opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Implement yet another syntax for Galaxy Markdown.

Browse Source 
The community took a vote (https://github.com/galaxyproject/galaxy/pull/8511#issuecomment-525886525) and the overwhelming favorite was this programming style declaration of a vaguely C-ish language embedded in quote fenced blocks.
This commit is contained in:
John Chilton
2019-08-30 09:46:14 -04:00
parent 664ab71653
commit fa637518e8
8 changed files with 245 additions and 143 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/galaxy/scripts/components/Markdown/Markdown.vue
+38 -13
View File
@@ -17,16 +17,12 @@ import JOB_STATES_MODEL from "mvc/history/job-states-model";
import HDCAModel from "mvc/history/hdca-model";
import HDCAListItemEdit from "mvc/history/hdca-li-edit";
const galaxy_blocks = /{galaxy_(\w+)(.*)}/;
const FUNCTION_CALL_LINE_TEMPLATE = /\s*(\w+)\s*\((\s*\w+\s*=\s*\w+\s*)\)\s*/m;
const md = MarkdownIt();
const default_fence = md.renderer.rules.fence;
function render_fenced_div(action, args, content) {
return `<div><pre>${content}</pre></div><br>\n`;
}
const RENDER_FUNCTIONS = {
history_dataset_display: (action, args, content) => {
const history_dataset_id = args.history_dataset_id;
@@ -82,10 +78,22 @@ const RENDER_FUNCTIONS = {
const history_dataset_id = args.history_dataset_id;
return `<img src="${getAppRoot()}dataset/display?dataset_id=${history_dataset_id}"></img>`;
},
history_dataset_peek: render_fenced_div,
history_dataset_info: render_fenced_div,
tool_stdout: render_fenced_div,
tool_stderr: render_fenced_div,
history_dataset_peek: (action, args, content) => {
const history_dataset_id = args.history_dataset_id;
return `<div class='dataset-peek' history_dataset_id="${history_dataset_id}"><pre><code></code></pre></div>`;
},
history_dataset_info: (action, args, content) => {
const history_dataset_id = args.history_dataset_id;
return `<div class='dataset-info' history_dataset_id="${history_dataset_id}"><pre><code></code></pre></div>`;
},
tool_stdout: (action, args, content) => {
const jobId = args.job_id;
return `<div class="tool-stdout" job_id="${jobId}"><pre><code></code></pre></div>`;
},
tool_stderr: (action, args, content) => {
const jobId = args.job_id;
return `<div class="tool-stderr" job_id="${jobId}"><pre><code></code></pre></div>`;
},
job_metrics: (action, args, content) => {
const jobId = args.job_id;
return `<div class="job-metrics" job_id="${jobId}"></div>`;
@@ -100,8 +108,8 @@ md.renderer.rules.fence = function(tokens, idx, options, env, slf) {
const token = tokens[idx],
info = token.info ? token.info.trim() : "",
content = token.content;
const arr = galaxy_blocks.exec(info);
if (arr) {
if (info == "galaxy") {
const arr = FUNCTION_CALL_LINE_TEMPLATE.exec(content);
const action = arr[1];
const arguments_str = arr[2].trim();
const args = {};
@@ -109,7 +117,7 @@ md.renderer.rules.fence = function(tokens, idx, options, env, slf) {
const parts = arguments_str.split(/(\s+)/);
for (const part of parts) {
const [key, val] = part.split("=");
args[key] = val;
args[key.trim()] = val.trim();
}
}
return RENDER_FUNCTIONS[action](action, args, content);
@@ -118,6 +126,16 @@ md.renderer.rules.fence = function(tokens, idx, options, env, slf) {
}
};
function render_fenced_output(tag, objects, idAttr, metadataKey) {
$("." + tag).each((i, el) => {
const objectId = $(el).attr(idAttr);
const meta = objects[objectId][metadataKey];
$(el)
.find("code")
.text(meta);
});
}
export default {
props: {
markdownConfig: {
@@ -129,7 +147,8 @@ export default {
markdownRendered: "",
historyDatasets: {},
historyDatasetCollections: {},
workflows: {}
workflows: {},
jobs: {}
