utils import right_trim
+from dcicutils.misc_utils import create_dict, right_trim
+
+# Forward type references for type hints.
+Excel = Type["Excel"]
 
 
 class RowReader(abc.ABC):
 
     def __init__(self):
         self.header = None
-        self.location = 0
+        self.row_number = 0
         self._warning_empty_headers = False
         self._warning_extra_values = []  # Line numbers.
         self.open()
 
     def __iter__(self) -> Iterator:
         for row in self.rows:
-            self.location += 1
+            self.row_number += 1
             if self.is_comment_row(row):
                 continue
             if self.is_terminating_row(row):
                 break
             if len(self.header) < len(row):  # Row values beyond what there are headers for are ignored.
-                self._warning_extra_values.append(self.location)
+                self._warning_extra_values.append(self.row_number)
             yield {column: self.cell_value(value) for column, value in zip(self.header, row)}
 
     def _define_header(self, header: List[Optional[Any]]) -> None:
@@ -49,13 +52,20 @@ def open(self) -> None:
         pass
 
     @property
-    def issues(self) -> Optional[List[str]]:
-        issues = []
+    def file(self) -> Optional[str]:
+        return self._file if hasattr(self, "_file") else None
+
+    @property
+    def warnings(self) -> List[str]:
+        warnings = []
         if self._warning_empty_headers:
-            issues.append("Empty header column encountered; ignoring it and all subsequent columns.")
+            warnings.append({"src": create_dict(file=self.file),
+                             "warning": "Empty header column encountered; ignoring it and all subsequent columns."})
         if self._warning_extra_values:
-            issues.extend([f"Extra column values on row [{row_number}]" for row_number in self._warning_extra_values])
-        return issues if issues else None
+            for row_number in self._warning_extra_values:
+                warnings.append({"src": create_dict(file=self.file, row=row_number),
+                                 "warning": f"Extra row column values."})
+        return warnings
 
 
 class ListReader(RowReader):
@@ -101,9 +111,10 @@ def __del__(self) -> None:
 
 class ExcelSheetReader(RowReader):
 
-    def __init__(self, sheet_name: str, workbook: openpyxl.workbook.workbook.Workbook) -> None:
+    def __init__(self, excel: Excel, sheet_name: str, workbook: openpyxl.workbook.workbook.Workbook) -> None:
         self.sheet_name = sheet_name or "Sheet1"
         self._workbook = workbook
+        self._file = excel._file
         self._rows = None
         super().__init__()
 
@@ -134,12 +145,13 @@ def __init__(self, file: str, reader_class: Optional[Type] = None) -> None:
         self.open()
 
     def sheet_reader(self, sheet_name: str) -> ExcelSheetReader:
-        return self._reader_class(sheet_name=sheet_name, workbook=self._workbook)
+        return self._reader_class(self, sheet_name=sheet_name, workbook=self._workbook)
 
     def open(self) -> None:
         if self._workbook is None:
             self._workbook = openpyxl.load_workbook(self._file, data_only=True)
-            self.sheet_names = self._workbook.sheetnames or []
+            self.sheet_names = [sheet_name for sheet_name in self._workbook.sheetnames
+                                if self._workbook[sheet_name].sheet_state != "hidden"]
 
     def __del__(self) -> None:
         if (workbook := self._workbook) is not None:

dcicutils/misc_utils.py

@@ -1501,6 +1501,14 @@ def right_trim(list_or_tuple: Union[List[Any], Tuple[Any]],
     return list_or_tuple[:i + 1]
 
 
+def create_dict(**kwargs) -> dict:
+    result = {}
+    for name in kwargs:
+        if kwargs[name]:
+            result[name] = kwargs[name]
+    return result
+
+
 def is_c4_arn(arn: str) -> bool:
     """
     Returns True iff the given (presumed) AWS ARN string value looks like it

