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-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--scripts/from_genbank_to_fasta_and_yaml.py12
-rw-r--r--scripts/sequences.acc396
-rw-r--r--setup.py2
7 files changed, 336 insertions, 198 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/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 0cc1a57..6a55b5e 100644
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -7,7 +7,7 @@ import os
path_ncbi_virus_accession = 'sequences.acc'
-date = '20200414'
+date = '20200415'
path_seq_fasta = 'seq_from_nuccore.{}.fasta'.format(date)
path_metadata_xml = 'metadata_from_nuccore.{}.xml'.format(date)
@@ -19,9 +19,15 @@ for term in term_list:
tmp_list = Entrez.read(
Entrez.esearch(db='nuccore', term=term, idtype='acc', retmax='10000')
)['IdList']
- print(term, len(tmp_list))
-
+
+ # Remove mRNAs, ncRNAs, Proteins, and predicted models (more information here: https://en.wikipedia.org/wiki/RefSeq)
+ tmp_list = [x for x in tmp_list if x[:2] not in ['NM', 'NR', 'NP', 'XM', 'XR', 'XP', 'WP']]
+
# Remove the version in the id
+ tmp_list = [x.split('.')[0] for x in tmp_list]
+
+ print(term, len(tmp_list))
+
id_set.update([x.split('.')[0] for x in tmp_list])
print(term_list, len(id_set))
diff --git a/scripts/sequences.acc b/scripts/sequences.acc
index 62bde2c..a420fb4 100644
--- a/scripts/sequences.acc
+++ b/scripts/sequences.acc
@@ -1,25 +1,159 @@
-MT325599
-MT325601
-MT325602
-MT325607
-MT325608
-MT325609
-MT325610
-MT325612
-MT325616
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-MT325600
-MT325606
-MT325611
-MT325613
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+NC_045512
+MT334522
+MT334523
+MT334524
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+MT334526
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+MT334529
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+MT334559
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+MT324684
+MT325573
+MT325574
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+MT325577
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+MT325580
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+MT325595
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+MT327745
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+MT325572
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+MT326095
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+MT326131
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+MT326164
+MT326166
+MT326167
+MT325570
+MT325579
+MT325581
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+MT325586
+MT325594
+MT325598
+MT325626
+MT325628
+MT325633
+MT325634
+MT326030
+MT326038
+MT326058
MT325565
MT325566
MT326147
@@ -56,7 +190,6 @@ MT326121
MT326119
MT326109
MT326100
-MT325568
MT324679
MT325561
MT325571
@@ -95,31 +228,11 @@ MT326177
MT326184
MT326185
MT326187
-MT325572
-MT325575
-MT325583
-MT325584
-MT325604
-MT325631
-MT325632
-MT325635
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-MT326095
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-MT326113
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-MT326115
-MT326122
-MT326131
-MT326132
-MT326133
-MT325563
-MT326164
-MT326166
-MT326167
+MT324681
+MT324682
+MT324683
+MT328032
+MT328035
MT325569
MT326097
MT326106
@@ -177,146 +290,83 @@ MT326101
MT326099
MT326098
MT326094
-MT326093
-MT326092
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-MT326030
-MT326038
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-MT324681
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+MT325599
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+MT325602
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+MT325625
+MT322394
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MT039874
MT077125
-MT322394
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MT322397
-MT322398
MT322399
+MT322403
+MT322406
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+MT322412
+MT322413
+MT322414
+MT322416
+MT322398
MT322400
MT322401
-MT322403
+MT322402
MT322404
MT322405
-MT322406
MT322408
MT322409
MT322410
MT322411
-MT322412
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MT322415
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MT322417
MT322418
MT322419
-MT322420
MT322421
MT322422
MT322423
-MT322424
-MT322396
-MT322402
-MT322395
-MT322407
-MT320538
MT320891
+MT320538
MT308692
MT308693
+MT308695
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MT308698
MT308699
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MT308703
MT308704
MT308694
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MT293547
MT304477
-MT304483
-MT300186
MT304478
MT304479
-MT304480
MT304481
MT304482
MT304484
@@ -324,9 +374,12 @@ MT304485
MT304486
MT304487
MT304488
+MT304491
+MT304480
+MT304483
MT304489
MT304490
-MT304491
+MT300186
MT291831
MT291836
MT291834
@@ -366,7 +419,6 @@ MT293168
MT293175
MT293190
MT293191
-MT273658
MT293159
MT292582
MT293162
@@ -376,7 +428,6 @@ MT293165
MT293156
MT293157
MT293158
-MT281577
MT293171
MT293174
MT293176
@@ -426,6 +477,8 @@ MT293223
MT291826
MT291832
MT291833
+MT273658
+MT281577
MT281530
MT276331
MT276325
@@ -645,8 +698,6 @@ MT253700
MT253705
MT253709
MT253708
-MT233526
-MT246667
MT246451
MT246453
MT246454
@@ -689,6 +740,8 @@ MT246472
MT246473
MT246483
MT246484
+MT233526
+MT246667
MT240479
MT232869
MT232870
@@ -774,8 +827,8 @@ MT127113
MT127114
MT127115
MT126808
-LC528233
LC528232
+LC528233
MT123290
MT123291
MT123292
@@ -807,8 +860,8 @@ MT066159
MT066175
MT066176
LC523807
-LC523808
LC523809
+LC523808
MT044258
MT044257
MT042777
@@ -830,7 +883,6 @@ LC522350
MT027062
MT027063
MT027064
-MT020781
MT019530
MT019531
MT020881
@@ -838,13 +890,14 @@ MT019533
MT019529
MT019532
MT020880
+MT020781
LR757995
LR757996
LR757997
LR757998
MT007544
-MT008023
MT008022
+MT008023
MN996530
MN996531
MN996527
@@ -856,22 +909,21 @@ MN988668
MN988669
MN994467
MN988713
-MN938387
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-MN975263
-MN975268
+MN938384
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MN975267
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MN938388
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MN938390
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MN938385
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+MN975265
MN970003
MN970004
-NC_045512
MN908947
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={