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-rw-r--r--bh20seqanalyzer/main.py12
-rw-r--r--bh20simplewebuploader/main.py112
-rw-r--r--bh20simplewebuploader/templates/status.html3
-rw-r--r--bh20simplewebuploader/templates/validated.html17
4 files changed, 114 insertions, 30 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index f18a93a..b3a439d 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -240,24 +240,26 @@ class SeqAnalyzer:
def move_fastq_to_fasta_results(self):
projects = self.api.groups().list(filters=[['owner_uuid', '=', self.fastq_project],
["properties.moved_output", "!=", True]],
- order="created_at desc",).execute()
+ order="created_at asc",).execute()
for p in projects["items"]:
wf = self.get_workflow_output_from_project(p["uuid"])
if not wf:
continue
logging.info("Moving completed fastq2fasta result %s back to uploader project", wf["output_uuid"])
- self.api.collections().update(uuid=wf["output_uuid"],
- body={"owner_uuid": self.uploader_project}).execute()
col = arvados.collection.Collection(wf["output_uuid"], api_client=self.api, keep_client=self.keepclient)
with col.open("metadata.yaml") as md:
metadata_content = ruamel.yaml.round_trip_load(md)
+ colprop = col.get_properties()
+ colprop["sequence_label"] = metadata_content["sample"]["sample_id"]
+ self.api.collections().update(uuid=wf["output_uuid"],
+ body={"owner_uuid": self.uploader_project,
+ "properties": colprop}).execute()
+
p["properties"]["moved_output"] = True
- p["properties"]["sequence_label"] = metadata_content["sample"]["sample_id"]
self.api.groups().update(uuid=p["uuid"], body={"properties": p["properties"]}).execute()
- break
def upload_schema(self):
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index c814f30..7dd07fe 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -144,6 +144,28 @@ def generate_form(components, options):
optional = False
is_list = False
+ # It may have documentation
+ docstring = field.get('doc', None)
+
+ # See if it has a more info/what goes here URL
+ predicate = field.get('jsonldPredicate', {})
+ # Predicate may be a URL, a dict with a URL in _id, maybe a
+ # dict with a URL in _type, or a dict with _id and _type but no
+ # URLs anywhere. Some of these may not technically be allowed
+ # by the format, but if they occur, we might as well try to
+ # handle them.
+ if isinstance(predicate, str):
+ if is_iri(predicate):
+ ref_iri = predicate
+ else:
+ # Assume it's a dict. Look at the fields we know about.
+ for field in ['_id', 'type']:
+ field_value = predicate.get(field, None)
+ if isinstance(field_value, str) and is_iri(field_value) and ref_iri is None:
+ # Take the first URL-looking thing we find
+ ref_iri = field_value
+ break
+
if isinstance(field_type, MutableSequence):
if field_type[0] == "null" and len(field_type) == 2:
optional = True
@@ -152,28 +174,6 @@ def generate_form(components, options):
raise Exception("Can't handle it")
if isinstance(field_type, MutableMapping):
- # It may have documentation
- docstring = field_type.get('doc', None)
-
- # See if it has a more info/what goes here URL
- predicate = field_type.get('jsonldPredicate', {})
- # Predicate may be a URL, a dict with a URL in _id, maybe a
- # dict with a URL in _type, or a dict with _id and _type but no
- # URLs anywhere. Some of these may not technically be allowed
- # by the format, but if they occur, we might as well try to
- # handle them.
- if isinstance(predicate, str):
- if is_iri(predicate):
- ref_iri = predicate
- else:
- # Assume it's a dict. Look at the fields we know about.
