aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--bh20sequploader/bh20seq-options.yml17
-rw-r--r--bh20sequploader/bh20seq-schema.yml2
-rw-r--r--bh20simplewebuploader/main.py86
-rw-r--r--bh20simplewebuploader/templates/form.html19
-rw-r--r--setup.py2
5 files changed, 103 insertions, 23 deletions
diff --git a/bh20sequploader/bh20seq-options.yml b/bh20sequploader/bh20seq-options.yml
new file mode 100644
index 0000000..d05be5a
--- /dev/null
+++ b/bh20sequploader/bh20seq-options.yml
@@ -0,0 +1,17 @@
+# Contains suggested human-readable field values and their corresponding IRIs.
+# Keyed on the field names in the types in the schema. Relies on field names
+# being unique or at least using the same options in different containing
+# types.
+
+host_age_unit:
+ Years: http://purl.obolibrary.org/obo/UO_0000036
+ Months: http://purl.obolibrary.org/obo/UO_0000035
+ Weeks: http://purl.obolibrary.org/obo/UO_0000034
+ Days: http://purl.obolibrary.org/obo/UO_0000033
+ Hours: http://purl.obolibrary.org/obo/UO_0000032
+
+host_sex:
+ Male: http://purl.obolibrary.org/obo/NCIT_C20197
+ Female: http://purl.obolibrary.org/obo/NCIT_C27993
+ Intersex: http://purl.obolibrary.org/obo/NCIT_C45908
+ Unknown: http://purl.obolibrary.org/obo/NCIT_C17998
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 7ffc15b..4cd0865 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -30,7 +30,7 @@ $graph:
# jsonldPredicate:
# _id: http://purl.obolibrary.org/obo/NOMEN_0000037
host_sex:
- doc: Sex of the host as define in NCIT, IRI expected (http://purl.obolibrary.org/obo/C20197 (Male), http://purl.obolibrary.org/obo/NCIT_C27993 (Female) or unkown (http://purl.obolibrary.org/obo/NCIT_C17998))
+ doc: Sex of the host as defined in NCIT, IRI expected (http://purl.obolibrary.org/obo/NCIT_C20197 (Male), http://purl.obolibrary.org/obo/NCIT_C27993 (Female), http://purl.obolibrary.org/obo/NCIT_C45908 (Intersex), or http://purl.obolibrary.org/obo/NCIT_C17998 (Unknown))
type: string
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/PATO_0000047
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index f5324a5..8c5c18c 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -7,7 +7,7 @@ import sys
import re
import string
import yaml
-import urllib.request
+import pkg_resources
from flask import Flask, request, redirect, send_file, send_from_directory, render_template
import os.path
@@ -25,7 +25,7 @@ app.config['MAX_CONTENT_LENGTH'] = 50 * 1024 * 1024
@app.errorhandler(413)
def handle_large_file(e):
return (render_template('error.html',
- error_message="One of your files is too large. The maximum file size is 1 megabyte."), 413)
+ error_message="One of your files is too large. The maximum file size is 50 megabytes."), 413)
def type_to_heading(type_name):
@@ -49,12 +49,32 @@ def name_to_label(field_name):
return string.capwords(field_name.replace('_', ' '))
-def generate_form(schema):
+def is_iri(string):
"""
- Linearize the schema and send a bunch of dicts.
+ Return True if the given string looks like an IRI, and False otherwise.
+
+ Used for finding type IRIs in the schema.
+
+ Right now only supports http(s) URLs because that's all we have in our schema.
+ """
+
+ return string.startswith('http')
+
+def generate_form(schema, options):
+ """
+ Linearize the schema into a list of dicts.
+
Each dict either has a 'heading' (in which case we put a heading for a
form section in the template) or an 'id', 'label', 'type', and 'required'
- (in which case we make a form field in the template).
+ (in which case we make a form field in the template). Non-heading dicts
+ with type 'select' will have an 'options' field, with a list of (name,
+ value) tuples, and represent a form dropdown element. Non-heading dicts may
+ have a human-readable 'docstring' field describing them.
+
+ Takes the deserialized metadata schema YAML, and also a deserialized YAML
+ of option values. The option values are keyed on (unscoped) field name in
+ the schema, and each is a dict of human readable option -> corresponding
+ IRI.