};
},
watch: {
@@ -139,6 +158,7 @@ export default {
this.historyDatasets = mConfig.history_datasets || {};
this.historyDatasetCollections = mConfig.history_dataset_collections || {};
this.workflows = mConfig.workflows || {};
this.jobs = mConfig.jobs || {};
this.$nextTick(() => {
render_embedded_items();
@@ -155,6 +175,11 @@ export default {
}
});
render_fenced_output("tool-stdout", this.jobs, "job_id", "tool_stdout");
render_fenced_output("tool-stderr", this.jobs, "job_id", "tool_stderr");
render_fenced_output("dataset-peek", this.historyDatasets, "history_dataset_id", "peek");
render_fenced_output("dataset-info", this.historyDatasets, "history_dataset_id", "info");
$(".dataset-collection").each((i, el) => {
const Galaxy = getGalaxyInstance();
const hdcaId = $(el).attr("history_dataset_collection_id");
client/galaxy/scripts/mvc/workflow/workflow-manager.js
+9 -6
View File
@@ -9,16 +9,19 @@ const DEFAULT_INVOCATION_REPORT = `
# Workflow Execution Report
## Workflow Inputs
::: invocation_inputs
:::
\`\`\`galaxy
invocation_inputs()
\`\`\`
## Workflow Outputs
::: invocation_outputs
:::
\`\`\`galaxy
invocation_outputs()
\`\`\`
## Workflow
::: workflow_display
:::
\`\`\`galaxy
workflow_display()
\`\`\`
`;
class Workflow {
lib/galaxy/managers/markdown_util.py
+93 -68
View File
@@ -37,8 +37,12 @@ INVOCATION_SECTIONS = [
"invocation_inputs",
"invocation_outputs",
]
GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = "(%s)" % "|".join(GALAXY_FLAVORED_MARKDOWN_CONTAINERS)
INVOCATION_SECTION_MARKDOWN_CONTAINER_REGEX = "(%s)" % "|".join(INVOCATION_SECTIONS)
ALL_CONTAINER_TYPES = GALAXY_FLAVORED_MARKDOWN_CONTAINERS + INVOCATION_SECTIONS
GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = "(%s)" % "|".join(ALL_CONTAINER_TYPES)
FUNCTION_ARG = r'\s*\w+\s*=\s*\w+\s*'
FUNCTION_CALL_LINE_TEMPLATE = r'\s*%s\s*\((?:' + FUNCTION_ARG + r')?\)\s*'
GALAXY_MARKDOWN_FUNCTION_CALL_LINE = re.compile(FUNCTION_CALL_LINE_TEMPLATE % GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX)
BLOCK_FENCE_START = re.compile(r'```.*')
BLOCK_FENCE_END = re.compile(r'```[\s]*')
@@ -49,14 +53,12 @@ INPUT_LABEL_PATTERN = re.compile(r'input=([\w_\-]+)')
STEP_LABEL_PATTERN = re.compile(r'step=([\w_\-]+)')
ID_PATTERN = re.compile(r'(workflow_id|history_dataset_id|history_dataset_collection_id|job_id)=([\d]+)')
GALAXY_FLAVORED_MARKDOWN_CONTAINER_LINE_PATTERN = re.compile(
r"```\s*\{galaxy_%s.*\}\s*" % GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX
)
FENCED_MARKDOWN_CONTAINER_LINE_PATTERN = re.compile(
r"```\s*\{.*"
r"```\s*galaxy\s*"
)
INVOCATION_SECTION_MARKDOWN_CONTAINER_LINE_PATTERN = re.compile(
r"```\s*\{galaxy_%s.*\}\s*" % INVOCATION_SECTION_MARKDOWN_CONTAINER_REGEX
r"```\s*galaxy\s*"
)
GALAXY_FENCED_BLOCK = re.compile(r'^```\s*galaxy\s*(.*?)^```', re.MULTILINE ^ re.DOTALL)
VALID_CONTAINER_START_PATTERN = re.compile(r"^```\s+[\w]+.*$")
VALID_CONTAINER_END_PATTERN = re.compile(r"^```\s*$")
WHITE_SPACE_ONLY_PATTERN = re.compile(r"^[\s]+$")
@@ -75,7 +77,6 @@ def ready_galaxy_markdown_for_export(trans, internal_galaxy_markdown):
extra_rendering_data = {}
def _remap(container, line):
remap_lines = []
id_match = re.search(ID_PATTERN, line)
object_id = None
encoded_id = None
@@ -83,44 +84,37 @@ def ready_galaxy_markdown_for_export(trans, internal_galaxy_markdown):
object_id = int(id_match.group(2))
encoded_id = trans.security.encode_id(object_id)
line = line.replace(id_match.group(), "%s=%s" % (id_match.group(1), encoded_id))
remap_lines.append(line)
def remap_with_fenced_output(output, default):
if output:
for line in output.splitlines(True):
if not line.endswith("\n"):
line += "\n"
remap_lines.append(line)
else:
