diff options
| -rw-r--r-- | bh20seqanalyzer/main.py | 12 | ||||
| -rw-r--r-- | bh20simplewebuploader/main.py | 112 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/status.html | 3 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/validated.html | 17 |
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> |