"""
# Get the list of form components, one of which is the root
@@ -90,16 +110,35 @@ def generate_form(schema):
for field_name, field_type in by_name.get(type_name, {}).get('fields', {}).items():
# For each field
- ref_url = None
+ 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', {})
- if not isinstance(predicate, str):
- ref_url = predicate.get('_id', None)
+ # 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:
- ref_url = predicate # not sure this is correct
- # Grab out its type field
+ # 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 ?)
@@ -115,14 +154,26 @@ def generate_form(schema):
for item in walk_fields(field_type, parent_keys + [field_name], subtree_optional or optional):
yield item
else:
- # We know how to make a string input
+ # This is a leaf field. We need an input for it.
record = {}
record['id'] = '.'.join(parent_keys + [field_name])
record['label'] = name_to_label(field_name)
record['required'] = not optional and not subtree_optional
- if ref_url:
- record['ref_url'] = ref_url
- if field_type == 'string':
+ if ref_iri:
+ record['ref_iri'] = ref_iri
+ if docstring:
+ record['docstring'] = docstring
+
+ if field_name in options:
+ # The field will be a 'select' type no matter what its real
+ # data type is.
+ record['type'] = 'select' # Not a real HTML input type. It's its own tag.
+ # We have a set of values to present
+ record['options'] = []
+ for name, value in options[field_name].items():
+ # Make a tuple for each one
+ record['options'].append((name, value))
+ elif field_type == 'string':
record['type'] = 'text' # HTML input type
elif field_type == 'int':
record['type'] = 'number'
@@ -133,9 +184,10 @@ def generate_form(schema):
return list(walk_fields(root_name))
-# At startup, we need to load the current metadata schema so we can make a form for it
-METADATA_SCHEMA = yaml.safe_load(urllib.request.urlopen('https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml'))
-FORM_ITEMS = generate_form(METADATA_SCHEMA)
+# 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)
@app.route('/')
def send_form():
diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html
index df66e8c..6993cf5 100644
--- a/bh20simplewebuploader/templates/form.html
+++ b/bh20simplewebuploader/templates/form.html
@@ -211,7 +211,6 @@
<div id="metadata_fill_form_spot">
<div id="metadata_fill_form">
- {{ record }}
{% for record in fields %}
{% if 'heading' in record %}
@@ -221,15 +220,27 @@
<div class="record">
<h4>{{ record['heading'] }}</h4>
{% else %}
- <label for="{{ record['id'] }}">
+ <label for="{{ record['id'] }}" title="{{ record.get('docstring', '') }}">
{{ record['label'] }}
{{ "*" if record['required'] else "" }}
- {% if 'ref_url' in record %}
- <a href="{{ record['ref_url'] }}" title="More Info" target="_blank">?</a>
+ {% if 'docstring' in record %}
+ <a href='javascript:alert({{ record['docstring'] | tojson }})'>❓</a>
+ {% endif %}
+ {% if 'ref_iri' in record %}
+ <a href="{{ record['ref_iri'] }}" target="_blank" title="Ontology Link">🔗</a>
{% endif %}
</label>
+ {% if record['type'] == 'select' %}
+ <select id="{{ record['id'] }}" name="{{ record['id'] }}" {{ "required" if record['required'] else "" }}>
+ <option value="" selected>Choose one...</option>
+ {% for option in record['options'] %}
+ <option value="{{ option[1] }}">{{ option[0] }}</option>
+ {% endfor %}
+ </select>
+ {% else %}
<input type="{{ record['type'] }}" id="{{ record['id'] }}" name="{{ record['id'] }}" {{ "required" if record['required'] else "" }}>
{% endif %}
+ {% endif %}
{% if loop.index == loop.length %}
</div>
{% endif %}
diff --git a/setup.py b/setup.py
index 18e858e..0e91274 100644
--- a/setup.py
+++ b/setup.py
@@ -31,7 +31,7 @@ setup(
author_email="peter.amstutz@curii.com",
license="Apache 2.0",
packages=["bh20sequploader", "bh20seqanalyzer", "bh20simplewebuploader"],
- package_data={"bh20sequploader": ["bh20seq-schema.yml", "validation/formats"],
+ package_data={"bh20sequploader": ["bh20seq-schema.yml", "bh20seq-options.yml", "validation/formats"],
},
install_requires=install_requires,
extras_require={