# TODO: handle this better... shouldn't be part of code block
# ideally.
remap_lines.append("%s\n" % default)
def ensure_rendering_data_for(object_type, encoded_id):
if object_type not in extra_rendering_data:
extra_rendering_data[object_type] = {}
object_type_data = extra_rendering_data[object_type]
if encoded_id not in object_type_data:
object_type_data[encoded_id] = {}
return object_type_data[encoded_id]
def extend_history_dataset_rendering_data(key, val, default_val):
ensure_rendering_data_for("history_datasets", encoded_id)[key] = val or default_val
if container == "history_dataset_display":
assert object_id is not None
hda = hdas_manager.get_accessible(object_id, trans.user)
if "history_datasets" not in extra_rendering_data:
extra_rendering_data["history_datasets"] = {}
extra_rendering_data["history_datasets"][encoded_id] = {
"name": hda.name,
}
extend_history_dataset_rendering_data("name", hda.name, "")
elif container == "history_dataset_peek":
assert object_id is not None
hda = hdas_manager.get_accessible(object_id, trans.user)
peek = hda.peek
remap_with_fenced_output(peek, "*No Dataset Peek Available*")
extend_history_dataset_rendering_data("peek", peek, "*No Dataset Peek Available*")
elif container == "history_dataset_info":
hda = hdas_manager.get_accessible(object_id, trans.user)
info = hda.info
remap_with_fenced_output(info, "*No Dataset Info Available*")
extend_history_dataset_rendering_data("info", info, "*No Dataset Peek Available*")
elif container == "workflow_display":
# TODO: should be workflow id...
stored_workflow = workflows_manager.get_stored_accessible_workflow(trans, encoded_id)
if "workflows" not in extra_rendering_data:
extra_rendering_data["workflows"] = {}
extra_rendering_data["workflows"][encoded_id] = {
"name": stored_workflow.name,
}
ensure_rendering_data_for("workflows", encoded_id)["name"] = stored_workflow.name
elif container == "history_dataset_collection_display":
collection_manager = DatasetCollectionManager(trans.app)
hdca = collection_manager.get_dataset_collection_instance(trans, "history", encoded_id)
@@ -130,18 +124,18 @@ def ready_galaxy_markdown_for_export(trans, internal_galaxy_markdown):
)
if "history_dataset_collections" not in extra_rendering_data:
extra_rendering_data["history_dataset_collections"] = {}
extra_rendering_data["history_dataset_collections"][encoded_id] = hdca_view
ensure_rendering_data_for("history_dataset_collections", encoded_id).update(hdca_view)
elif container == "tool_stdout":
job_manager = JobManager(trans.app)
job = job_manager.get_accessible_job(trans, object_id)
remap_with_fenced_output(job.tool_stdout, "*No Standard Output Available*")
ensure_rendering_data_for("jobs", encoded_id)["tool_stdout"] = job.tool_stdout or "*No Standard Output Available*"
elif container == "tool_stderr":
job_manager = JobManager(trans.app)
job = job_manager.get_accessible_job(trans, object_id)
remap_with_fenced_output(job.tool_stderr, "*No Standard Error Available*")
return remap_lines
ensure_rendering_data_for("jobs", encoded_id)["tool_stderr"] = job.tool_stderr or "*No Standard Error Available*"
return (line, False)
export_markdown = _remap_galaxy_markdown_containers(_remap, internal_galaxy_markdown)
export_markdown = _remap_galaxy_markdown_calls(_remap, internal_galaxy_markdown)
return export_markdown, extra_rendering_data
@@ -171,12 +165,14 @@ def resolve_invocation_markdown(trans, invocation, workflow_markdown):
if output_assoc.history_content_type == "dataset":
section_markdown += """#### Output Dataset: %s
```{galaxy_history_dataset_display output=%s}
