diff options
| -rw-r--r-- | bh20simplewebuploader/main.py | 86 | ||||
| -rw-r--r-- | bh20simplewebuploader/static/main.css | 17 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/footer.html | 5 |
3 files changed, 64 insertions, 44 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 3173d60..62b68d9 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 +50,8 @@ 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) @@ -78,7 +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. @@ -101,9 +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 @@ -131,14 +133,25 @@ 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 + optional = False + is_list = False + + 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): # It may have documentation docstring = field_type.get('doc', None) @@ -161,25 +174,13 @@ def generate_form(schema, options): 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] + 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 @@ -227,15 +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 -if os.path.isfile("bh20sequploader/bh20seq-schema.yml"): - METADATA_SCHEMA = yaml.safe_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.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-schema.yml")) - METADATA_OPTION_DEFINITIONS = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-options.yml")) -# print(METADATA_SCHEMA,file=sys.stderr) -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(): @@ -543,10 +553,10 @@ def status_page(): for s in (("passed", "/download"), ("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("<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) return render_template('status.html', table=Markup(output.getvalue()), menu='STATUS') diff --git a/bh20simplewebuploader/static/main.css b/bh20simplewebuploader/static/main.css index 47fb408..b28ee9c 100644 --- a/bh20simplewebuploader/static/main.css +++ b/bh20simplewebuploader/static/main.css @@ -178,7 +178,7 @@ span.dropt:hover {text-decoration: none; background: #ffffff; z-index: 6; } .about { display: grid; - grid-template-columns: repeat(2, 1fr); + grid-template-columns: 1fr 1fr; grid-auto-flow: row; } @@ -229,7 +229,7 @@ a { #metadata_fill_form { column-count: 4; margin-top: 0.5em; - column-width: 250px; + column-width: 15em; } .record, .record .field-group, .record .field-group .field { @@ -238,6 +238,8 @@ a { -webkit-column-break-inside: avoid; /* Chrome, Safari, Opera */ page-break-inside: avoid; /* Firefox */ break-inside: avoid; + display: block; + width: 90%; } .record { @@ -258,6 +260,10 @@ a { width: max-content; } +.control { + width: 100%; +} + .filter-options { width: 100%; } @@ -304,9 +310,10 @@ footer { } .sponsors img { - width: 80%; - display:block; - margin:auto; + width: auto; + display: block; + margin: auto; + height: 4em; } .loader { diff --git a/bh20simplewebuploader/templates/footer.html b/bh20simplewebuploader/templates/footer.html index 37a6b64..5a1f3c9 100644 --- a/bh20simplewebuploader/templates/footer.html +++ b/bh20simplewebuploader/templates/footer.html @@ -21,12 +21,15 @@ <img src="static/image/covid19biohackathon.png"></a> </div> <div class="sponsorimg"> - <a href="https://www.commonwl.org/"><img src="static/image/CWL.png"></a> + <a href="https://www.curii.com/"><img src="static/image/curii.logo.ai.svg"></a> </div> <div class="sponsorimg"> <a href="https://arvados.org/"><img src="static/image/arvados-logo.png"></a> </div> <div class="sponsorimg"> + <a href="https://www.commonwl.org/"><img src="static/image/CWL.png"></a> + </div> + <div class="sponsorimg"> <a href="https://uthsc.edu/"><img src="static/image/UTHSC-primary-stacked-logo-4c.png"></a> </div> <div class="sponsorimg"> |