diff options
Diffstat (limited to 'bh20simplewebuploader/main.py')
| -rw-r--r-- | bh20simplewebuploader/main.py | 242 |
1 files changed, 164 insertions, 78 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 77e345b..206f884 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -8,7 +8,7 @@ import os import sys import re import string -import yaml +import ruamel.yaml as yaml import pkg_resources from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify import os.path @@ -16,6 +16,9 @@ import requests import io import arvados from markupsafe import Markup +from schema_salad.sourceline import add_lc_filename +from schema_salad.schema import shortname +from typing import MutableSequence, MutableMapping ARVADOS_API = 'lugli.arvadosapi.com' ANONYMOUS_TOKEN = '5o42qdxpxp5cj15jqjf7vnxx5xduhm4ret703suuoa3ivfglfh' @@ -47,6 +50,9 @@ def type_to_heading(type_name): Turn a type name like "sampleSchema" from the metadata schema into a human-readable heading. """ + type_name = shortname(type_name) + + print(type_name,file=sys.stderr) # Remove camel case decamel = re.sub('([A-Z])', r' \1', type_name) # Split @@ -77,7 +83,7 @@ def is_iri(string): return string.startswith('http') -def generate_form(schema, options): +def generate_form(components, options): """ Linearize the schema into a list of dicts. @@ -100,9 +106,6 @@ def generate_form(schema, options): IRI. """ - # Get the list of form components, one of which is the root - components = schema.get('$graph', []) - # Find the root root_name = None # And also index components by type name @@ -130,55 +133,54 @@ def generate_form(schema, options): # First make a heading, if we aren't the very root of the form yield {'heading': type_to_heading(type_name)} - for field_name, field_type in by_name.get(type_name, {}).get('fields', {}).items(): + for field in by_name.get(type_name, {}).get('fields', []): + field_name = shortname(field["name"]) + field_type = field["type"] # For each field ref_iri = None docstring = None - if not isinstance(field_type, str): - # If the type isn't a string - - # 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 - - # Now overwrite the field type with the actual type string - field_type = field_type.get('type', '') - - # Decide if the field is optional (type ends in ?) optional = False - if field_type.endswith('?'): - # It's optional - optional = True - # Drop the ? - field_type = field_type[:-1] - - # Decide if the field is a list (type ends in []) is_list = False - if field_type.endswith('[]'): - # It's a list - is_list = True - # Reduce to the normal type - field_type = field_type[:-2] + + # 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 + field_type = field_type[1] + else: + raise Exception("Can't handle it") + + if isinstance(field_type, MutableMapping): + if field_type["type"] == "array": + # Now replace the field type with the actual type string + is_list = True + field_type = field_type.get('items', '') + else: + field_type = field_type.get('type', '') + pass if field_type in by_name: # This is a subrecord. We need to recurse @@ -226,10 +228,24 @@ def generate_form(schema, options): return list(walk_fields(root_name)) -# At startup, we need to load the metadata schema from the uploader module, so we can make a form for it -METADATA_SCHEMA = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-schema.yml")) -METADATA_OPTION_DEFINITIONS = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-options.yml")) -FORM_ITEMS = generate_form(METADATA_SCHEMA, METADATA_OPTION_DEFINITIONS) +import schema_salad.schema +def load_schema_generate_form(): + # At startup, we need to load the metadata schema from the uploader module, so we can make a form for it + if os.path.isfile("bh20sequploader/bh20seq-schema.yml"): + METADATA_SCHEMA = yaml.round_trip_load(open("bh20sequploader/bh20seq-schema.yml","r").read()) + METADATA_OPTION_DEFINITIONS = yaml.safe_load(open("bh20sequploader/bh20seq-options.yml","r").read()) + else: + METADATA_SCHEMA = yaml.round_trip_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-schema.yml")) + METADATA_OPTION_DEFINITIONS = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-options.yml")) + + METADATA_SCHEMA["name"] = "bh20seq-schema.yml" + add_lc_filename(METADATA_SCHEMA, "bh20seq-schema.yml") + metaschema_names, _metaschema_doc, metaschema_loader = schema_salad.schema.get_metaschema() + schema_doc, schema_metadata = metaschema_loader.resolve_ref(METADATA_SCHEMA, "") + + return generate_form(schema_doc, METADATA_OPTION_DEFINITIONS) + +FORM_ITEMS = load_schema_generate_form() @app.route('/') def send_home(): @@ -237,7 +253,7 @@ def send_home(): Send the front page. """ - return render_template('home.html', menu='HOME') + return render_template('home.html', menu='HOME', load_map=True) @app.route('/upload') @@ -429,17 +445,21 @@ def receive_files(): if result.returncode != 0: # It didn't work. Complain. - error_message="Uploader returned value {} and said:".format(result.returncode) + str(result.stderr.decode('utf-8')) + error_message="Uploader returned value {} and said:\n".format(result.returncode) + str(result.stderr.decode('utf-8')) print(error_message, file=sys.stderr) return (render_template('error.html', error_message=error_message), 403) else: # It worked. Say so. - return render_template('success.html', log=result.stdout.decode('utf-8', errors='replace')) + return render_template('success.html', log=result.stderr.decode('utf-8', errors='replace')) finally: shutil.rmtree(dest_dir) -def get_html_body(fn): - buf = "" + +def edit_button(url,text="Edit text!"): + return '<p class="editbutton"><a href="'+url+'">'+text+'<img src="static/image/edit.png"></a></p>' + +def get_html_body(fn,source="https://github.com/arvados/bh20-seq-resource/tree/master/doc"): + buf = edit_button(source) in_body = False begin_body = re.compile(r"<body>",re.IGNORECASE) end_body = re.compile(r"(</body>|.*=\"postamble\")",re.IGNORECASE) @@ -451,11 +471,12 @@ def get_html_body(fn): buf += line elif begin_body.match(line): in_body = True + buf += edit_button(source) return buf @app.route('/download') def download_page(): - buf = get_html_body('doc/web/download.html') + buf = get_html_body('doc/web/download.html','https://github.com/arvados/bh20-seq-resource/blob/master/doc/web/download.org') return render_template('resource.html',menu='DOWNLOAD',embed=buf) def pending_table(output, items): @@ -468,10 +489,13 @@ def pending_table(output, items): for r in items: if r["status"] != "pending": continue - 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["sequence_label"])) - output.write("</tr>") + 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.get("sequence_label"))) + output.write("</tr>") + except: + pass output.write( """ </table> @@ -486,18 +510,69 @@ def rejected_table(output, items): <th>Errors</th></tr> """) for r in items: - if r["status"] != "rejected": - continue + try: + if r["status"] != "rejected": + continue + 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.get("sequence_label"))) + output.write("<td><pre>%s</pre></td>" % Markup.escape("\n".join(r.get("errors", [])))) + output.write("</tr>") + except: + pass + output.write( +""" +</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>") - 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["sequence_label"])) - output.write("<td><pre>%s</pre></td>" % Markup.escape("\n".join(r.get("errors", [])))) + 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(): @@ -518,46 +593,57 @@ 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("<a id='pending'><h1>Pending</h1>") + 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>") + 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') + return render_template('demo.html',menu='DEMO',load_map=True) @app.route('/blog',methods=['GET']) def blog_page(): blog_content = request.args.get('id') # e.g. using-covid-19-pubseq-part3 buf = None; if blog_content: - buf = get_html_body('doc/blog/'+blog_content+'.html') + buf = get_html_body('doc/blog/'+blog_content+'.html',"https://github.com/arvados/bh20-seq-resource/blob/master/doc/blog/"+blog_content+".org") return render_template('blog.html',menu='BLOG',embed=buf,blog=blog_content) @app.route('/about') def about_page(): - buf = get_html_body('doc/web/about.html') + buf = get_html_body('doc/web/about.html','https://github.com/arvados/bh20-seq-resource/blob/master/doc/web/about.org') return render_template('about.html',menu='ABOUT',embed=buf) -## -@app.route('/map') -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 |