From d49f6b5e11a41a51cb257bbafdcba410544f8486 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Thu, 16 Jul 2020 16:27:32 -0400 Subject: Add "validated" and "running workflows" tables to status Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- bh20simplewebuploader/main.py | 112 +++++++++++++++++++------ bh20simplewebuploader/templates/status.html | 3 +- bh20simplewebuploader/templates/validated.html | 17 ++++ 3 files changed, 107 insertions(+), 25 deletions(-) create mode 100644 bh20simplewebuploader/templates/validated.html (limited to 'bh20simplewebuploader') 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): """) +def workflows_table(output, items): + output.write( +""" + + + + + + + +""") + for r in items: + output.write("") + try: + sid = r["mounts"]["/var/lib/cwl/cwl.input.json"]["content"]["sample_id"] + output.write("" % Markup.escape(r["name"])) + output.write("" % Markup.escape(sid)) + output.write("" % Markup.escape(r["created_at"])) + output.write("" % (r["uuid"], r["uuid"])) + except: + pass + output.write("") + output.write( +""" +
NameSample idStartedContainer request
%s%s%s%s
+""") + +def validated_table(output, items): + output.write( +""" + + + + + +""") + for r in items: + try: + output.write("") + output.write("" % (r["uuid"], r["uuid"])) + output.write("" % Markup.escape(r["properties"].get("sequence_label"))) + output.write("") + except: + pass + output.write( +""" +
CollectionSequence label
%s%s
+""") @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("

%s sequences QC %s

" % (s[1], status.get(s[0], 0), s[0])) + output.write("

%s analysis workflows running

" % ('#workflows', len(workflows))) + output.write("

Pending

") pending_table(output, out) output.write("

Rejected

") rejected_table(output, out) + output.write("

Running Workflows

") + 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 @@

Sequence upload processing status

-
+
+ {{ table }}
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 @@ + + + {% include 'header.html' %} + + {% include 'banner.html' %} + {% include 'menu.html' %} + +

Validated sequences

+ +
+ {{ table }} +
+ +{% include 'footer.html' %} + + + -- cgit v1.2.3