dcicutils/portal_utils.py

@@ -0,0 +1,278 @@
+from collections import deque
+from pyramid.paster import get_app
+from pyramid.router import Router
+import re
+import requests
+from requests.models import Response as RequestResponse
+from typing import Optional, Type, Union
+from webtest.app import TestApp, TestResponse
+from dcicutils.common import OrchestratedApp, APP_CGAP, APP_FOURFRONT, APP_SMAHT, ORCHESTRATED_APPS
+from dcicutils.creds_utils import CGAPKeyManager, FourfrontKeyManager, SMaHTKeyManager
+from dcicutils.ff_utils import get_metadata, get_schema, patch_metadata, post_metadata
+from dcicutils.misc_utils import to_camel_case, VirtualApp
+from dcicutils.zip_utils import temporary_file
+
+Portal = Type["Portal"]  # Forward type reference for type hints.
+FILE_SCHEMA_NAME = "File"
+
+
+class Portal:
+    """
+    This is meant to be an uber wrapper for Portal access. It can be created in a variety of ways:
+    1. From a (Portal) .ini file (e.g. development.ini)
+    2. From a key dictionary, containing "key" and "secret" property values.
+    3. From a key tuple, containing (in order) a key and secret values.
+    4. From a keys file assumed to reside in ~/.{app}-keys.json where the given "app" value is either "smaht", "cgap",
+       or "fourfront"; and where this file is assumed to contain a dictionary with a key equal to the given "env"
+       value (e.g. smaht-localhost) and with a dictionary value containing "key" and "secret" property values; if
+       an "app" value is not specified but the given "env" value begins with one of the app values then that value
+       will be used, i.e. e.g. if env is "smaht-localhost" and app is unspecified than it is assumed to be "smaht".
+    5. From a keys file as described above (#4) but rather than be identified by the given "env" value it
+       is looked up by the given "server" name and the "server" key dictionary value in the key file.
+    6. From a given "vapp" value (which is assumed to be a TestApp or VirtualApp).
+    7. From another Portal object.
+    8. From a a pyramid Router object.
+    """
+    def __init__(self,
+                 arg: Optional[Union[VirtualApp, TestApp, Router, Portal, dict, tuple, str]] = None,
+                 env: Optional[str] = None, app: Optional[OrchestratedApp] = None, server: Optional[str] = None,
+                 key: Optional[Union[dict, tuple]] = None,
+                 vapp: Optional[Union[VirtualApp, TestApp, Router, Portal, str]] = None,
+                 portal: Optional[Union[VirtualApp, TestApp, Router, Portal, str]] = None) -> Portal:
+        if vapp and not portal:
+            portal = vapp
+        if ((isinstance(arg, (VirtualApp, TestApp, Router, Portal)) or
+             isinstance(arg, str) and arg.endswith(".ini")) and not portal):
+            portal = arg
+        elif isinstance(arg, str) and not env:
+            env = arg
+        elif (isinstance(arg, dict) or isinstance(arg, tuple)) and not key:
+            key = arg
+        if not app and env:
+            if env.startswith(APP_SMAHT):
+                app = APP_SMAHT
+            elif env.startswith(APP_CGAP):
+                app = APP_CGAP
+            elif env.startswith(APP_FOURFRONT):
+                app = APP_FOURFRONT
+        if isinstance(portal, Portal):
+            self._vapp = portal._vapp
+            self._env = portal._env
+            self._app = portal._app
+            self._server = portal._server
+            self._key = portal._key
+            self._key_pair = portal._key_pair
+            self._key_file = portal._key_file
+            return
+        self._vapp = None
+        self._env = env
+        self._app = app
+        self._server = server
+        self._key = None
+        self._key_pair = None
+        self._key_file = None
+        if isinstance(portal, (VirtualApp, TestApp)):
+            self._vapp = portal
+        elif isinstance(portal, (Router, str)):
+            self._vapp = Portal._create_vapp(portal)
+        elif isinstance(key, dict):
+            self._key = key
+            self._key_pair = (key.get("key"), key.get("secret")) if key else None
+            if key_server := key.get("server"):
+                self._server = key_server
+        elif isinstance(key, tuple) and len(key) >= 2:
+            self._key = {"key": key[0], "secret": key[1]}
+            self._key_pair = key
+        elif isinstance(env, str):
+            key_managers = {APP_CGAP: CGAPKeyManager, APP_FOURFRONT: FourfrontKeyManager, APP_SMAHT: SMaHTKeyManager}
+            if not (key_manager := key_managers.get(self._app)) or not (key_manager := key_manager()):
+                raise Exception(f"Invalid app name: {self._app} (valid: {', '.join(ORCHESTRATED_APPS)}).")
+            if isinstance(env, str):