```galaxy
history_dataset_display(output=%s)
```
""" % (output_assoc.workflow_output.label, output_assoc.workflow_output.label)
else:
section_markdown += """#### Output Dataset Collection: %s
```{galaxy_history_dataset_collection_display output=%s}
```galaxy
history_dataset_collection_display(output=%s)
```
""" % (output_assoc.workflow_output.label)
elif container == "invocation_inputs":
@@ -186,21 +182,25 @@ def resolve_invocation_markdown(trans, invocation, workflow_markdown):
if input_assoc.history_content_type == "dataset":
section_markdown += """#### Input Dataset: %s
```{galaxy_history_dataset_display input=%s}
```galaxy
history_dataset_display(input=%s)
```
""" % (input_assoc.workflow_step.label, input_assoc.workflow_step.label)
else:
section_markdown += """#### Input Dataset Collection: %s
```{galaxy_history_dataset_collection_display input=%s}
```galaxy
history_dataset_collection_display(input=%s)
```
""" % (input_assoc.workflow_step.label, input_assoc.workflow_step.label)
return section_markdown
else:
return line, False
return section_markdown, True
def _remap(container, line):
if container == "workflow_display":
# TODO: this really should be workflow id not stored workflow id but the API
# it consumes wants the stored id.
return "```{galaxy_workflow_display workflow_id=%s}\n" % invocation.workflow.stored_workflow.id
return ("workflow_display(workflow_id=%s)\n" % invocation.workflow.stored_workflow.id, False)
ref_object_type = None
output_match = re.search(OUTPUT_LABEL_PATTERN, line)
input_match = re.search(INPUT_LABEL_PATTERN, line)
@@ -228,16 +228,14 @@ def resolve_invocation_markdown(trans, invocation, workflow_markdown):
else:
ref_object_type = "history_dataset_collection"
line = line.replace(target_match.group(), "%s_id=%s" % (ref_object_type, ref_object.id))
return line
return (line, False)
log.debug("workflow markdown is \n%s" % workflow_markdown)
workflow_markdown = _remap_galaxy_markdown_containers(
workflow_markdown = _remap_galaxy_markdown_calls(
_section_remap,
workflow_markdown,
container_pattern=INVOCATION_SECTION_MARKDOWN_CONTAINER_LINE_PATTERN,
replace_whole_container=True
)
galaxy_markdown = _remap_galaxy_markdown_containers(_remap, workflow_markdown)
galaxy_markdown = _remap_galaxy_markdown_calls(_remap, workflow_markdown)
log.debug("galaxy markdown is \n%s" % galaxy_markdown)
return galaxy_markdown
@@ -245,6 +243,7 @@ def resolve_invocation_markdown(trans, invocation, workflow_markdown):
def validate_galaxy_markdown(galaxy_markdown, internal=True):
expecting_container_close_for = None
last_line_no = 0
function_calls = 0
for (line, fenced, open_fence, line_no) in _split_markdown_lines(galaxy_markdown):
last_line_no = line_no
@@ -261,7 +260,7 @@ def validate_galaxy_markdown(galaxy_markdown, internal=True):
continue
elif fenced and expecting_container_close and BLOCK_FENCE_END.match(line):
expecting_container_close_for = None
elif open_fence and FENCED_MARKDOWN_CONTAINER_LINE_PATTERN.match(line):
elif open_fence and GALAXY_FLAVORED_MARKDOWN_CONTAINER_LINE_PATTERN.match(line):
if expecting_container_close:
if not VALID_CONTAINER_END_PATTERN.match(line):
invalid_line("Invalid command close line [{line}] for [{expected_for}]", line=line, expected_for=expecting_container_close_for)
@@ -269,11 +268,16 @@ def validate_galaxy_markdown(galaxy_markdown, internal=True):
expecting_container_close_for = None
continue
if not GALAXY_FLAVORED_MARKDOWN_CONTAINER_LINE_PATTERN.match(line):
invalid_line("Invalid markdown command line [{line}]", line=line)
