Galaxy Markdown - add workflow image and license to Galaxy markdown.

client/src/components/Markdown/Elements/Workflow/WorkflowImage.vue

@@ -0,0 +1,32 @@
+<script setup lang="ts">
+import { computed } from "vue";
+
+import { getAppRoot } from "@/onload/loadConfig";
+
+interface WorkflowImageProps {
+    workflowId: string;
+    size?: string;
+}
+
+const props = withDefaults(defineProps<WorkflowImageProps>(), {
+    size: "lg",
+});
+
+const src = computed(() => {
+    return `${getAppRoot()}workflow/gen_image?id=${props.workflowId}&embed=true`;
+});
+const width = computed(() => {
+    const size = props.size;
+    if (size == "sm") {
+        return "300px";
+    } else if (size == "md") {
+        return "550px";
+    } else {
+        return "100%";
+    }
+});
+</script>
+
+<template>
+    <img alt="Preview of Galaxy Workflow" :src="src" :width="width" height="auto" />
+</template>

client/src/components/Markdown/Elements/Workflow/WorkflowLicense.vue

@@ -0,0 +1,20 @@
+<script setup lang="ts">
+import License from "@/components/License/License.vue";
+
+interface WorkflowLicenseProps {
+    licenseId?: string;
+}
+
+const props = withDefaults(defineProps<WorkflowLicenseProps>(), {
+    licenseId: null,
+});
+</script>
+
+<template>
+    <span>
+        <p v-if="!props.licenseId">
+            <i>Workflow does not define a license.</i>
+        </p>
+        <License v-else :license-id="props.licenseId" />
+    </span>
+</template>

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);
             <div v-else-if="name == 'generate_time'" class="galaxy-time">
                 <pre><code>{{ time }}</code></pre>
             </div>
+            <div v-else-if="name == 'workflow_image'" class="workflow-image" style="text-align: center">
+                <WorkflowImage :workflow-id="args.workflow_id" :size="args.size || 'lg'" />
+            </div>
+            <div v-else-if="name == 'workflow_license'" class="workflow-license">
+                <WorkflowLicense :license-id="workflows[args.workflow_id]['license']" />
+            </div>
             <HistoryLink v-else-if="name == 'history_link'" :args="args" :histories="histories" />
             <HistoryDatasetAsImage v-else-if="name == 'history_dataset_as_image'" :args="args" />
             <HistoryDatasetLink v-else-if="name == 'history_dataset_link'" :args="args" />

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;

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: {

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"],

lib/galaxy/managers/markdown_util.py

@@ -36,6 +36,7 @@
 from galaxy.config import GalaxyAppConfiguration
 from galaxy.exceptions import (
     MalformedContents,
+    ObjectNotFound,
     ServerNotConfiguredForRequest,
 )
 from galaxy.managers.hdcas import HDCASerializer
@@ -44,6 +45,7 @@
     summarize_job_metrics,
     summarize_job_parameters,
 )
+from galaxy.managers.licenses import LicensesManager
 from galaxy.model.item_attrs import get_item_annotation_str
 from galaxy.model.orm.now import now
 from galaxy.schema import PdfDocumentType
@@ -67,6 +69,7 @@
 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 +157,12 @@ 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 +251,14 @@ 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 +330,14 @@ 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 +456,14 @@ 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 +500,25 @@ 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
+        license_manager = LicensesManager()
+        license_id = stored_workflow.latest_workflow.license
+        markdown = "*No license specified.*"
+        if license_id:
+            try:
+                license_metadata = license_manager.get_license_by_id(license_id)
+                markdown = f"[{license_metadata.name}]({license_metadata.url})"
+            except ObjectNotFound:
+                markdown = f"Unknown license ({license_id})"
+        return (f"\n\n{markdown}\n\n", 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, for_embed=True)
+        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.

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:

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()

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):