+                self._key = key_manager.get_keydict_for_env(env)
+                if key_server := self._key.get("server"):
+                    self._server = key_server
+            elif isinstance(self._server, str):
+                self._key = key_manager.get_keydict_for_server(self._server)
+            self._key_pair = key_manager.keydict_to_keypair(self._key) if self._key else None
+            self._key_file = key_manager.keys_file
+
+    @property
+    def env(self):
+        return self._env
+
+    @property
+    def app(self):
+        return self._app
+
+    @property
+    def server(self):
+        return self._server
+
+    @property
+    def key(self):
+        return self._key
+
+    @property
+    def key_pair(self):
+        return self._key_pair
+
+    @property
+    def key_file(self):
+        return self._key_file
+
+    @property
+    def vapp(self):
+        return self._vapp
+
+    def get_metadata(self, object_id: str) -> Optional[dict]:
+        return get_metadata(obj_id=object_id, vapp=self._vapp, key=self._key)
+
+    def patch_metadata(self, object_id: str, data: str) -> Optional[dict]:
+        if self._key:
+            return patch_metadata(obj_id=object_id, patch_item=data, key=self._key)
+        return self.patch(f"/{object_id}", data)
+
+    def post_metadata(self, object_type: str, data: str) -> Optional[dict]:
+        if self._key:
+            return post_metadata(schema_name=object_type, post_item=data, key=self._key)
+        return self.post(f"/{object_type}", data)
+
+    def get(self, uri: str, follow: bool = True, **kwargs) -> Optional[Union[RequestResponse, TestResponse]]:
+        if isinstance(self._vapp, (VirtualApp, TestApp)):
+            response = self._vapp.get(self._uri(uri), **self._kwargs(**kwargs))
+            if response and response.status_code in [301, 302, 303, 307, 308] and follow:
+                response = response.follow()
+            return self._response(response)
+        return requests.get(self._uri(uri), allow_redirects=follow, **self._kwargs(**kwargs))
+
+    def patch(self, uri: str, data: Optional[dict] = None,
+              json: Optional[dict] = None, **kwargs) -> Optional[Union[RequestResponse, TestResponse]]:
+        if isinstance(self._vapp, (VirtualApp, TestApp)):
+            return self._vapp.patch_json(self._uri(uri), json or data, **self._kwargs(**kwargs))
+        return requests.patch(self._uri(uri), json=json or data, **self._kwargs(**kwargs))
+
+    def post(self, uri: str, data: Optional[dict] = None, json: Optional[dict] = None,
+             files: Optional[dict] = None, **kwargs) -> Optional[Union[RequestResponse, TestResponse]]:
+        if isinstance(self._vapp, (VirtualApp, TestApp)):
+            if files:
+                return self._vapp.post(self._uri(uri), json or data, upload_files=files, **self._kwargs(**kwargs))
+            else:
+                return self._vapp.post_json(self._uri(uri), json or data, upload_files=files, **self._kwargs(**kwargs))
+        return requests.post(self._uri(uri), json=json or data, files=files, **self._kwargs(**kwargs))
+
+    def get_schema(self, schema_name: str) -> Optional[dict]:
+        return get_schema(self.schema_name(schema_name), portal_vapp=self._vapp, key=self._key)
+
+    def get_schemas(self) -> dict:
+        return self.get("/profiles/").json()
+
+    @staticmethod
+    def schema_name(name: str) -> str:
+        return to_camel_case(name)
+
+    def is_file_schema(self, schema_name: str) -> bool:
+        if super_type_map := self.get_schemas_super_type_map():
+            if file_super_type := super_type_map.get(FILE_SCHEMA_NAME):
+                return self.schema_name(schema_name) in file_super_type
+        return False
+
+    def get_schemas_super_type_map(self) -> dict:
+        """
+        Returns the "super type map" for all of the known schemas (via /profiles).
+        This is a dictionary of all types which have (one or more) sub-types whose value is
+        an array of all of those sub-types (direct and all descendents), in breadth first order.
+        """
+        def breadth_first(super_type_map: dict, super_type_name: str) -> dict:
+            result = []
+            queue = deque(super_type_map.get(super_type_name, []))
+            while queue:
+                result.append(sub_type_name := queue.popleft())
+                if sub_type_name in super_type_map:
+                    queue.extend(super_type_map[sub_type_name])
+            return result
+        if not (schemas := self.get_schemas()):
+            return {}
+        super_type_map = {}
+        for type_name in schemas:
+            if super_type_name := schemas[type_name].get("rdfs:subClassOf"):
+                super_type_name = super_type_name.replace("/profiles/", "").replace(".json", "")