# TODO: check IDs and attributes and stuff...
expecting_container_close_for = line
continue
elif fenced and line and expecting_container_close_for:
if GALAXY_MARKDOWN_FUNCTION_CALL_LINE.match(line):
function_calls += 1
if function_calls > 1:
invalid_line("Only one Galaxy directive is allowed per fenced Galaxy block (```galaxy)")
continue
else:
invalid_line("Invalid embedded Galaxy markup line [{line}]", line=line)
# Markdown unrelated to Galaxy object containers.
continue
@@ -282,26 +286,47 @@ def validate_galaxy_markdown(galaxy_markdown, internal=True):
raise Exception("Invalid line %d: %s" % (last_line_no, "close of block for [{expected_for}] expected".format(expected_for=expecting_container_close_for)))
def _remap_galaxy_markdown_containers(func, markdown, container_pattern=GALAXY_FLAVORED_MARKDOWN_CONTAINER_LINE_PATTERN, replace_whole_container=False):
remapped_lines = []
replaced_container = False
for (line, fenced, open_fence, _) in _split_markdown_lines(markdown):
if replaced_container:
# Replaced whole container, no need to keep container close.
assert line.startswith("```")
replaced_container = False
continue
container_match = container_pattern.match(line)
if container_match:
remap_line = func(container_match.group(1), line)
if not isinstance(remap_line, list):
remap_line = [remap_line]
remapped_lines.extend(remap_line)
replaced_container = replace_whole_container
def _remap_galaxy_markdown_containers(func, markdown):
new_markdown = markdown
searching_from = 0
while True:
from_markdown = new_markdown[searching_from:]
match = re.search(GALAXY_FENCED_BLOCK, from_markdown)
if match is not None:
(replacement, whole_block) = func(match.group(1))
if whole_block:
start_pos = match.start()
end_pos = match.end()
else:
start_pos = match.start(1)
end_pos = match.end(1)
start_pos = start_pos + searching_from
end_pos = end_pos + searching_from
new_markdown = new_markdown[:start_pos] + replacement + new_markdown[end_pos:]
searching_from = end_pos
else:
remapped_lines.append(line)
rval = "".join(remapped_lines)
return rval
break
return new_markdown
def _remap_galaxy_markdown_calls(func, markdown):
def _remap_container(container):
matching_line = None
for line in container.splitlines():
if GALAXY_MARKDOWN_FUNCTION_CALL_LINE.match(line):
assert matching_line is None
matching_line = line
assert matching_line, "Failed to find func call line in [%s]" % container
match = GALAXY_MARKDOWN_FUNCTION_CALL_LINE.match(line)
return func(match.group(1), matching_line + "\n")
return _remap_galaxy_markdown_containers(_remap_container, markdown)
def _split_markdown_lines(markdown):
lib/galaxy/workflow/reports/generators/markdown.py
+9 -6
View File
@@ -11,16 +11,19 @@ DEFAULT_MARKDOWN = """
# ${title}
## Workflow Inputs
::: invocation_inputs
:::
```galaxy
invocation_inputs()
```
## Workflow Outputs
::: invocation_outputs
:::
```galaxy
invocation_outputs()
```
## Workflow
::: workflow_display
:::
```galaxy
workflow_display()
```
"""
test/api/test_workflows.py
+1 -1
View File
@@ -1284,7 +1284,7 @@ steps:
assert report_json["render_format"] == "markdown"
markdown_content = report_json["markdown"]
assert "## Workflow Outputs" in markdown_content
assert "\n```{galaxy_history_dataset_display history_dataset_id=" in markdown_content
assert "\n```galaxy\nhistory_dataset_display(history_dataset_id=" in markdown_content
assert "## Workflow Inputs" in markdown_content
assert "## About This Report" in markdown_content
test/base/workflow_fixtures.py
+52 -26
View File
@@ -500,19 +500,23 @@ report:
in the default workflow invocation report template.
