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Merge pull request galaxyproject#16672 from jmchilton/markdown
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Galaxy Markdown - add workflow image and license to Galaxy markdown.
martenson authored Nov 3, 2023

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2 parents d3d812c + c09b62f commit aa1702d
Showing 10 changed files with 183 additions and 41 deletions.
32 changes: 32 additions & 0 deletions client/src/components/Markdown/Elements/Workflow/WorkflowImage.vue
Original file line number Diff line number Diff line change
@@ -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>
Original file line number Diff line number Diff line change
@@ -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>
8 changes: 8 additions & 0 deletions client/src/components/Markdown/MarkdownContainer.vue
Original file line number Diff line number Diff line change
@@ -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" />
2 changes: 1 addition & 1 deletion client/src/components/Markdown/MarkdownDialog.vue
Original file line number Diff line number Diff line change
@@ -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;
18 changes: 18 additions & 0 deletions client/src/components/Markdown/MarkdownToolBox.vue
Original file line number Diff line number Diff line change
@@ -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: {
2 changes: 2 additions & 0 deletions lib/galaxy/managers/markdown_parse.py
Original file line number Diff line number Diff line change
@@ -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"],
52 changes: 50 additions & 2 deletions lib/galaxy/managers/markdown_util.py
Original file line number Diff line number Diff line change
@@ -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")
@@ -433,10 +458,14 @@ 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)
@@ -473,6 +502,25 @@ 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.
36 changes: 36 additions & 0 deletions lib/galaxy/managers/workflows.py
Original file line number Diff line number Diff line change
@@ -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:
47 changes: 10 additions & 37 deletions lib/galaxy/webapps/galaxy/controllers/workflow.py
Original file line number Diff line number Diff line change
@@ -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()
7 changes: 6 additions & 1 deletion lib/galaxy/workflow/render.py
Original file line number Diff line number Diff line change
@@ -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):

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