+                if super_type_name != "Item":
+                    if not super_type_map.get(super_type_name):
+                        super_type_map[super_type_name] = [type_name]
+                    elif type_name not in super_type_map[super_type_name]:
+                        super_type_map[super_type_name].append(type_name)
+        super_type_map_flattened = {}
+        for super_type_name in super_type_map:
+            super_type_map_flattened[super_type_name] = breadth_first(super_type_map, super_type_name)
+        return super_type_map_flattened
+
+    def _uri(self, uri: str) -> str:
+        if not isinstance(uri, str) or not uri:
+            return "/"
+        if uri.lower().startswith("http://") or uri.lower().startswith("https://"):
+            return uri
+        uri = re.sub(r"/+", "/", uri)
+        return (self._server + ("/" if uri.startswith("/") else "") + uri) if self._server else uri
+
+    def _kwargs(self, **kwargs) -> dict:
+        result_kwargs = {"headers":
+                         kwargs.get("headers", {"Content-type": "application/json", "Accept": "application/json"})}
+        if self._key_pair:
+            result_kwargs["auth"] = self._key_pair
+        if isinstance(timeout := kwargs.get("timeout"), int):
+            result_kwargs["timeout"] = timeout
+        return result_kwargs
+
+    def _response(self, response) -> Optional[RequestResponse]:
+        if response and isinstance(getattr(response.__class__, "json"), property):
+            class RequestResponseWrapper:  # For consistency change json property to method.
+                def __init__(self, response, **kwargs):
+                    super().__init__(**kwargs)
+                    self._response = response
+                def __getattr__(self, attr):  # noqa
+                    return getattr(self._response, attr)
+                def json(self):  # noqa
+                    return self._response.json
+            response = RequestResponseWrapper(response)
+        return response
+
+    @staticmethod
+    def create_for_testing(ini_file: Optional[str] = None) -> Portal:
+        if isinstance(ini_file, str):
+            return Portal(Portal._create_vapp(ini_file))
+        minimal_ini_for_unit_testing = "[app:app]\nuse = egg:encoded\nsqlalchemy.url = postgresql://dummy\n"
+        with temporary_file(content=minimal_ini_for_unit_testing, suffix=".ini") as ini_file:
+            return Portal(Portal._create_vapp(ini_file))
+
+    @staticmethod
+    def create_for_testing_local(ini_file: Optional[str] = None) -> Portal:
+        if isinstance(ini_file, str) and ini_file:
+            return Portal(Portal._create_vapp(ini_file))
+        minimal_ini_for_testing_local = "\n".join([
+            "[app:app]\nuse = egg:encoded\nfile_upload_bucket = dummy",
+            "sqlalchemy.url = postgresql://postgres@localhost:5441/postgres?host=/tmp/snovault/pgdata",
+            "multiauth.groupfinder = encoded.authorization.smaht_groupfinder",
+            "multiauth.policies = auth0 session remoteuser accesskey",
+            "multiauth.policy.session.namespace = mailto",
+            "multiauth.policy.session.use = encoded.authentication.NamespacedAuthenticationPolicy",
+            "multiauth.policy.session.base = pyramid.authentication.SessionAuthenticationPolicy",
+            "multiauth.policy.remoteuser.namespace = remoteuser",
+            "multiauth.policy.remoteuser.use = encoded.authentication.NamespacedAuthenticationPolicy",
+            "multiauth.policy.remoteuser.base = pyramid.authentication.RemoteUserAuthenticationPolicy",
+            "multiauth.policy.accesskey.namespace = accesskey",
+            "multiauth.policy.accesskey.use = encoded.authentication.NamespacedAuthenticationPolicy",
+            "multiauth.policy.accesskey.base = encoded.authentication.BasicAuthAuthenticationPolicy",
+            "multiauth.policy.accesskey.check = encoded.authentication.basic_auth_check",
+            "multiauth.policy.auth0.use = encoded.authentication.NamespacedAuthenticationPolicy",
+            "multiauth.policy.auth0.namespace = auth0",
+            "multiauth.policy.auth0.base = encoded.authentication.Auth0AuthenticationPolicy"
+        ])
+        with temporary_file(content=minimal_ini_for_testing_local, suffix=".ini") as minimal_ini_file:
+            return Portal(Portal._create_vapp(minimal_ini_file))
+
+    @staticmethod
+    def _create_vapp(value: Union[str, Router, TestApp] = "development.ini", app_name: str = "app") -> TestApp:
+        if isinstance(value, TestApp):
+            return value
+        app = value if isinstance(value, Router) else get_app(value, app_name)
+        return TestApp(app, {"HTTP_ACCEPT": "application/json", "REMOTE_USER": "TEST"})