## Workflow Inputs
```{galaxy_invocation_inputs}
```galaxy
invocation_inputs()
```
## Workflow Outputs
```{galaxy_invocation_outputs}
```galaxy
invocation_outputs()
```
## Workflow Inputs
```{galaxy_invocation_inputs}
```galaxy
invocation_inputs()
```
## Workflow Outputs
```{galaxy_invocation_outputs}
```galaxy
invocation_outputs()
```
The auto-generated sections could be hand-crafted from workflow markdown also,
@@ -530,28 +534,34 @@ report:
Once can reference an output and embed a display of it as follows:
```{galaxy_history_dataset_display output=output_1}
```galaxy
history_dataset_display(output=output_1)
```
```{galaxy_history_dataset_display output=output_1}
```galaxy
history_dataset_display(output=output_1)
```
Inputs can be referenced and displayed the same way:
```{galaxy_history_dataset_display input=input_1}
```galaxy
history_dataset_display(input=input_1)
```
```{galaxy_history_dataset_display input=input_1}
```galaxy
history_dataset_display(input=input_1)
```
---
Images can be embedded directly into the report as follows:
```{galaxy_history_dataset_as_image output=output_image}
```galaxy
history_dataset_as_image(output=output_image)
```
```{galaxy_history_dataset_as_image output=output_image}
```galaxy
history_dataset_as_image(output=output_image)
```
---
@@ -559,30 +569,36 @@ report:
Dataset peek content can be displayed to quickly provided an embedded
summary of an input or output:
```{galaxy_history_dataset_peek output=output_1}
```galaxy
history_dataset_peek(output=output_1)
```
```{galaxy_history_dataset_peek output=output_1}
```galaxy
history_dataset_peek(output=output_1)
```
---
Dataset "info" content can be displayed as well:
```{galaxy_history_dataset_info input=input_1}
```galaxy
history_dataset_info(input=input_1)
```
```{galaxy_history_dataset_info input=input_1}
```galaxy
history_dataset_info(input=input_1)
```
---
Collections can be displayed:
```{galaxy_history_dataset_collection_display input=input_list}
```galaxy
history_dataset_collection_display(input=input_list)
```
```{galaxy_history_dataset_collection_display input=input_list}
```galaxy
history_dataset_collection_display(input=input_list)
```
---
@@ -590,46 +606,56 @@ report:
The whole workflow can be embedded to provide some context and display
annotations and steps.
```{galaxy_workflow_display}
```galaxy
workflow_display()
```
```{galaxy_workflow_display}
```galaxy
workflow_display()
```
---
Job parameters can be summarized:
```{galaxy_job_parameters step=qc_step}
```galaxy
job_parameters(step=qc_step)
```
```{galaxy_job_parameters step=qc_step}
```galaxy
job_parameters(step=qc_step)
```
---
Job metrics can be summarized as well:
```{galaxy_job_metrics step=image_cat}
```galaxy
job_metrics(step=image_cat)
```
```{galaxy_job_metrics step=image_cat}
```galaxy
job_metrics(step=image_cat)
```
---
Tool standard out and error are also available for steps.
```{galaxy_tool_stdout step=qc_step}
```galaxy
tool_stdout(step=qc_step)
```
```{galaxy_tool_stdout step=qc_step}
```galaxy
tool_stdout(step=qc_step)
```
```{galaxy_tool_stderr step=qc_step}
```galaxy
tool_stderr(step=qc_step)
```
```{galaxy_tool_stderr step=qc_step}
```galaxy
tool_stderr(step=qc_step)
```
---
test/unit/test_markdown_validate.py
+26 -12
View File
@@ -32,26 +32,40 @@ printf('hello')
""")
# assert valid container is fine.
assert_markdown_valid("""
```{galaxy_job_metrics job_id=THISFAKEID}
```galaxy
job_metrics(job_id=THISFAKEID)
```
""")
# assert valid container is fine.
# assert valid container is fine at end of document.
assert_markdown_valid("""
```{galaxy_job_metrics job_id=THISFAKEID}
```galaxy
job_metrics(job_id=THISFAKEID)
```""")
# assert valid containers require container close
assert_markdown_invalid("""
```{galaxy_job_metrics job_id=THISFAKEID}
foo
```galaxy
job_metrics(job_id=THISFAKEID)
""", at_line=1)
# assert valid containers require container close, even at end...
assert_markdown_invalid("""
```{galaxy_job_metrics job_id=THISFAKEID""")
