From fd3e3290df516c735d09a91d08e88cb572a3fcce Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 7 Sep 2023 16:24:49 -0400 Subject: [PATCH] Galaxy Markdown - add workflow image and license to Galaxy markdown. --- .../Elements/Workflow/WorkflowImage.vue | 32 +++++++++++++ .../Elements/Workflow/WorkflowLicense.vue | 20 ++++++++ .../components/Markdown/MarkdownContainer.vue | 8 ++++ .../components/Markdown/MarkdownDialog.vue | 2 +- .../components/Markdown/MarkdownToolBox.vue | 18 +++++++ lib/galaxy/managers/markdown_parse.py | 2 + lib/galaxy/managers/markdown_util.py | 42 ++++++++++++++++- lib/galaxy/managers/workflows.py | 36 ++++++++++++++ .../webapps/galaxy/controllers/workflow.py | 47 ++++--------------- lib/galaxy/workflow/render.py | 7 ++- 10 files changed, 173 insertions(+), 41 deletions(-) create mode 100644 client/src/components/Markdown/Elements/Workflow/WorkflowImage.vue create mode 100644 client/src/components/Markdown/Elements/Workflow/WorkflowLicense.vue diff --git a/client/src/components/Markdown/Elements/Workflow/WorkflowImage.vue b/client/src/components/Markdown/Elements/Workflow/WorkflowImage.vue new file mode 100644 index 000000000000..3ebf725ed304 --- /dev/null +++ b/client/src/components/Markdown/Elements/Workflow/WorkflowImage.vue @@ -0,0 +1,32 @@ + + + diff --git a/client/src/components/Markdown/Elements/Workflow/WorkflowLicense.vue b/client/src/components/Markdown/Elements/Workflow/WorkflowLicense.vue new file mode 100644 index 000000000000..a4b0f3dd46d0 --- /dev/null +++ b/client/src/components/Markdown/Elements/Workflow/WorkflowLicense.vue @@ -0,0 +1,20 @@ + + + diff --git a/client/src/components/Markdown/MarkdownContainer.vue b/client/src/components/Markdown/MarkdownContainer.vue index 9ece148b02b6..b544ae3d71e2 100644 --- a/client/src/components/Markdown/MarkdownContainer.vue +++ b/client/src/components/Markdown/MarkdownContainer.vue @@ -14,6 +14,8 @@ import JobParameters from "./Elements/JobParameters.vue"; import ToolStd from "./Elements/ToolStd.vue"; import Visualization from "./Elements/Visualization.vue"; import WorkflowDisplay from "./Elements/Workflow/WorkflowDisplay.vue"; +import WorkflowImage from "./Elements/Workflow/WorkflowImage.vue"; +import WorkflowLicense from "./Elements/Workflow/WorkflowLicense.vue"; const toggle = ref(false); const props = defineProps({ @@ -75,6 +77,12 @@ const isVisible = computed(() => !isCollapsible.value || toggle.value); 
{{ time }}
+
+ +
+
+ +
diff --git a/client/src/components/Markdown/MarkdownDialog.vue b/client/src/components/Markdown/MarkdownDialog.vue index 8303870b7ca7..648c9696c4f7 100644 --- a/client/src/components/Markdown/MarkdownDialog.vue +++ b/client/src/components/Markdown/MarkdownDialog.vue @@ -177,7 +177,7 @@ export default { }, onWorkflow(response) { this.workflowShow = false; - this.$emit("onInsert", `workflow_display(workflow_id=${response.id})`); + this.$emit("onInsert", `${this.argumentName}(workflow_id=${response.id})`); }, onVisualization(response) { this.visualizationShow = false; diff --git a/client/src/components/Markdown/MarkdownToolBox.vue b/client/src/components/Markdown/MarkdownToolBox.vue index 19b3caa3bcee..6e75bd71a1b5 100644 --- a/client/src/components/Markdown/MarkdownToolBox.vue +++ b/client/src/components/Markdown/MarkdownToolBox.vue @@ -190,6 +190,16 @@ export default { name: "Workflow Display", emitter: "onWorkflowId", }, + { + id: "workflow_license", + name: "Workflow License", + emitter: "onWorkflowId", + }, + { + id: "workflow_image", + name: "Workflow Image", + emitter: "onWorkflowId", + }, ], }, workflowInEditorSection: { @@ -214,6 +224,14 @@ export default { name: "Current Workflow", description: "containing all steps", }, + { + id: "workflow_image", + name: "Current Workflow Image", + }, + { + id: "workflow_license", + name: "Current Workflow License", + }, ], }, otherSection: { diff --git a/lib/galaxy/managers/markdown_parse.py b/lib/galaxy/managers/markdown_parse.py index ca486283f844..c93827a3ad14 100644 --- a/lib/galaxy/managers/markdown_parse.py +++ b/lib/galaxy/managers/markdown_parse.py @@ -38,6 +38,8 @@ class DynamicArguments: "history_dataset_type": ["input", "output", "history_dataset_id"], "history_dataset_collection_display": ["input", "output", "history_dataset_collection_id"], "workflow_display": ["workflow_id"], + "workflow_license": ["workflow_id"], + "workflow_image": ["workflow_id", "size"], "job_metrics": ["step", "job_id"], "job_parameters": ["step", "job_id"], "tool_stderr": ["step", "job_id"], diff --git a/lib/galaxy/managers/markdown_util.py