- for field in ['_id', 'type']:
- field_value = predicate.get(field, None)
- if isinstance(field_value, str) and is_iri(field_value) and ref_iri is None:
- # Take the first URL-looking thing we find
- ref_iri = field_value
- break
-
if field_type["type"] == "array":
# Now replace the field type with the actual type string
is_list = True
@@ -525,6 +525,54 @@ def rejected_table(output, items):
</table>
""")
+def workflows_table(output, items):
+ output.write(
+"""
+<table>
+<tr>
+<th>Name</th>
+<th>Sample id</th>
+<th>Started</th>
+<th>Container request</th>
+</tr>
+""")
+ for r in items:
+ output.write("<tr>")
+ try:
+ sid = r["mounts"]["/var/lib/cwl/cwl.input.json"]["content"]["sample_id"]
+ output.write("<td>%s</td>" % Markup.escape(r["name"]))
+ output.write("<td>%s</td>" % Markup.escape(sid))
+ output.write("<td>%s</td>" % Markup.escape(r["created_at"]))
+ output.write("<td><a href='https://workbench.lugli.arvadosapi.com/container_requests/%s'>%s</a></td>" % (r["uuid"], r["uuid"]))
+ except:
+ pass
+ output.write("</tr>")
+ output.write(
+"""
+</table>
+""")
+
+def validated_table(output, items):
+ output.write(
+"""
+<table>
+<tr>
+<th>Collection</th>
+<th>Sequence label</th>
+</tr>
+""")
+ for r in items:
+ try:
+ output.write("<tr>")
+ output.write("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"]))
+ output.write("<td>%s</td>" % Markup.escape(r["properties"].get("sequence_label")))
+ output.write("</tr>")
+ except:
+ pass
+ output.write(
+"""
+</table>
+""")
@app.route('/status')
def status_page():
@@ -545,22 +593,39 @@ def status_page():
prop["uuid"] = p["uuid"]
status[prop["status"]] = status.get(prop["status"], 0) + 1
+ workflows = arvados.util.list_all(api.container_requests().list,
+ filters=[["name", "in", ["fastq2fasta.cwl"]], ["state", "=", "Committed"]],
+ order="created_at asc")
+
output = io.StringIO()
validated = api.collections().list(filters=[["owner_uuid", "=", VALIDATED_PROJECT]], limit=1).execute()
status["passed"] = validated["items_available"]
- for s in (("passed", "/download"), ("pending", "#pending"), ("rejected", "#rejected")):
+ for s in (("passed", "/validated"), ("pending", "#pending"), ("rejected", "#rejected")):
output.write("<p><a href='%s'>%s sequences QC %s</a></p>" % (s[1], status.get(s[0], 0), s[0]))
+ output.write("<p><a href='%s'>%s analysis workflows running</a></p>" % ('#workflows', len(workflows)))
+
output.write("<a id='pending'><h1>Pending</h1></a>")
pending_table(output, out)
output.write("<a id='rejected'><h1>Rejected</h1></a>")
rejected_table(output, out)
+ output.write("<a id='workflows'><h1>Running Workflows</h1></a>")
+ workflows_table(output, workflows)
+
return render_template('status.html', table=Markup(output.getvalue()), menu='STATUS')
+@app.route('/validated')
+def validated_page():
+ api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN, insecure=True)
+ output = io.StringIO()
+ validated = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", VALIDATED_PROJECT]])
+ validated_table(output, validated)
+ return render_template('validated.html', table=Markup(output.getvalue()), menu='STATUS')
+
@app.route('/demo')
def demo_page():
return render_template('demo.html',menu='DEMO')
@@ -585,7 +650,6 @@ def map_page():
return render_template('map.html',menu='DEMO')
-
## Dynamic API functions starting here
## This is quick and dirty for now, just to get something out and demonstrate the queries
## Feel free to rename the functions/endpoints, feel free to process result so we get nicer JSON
diff --git a/bh20simplewebuploader/templates/status.html b/bh20simplewebuploader/templates/status.html
index a1cf28f..e89437e 100644
--- a/bh20simplewebuploader/templates/status.html
+++ b/bh20simplewebuploader/templates/status.html
@@ -7,7 +7,8 @@
<h1>Sequence upload processing status</h1>
- <div class="status">
+ <div class="status">
+
{{ table }}
</div>
diff --git a/bh20simplewebuploader/templates/validated.html b/bh20simplewebuploader/templates/validated.html
new file mode 100644
index 0000000..cee94bd
--- /dev/null
+++ b/bh20simplewebuploader/templates/validated.html
@@ -0,0 +1,17 @@
+<!DOCTYPE html>
+<html>
+ {% include 'header.html' %}
+ <body>
+ {% include 'banner.html' %}
+ {% include 'menu.html' %}
+
+ <h1>Validated sequences</h1>
+
+ <div class="status">
+ {{ table }}
+ </div>
+
+{% include 'footer.html' %}
+
+ </body>
+</html>