# assert valid containers require container close, even at end...
```galaxy
job_metrics(job_id=THISFAKEID)""")
# assert only one command allowed
assert_markdown_invalid("""
```{galaxy_not_a_command}
```""")
```galaxy
job_metrics(job_id=THISFAKEID)
job_metrics(job_id=THISFAKEID2)
```
""")
# assert command paren is closed
assert_markdown_invalid("""
```{not_a_command}
```""")
```galaxy
job_metrics(job_id=THISFAKEID
```
""")
# assert command arg is named.
assert_markdown_invalid("""
```galaxy
job_metrics(THISFAKEID)
```
""")
test/unit/workflows/test_workflow_markdown.py
+17 -11
View File
@@ -1,5 +1,5 @@
from galaxy import model
from galaxy.managers.markdown_util import resolve_invocation_markdown
from galaxy.managers.markdown_util import resolve_invocation_markdown, validate_galaxy_markdown
from .test_workflow_progress import TEST_WORKFLOW_YAML
from .workflow_support import MockTrans, yaml_to_model
@@ -7,63 +7,69 @@ from .workflow_support import MockTrans, yaml_to_model
def test_workflow_section_expansion():
workflow_markdown = """
## Workflow
```{galaxy_workflow_display}
```galaxy
workflow_display()
```
"""
galaxy_markdown = resolved_markdown(workflow_markdown)
assert "## Workflow\n" in galaxy_markdown
assert "```{galaxy_workflow_display workflow_id=342}\n```\n" in galaxy_markdown
assert "```galaxy\nworkflow_display(workflow_id=342)\n```\n" in galaxy_markdown
def test_inputs_section_expansion():
workflow_markdown = """
## Workflow Inputs
```{galaxy_invocation_inputs}
```galaxy
invocation_inputs()
```
"""
galaxy_markdown = resolved_markdown(workflow_markdown)
assert "## Workflow Inputs" in galaxy_markdown
assert "```{galaxy_history_dataset_display history_dataset_id=567}" in galaxy_markdown
assert "```galaxy\nhistory_dataset_display(history_dataset_id=567)\n" in galaxy_markdown
assert len(galaxy_markdown.split("```")) == 3
def test_outputs_section_expansion():
workflow_markdown = """
## Workflow Outputs
```{galaxy_invocation_outputs}
```galaxy
invocation_outputs()
```
"""
galaxy_markdown = resolved_markdown(workflow_markdown)
assert "## Workflow Outputs" in galaxy_markdown
assert "```{galaxy_history_dataset_display history_dataset_id=563}" in galaxy_markdown
assert "```galaxy\nhistory_dataset_display(history_dataset_id=563)" in galaxy_markdown
def test_input_reference_mapping():
workflow_markdown = """
And outputs...
```{galaxy_history_dataset_peek input=input1}
```galaxy
history_dataset_peek(input=input1)
```
"""
galaxy_markdown = resolved_markdown(workflow_markdown)
assert "```{galaxy_history_dataset_peek history_dataset_id=567}\n```" in galaxy_markdown
assert "```galaxy\nhistory_dataset_peek(history_dataset_id=567)\n```" in galaxy_markdown
def test_output_reference_mapping():
workflow_markdown = """
And outputs...
```{galaxy_history_dataset_as_image output=output_label}
```galaxy
history_dataset_as_image(output=output_label)
```
"""
galaxy_markdown = resolved_markdown(workflow_markdown)
assert "```{galaxy_history_dataset_as_image history_dataset_id=563}" in galaxy_markdown
assert "```galaxy\nhistory_dataset_as_image(history_dataset_id=563)\n```" in galaxy_markdown
def resolved_markdown(workflow_markdown):
# Convert workflow markdown to internal Galaxy markdown with object id references
# and with sections expanded.
trans = MockTrans()
validate_galaxy_markdown(workflow_markdown)
galaxy_markdown = resolve_invocation_markdown(trans, example_invocation(trans), workflow_markdown)
return galaxy_markdown