b/lib/galaxy/managers/markdown_util.py index 4e5219251ccc..7d2ff714022c 100644 --- a/lib/galaxy/managers/markdown_util.py +++ b/lib/galaxy/managers/markdown_util.py @@ -67,6 +67,7 @@ INPUT_LABEL_PATTERN = re.compile(r"input=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX) STEP_LABEL_PATTERN = re.compile(r"step=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX) PATH_LABEL_PATTERN = re.compile(r"path=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX) +SIZE_PATTERN = re.compile(r"size=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX) # STEP_OUTPUT_LABEL_PATTERN = re.compile(r'step_output=([\w_\-]+)/([\w_\-]+)') UNENCODED_ID_PATTERN = re.compile( r"(history_id|workflow_id|history_dataset_id|history_dataset_collection_id|job_id|invocation_id)=([\d]+)" @@ -154,6 +155,12 @@ def _remap(container, line): elif container == "workflow_display": stored_workflow = workflow_manager.get_stored_accessible_workflow(trans, encoded_id) rval = self.handle_workflow_display(line, stored_workflow) + elif container == "workflow_image": + stored_workflow = workflow_manager.get_stored_accessible_workflow(trans, encoded_id) + rval = self.handle_workflow_image(line, stored_workflow) + elif container == "workflow_license": + stored_workflow = workflow_manager.get_stored_accessible_workflow(trans, encoded_id) + rval = self.handle_workflow_license(line, stored_workflow) elif container == "history_dataset_collection_display": hdca = collection_manager.get_dataset_collection_instance(trans, "history", encoded_id) rval = self.handle_dataset_collection_display(line, hdca) @@ -242,6 +249,14 @@ def handle_dataset_type(self, line, hda): def handle_workflow_display(self, line, stored_workflow): pass + @abc.abstractmethod + def handle_workflow_image(self, line, stored_workflow): + pass + + @abc.abstractmethod + def handle_workflow_license(self, line, stored_workflow): + pass + @abc.abstractmethod def handle_dataset_collection_display(self, line, hdca): pass @@ -313,6 +328,14 @@ def handle_dataset_info(self, line, hda): def handle_workflow_display(self, line, stored_workflow): self.ensure_rendering_data_for("workflows", stored_workflow)["name"] = stored_workflow.name + def handle_workflow_image(self, line, stored_workflow): + pass + + def handle_workflow_license(self, line, stored_workflow): + self.ensure_rendering_data_for("workflows", stored_workflow)[ + "license" + ] = stored_workflow.latest_workflow.license + def handle_dataset_collection_display(self, line, hdca): hdca_serializer = HDCASerializer(self.trans.app) hdca_view = hdca_serializer.serialize_to_view(hdca, user=self.trans.user, trans=self.trans, view="summary") @@ -431,10 +454,14 @@ def handle_dataset_as_image(self, line, hda): file = dataset.file_name with open(file, "rb") as f: - base64_image_data = base64.b64encode(f.read()).decode("utf-8") - rval = (f"![{name}](data:image/png;base64,{base64_image_data})", True) + image_data = f.read() + rval = (self._embed_image(name, "png", image_data), True) return rval + def _embed_image(self, name: str, image_type: str, image_data: bytes): + base64_image_data = base64.b64encode(image_data).decode("utf-8") + return f"![{name}](data:image/{image_type};base64,{base64_image_data})" + def handle_history_link(self, line, history): if history: content = literal_via_fence(history.name) @@ -471,6 +498,17 @@ def handle_workflow_display(self, line, stored_workflow): markdown += "\n---\n" return (markdown, True) + def handle_workflow_license(self, line, stored_workflow): + # workflow_manager = self.trans.app.workflow_manager + # TODO: make this a link + return (f"Workflow License: {stored_workflow.latest_workflow.license}", True) + + def handle_workflow_image(self, line, stored_workflow): + workflow_manager = self.trans.app.workflow_manager + image_data = workflow_manager.get_workflow_svg(self.trans, stored_workflow.latest_workflow) + rval = (self._embed_image("Workflow", "svg+xml", image_data), True) + return rval + def handle_dataset_collection_display(self, line, hdca): name = hdca.name or "" # put it in a list to hack around no nonlocal on Python 2. diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py index 4d84e834cd85..157f9cad7dda 100644 --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -96,6 +96,10 @@ RefactorActionExecution, RefactorActions, ) +from galaxy.workflow.render import ( + STANDALONE_SVG_TEMPLATE, + WorkflowCanvas, +) from galaxy.workflow.reports import generate_report from galaxy.workflow.resources import get_resource_mapper_function from galaxy.workflow.steps import ( @@ -367,6 +371,38 @@ def check_security(self, trans, has_workflow, check_ownership=True, check_access return True + def get_workflow_svg_from_id(self, trans, id, for_embed=False) -> bytes: + stored = self.get_stored_accessible_workflow(trans, id) + return self.get_workflow_svg(trans, stored.latest_workflow, for_embed=for_embed) + + def get_workflow_svg(self, trans, workflow, for_embed=False) -> bytes: + try: + svg = self._workflow_to_svg_canvas(trans, workflow, for_embed=for_embed) + s = STANDALONE_SVG_TEMPLATE % svg.tostring() + return s.encode("utf-8") + except Exception: + message = ( + "Galaxy is unable to create the SVG image. Please check your workflow, there might be missing tools." + ) + raise exceptions.MessageException(message) + + def _workflow_to_svg_canvas(self, trans, workflow, for_embed=False): + workflow_canvas = WorkflowCanvas() + for step in workflow.steps: + # Load from database representation + module = module_factory.from_workflow_step(trans, step) + module_name = module.get_name() + module_data_inputs = module.get_data_inputs() + module_data_outputs = module.get_data_outputs() + workflow_canvas.populate_data_for_step( + step, + module_name, + module_data_inputs, + module_data_outputs, + ) + workflow_canvas.add_steps() + return workflow_canvas.finish(for_embed=for_embed) + def get_invocation(self, trans, decoded_invocation_id, eager=False) -> model.WorkflowInvocation: q = trans.sa_session.query(model.WorkflowInvocation) if eager: diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py index 3772a29cd10c..b2dd07de100f 100644 --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -39,14 +39,7 @@ extract_workflow, summarize, ) -from galaxy.workflow.modules import ( - load_module_sections, - module_factory, -) -from galaxy.workflow.render import ( - STANDALONE_SVG_TEMPLATE, - WorkflowCanvas, -) +from galaxy.workflow.modules import load_module_sections log = logging.getLogger(__name__) @@ -333,18 +326,16 @@ def annotate_async(self, trans, id, new_annotation=None, **kwargs): @web.expose @web.require_login("use Galaxy workflows") - def gen_image(self, trans, id, **kwargs): - stored = self.get_stored_workflow(trans, id, check_ownership=True) + def gen_image(self, trans, id, embed="false", **kwargs): + embed = util.asbool(embed) try: - svg = self._workflow_to_svg_canvas(trans, stored) - except Exception: - message = ( - "Galaxy is unable to create the SVG image. Please check your workflow, there might be missing tools." - ) - return trans.show_error_message(message) - trans.response.set_content_type("image/svg+xml") - s = STANDALONE_SVG_TEMPLATE % svg.tostring() - return s.encode("utf-8") + s = trans.app.workflow_manager.get_workflow_svg_from_id(trans, id, for_embed=embed) + trans.response.set_content_type("image/svg+xml") + return s + except Exception as e: + log.exception("Failed to generate SVG image") + error_message = str(e) + return trans.show_error_message(error_message) @web.legacy_expose_api def create(self, trans, payload=None, **kwd): @@ -630,21 +621,3 @@ def build_from_current_history( def get_item(self, trans, id): return self.get_stored_workflow(trans, id) - - def _workflow_to_svg_canvas(self, trans, stored): - workflow = stored.latest_workflow - workflow_canvas = WorkflowCanvas() - for step in workflow.steps: - # Load from database representation - module = module_factory.from_workflow_step(trans, step) - module_name = module.get_name() - module_data_inputs = module.get_data_inputs() - module_data_outputs = module.get_data_outputs() - workflow_canvas.populate_data_for_step( - step, - module_name, - module_data_inputs, - module_data_outputs, - ) - workflow_canvas.add_steps() - return workflow_canvas.finish() diff --git a/lib/galaxy/workflow/render.py b/lib/galaxy/workflow/render.py index cc9f6bd7ab8f..b5ee044bbc2f 100644 --- a/lib/galaxy/workflow/render.py +++ b/lib/galaxy/workflow/render.py @@ -23,7 +23,7 @@ def __init__(self): self.max_width = 0 self.data = [] - def finish(self): + def finish(self, for_embed=False): # max_x, max_y, max_width = self.max_x, self.max_y, self.max_width for box in self.boxes: self.canvas.add(box) @@ -33,6 +33,11 @@ def finish(self): for text in self.text: text_style_layer.add(text) self.canvas.add(text_style_layer) + # if we're embedding this in HTML - setup a viewbox and preserve aspect ratio + # https://css-tricks.com/scale-svg/#aa-the-viewbox-attribute + if for_embed: + self.canvas.viewbox(-5, -5, self.max_x + self.max_width, self.max_y + 150) + self.canvas.fit() return self.canvas def add_boxes(self, step_dict, width, name_fill):