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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/dict_ontology_standardization/ncbi_countries.csv243
-rw-r--r--scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv15
-rw-r--r--scripts/dict_ontology_standardization/ncbi_speciesman_source.csv22
-rw-r--r--scripts/from_genbank_to_fasta_and_yaml.py270
-rw-r--r--setup.py2
9 files changed, 553 insertions, 123 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/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv
new file mode 100644
index 0000000..9813f52
--- /dev/null
+++ b/scripts/dict_ontology_standardization/ncbi_countries.csv
@@ -0,0 +1,243 @@
+USA,http://www.wikidata.org/entity/Q30
+USA: CA,http://www.wikidata.org/entity/Q99
+USA: ME,http://www.wikidata.org/entity/Q724
+USA: NH,http://www.wikidata.org/entity/Q759
+USA: AL,http://www.wikidata.org/entity/Q173
+USA: MA,http://www.wikidata.org/entity/Q771
+USA: CT,http://www.wikidata.org/entity/Q779
+USA: AK,http://www.wikidata.org/entity/Q797
+USA: HI,http://www.wikidata.org/entity/Q782
+USA: FL,http://www.wikidata.org/entity/Q812
+USA: AZ,http://www.wikidata.org/entity/Q816
+USA: OR,http://www.wikidata.org/entity/Q824
+USA: UT,http://www.wikidata.org/entity/Q829
+USA: MI,http://www.wikidata.org/entity/Q1166
+USA: IL,http://www.wikidata.org/entity/Q1204
+USA: ND,http://www.wikidata.org/entity/Q1207
+USA: SD,http://www.wikidata.org/entity/Q1211
+USA: ID,http://www.wikidata.org/entity/Q1221
+USA: MT,http://www.wikidata.org/entity/Q1212
+USA: WY,http://www.wikidata.org/entity/Q1214
+USA: WA,http://www.wikidata.org/entity/Q1223
+USA: NV,http://www.wikidata.org/entity/Q1227
+USA: CO,http://www.wikidata.org/entity/Q1261
+USA: WV,http://www.wikidata.org/entity/Q1371
+USA: VA,http://www.wikidata.org/entity/Q1370
+USA: RI,http://www.wikidata.org/entity/Q1387
+USA: NY,http://www.wikidata.org/entity/Q1384
+USA: DE,http://www.wikidata.org/entity/Q1393
+USA: OH,http://www.wikidata.org/entity/Q1397
+USA: MD,http://www.wikidata.org/entity/Q1391
+USA: NJ,http://www.wikidata.org/entity/Q1408
+USA: GA,http://www.wikidata.org/entity/Q1428
+USA: PA,http://www.wikidata.org/entity/Q1400
+USA: IN,http://www.wikidata.org/entity/Q1415
+USA: TX,http://www.wikidata.org/entity/Q1439
+USA: NC,http://www.wikidata.org/entity/Q1454
+USA: MS,http://www.wikidata.org/entity/Q1494
+USA: SC,http://www.wikidata.org/entity/Q1456
+USA: NM,http://www.wikidata.org/entity/Q1522
+USA: TN,http://www.wikidata.org/entity/Q1509
+USA: MN,http://www.wikidata.org/entity/Q1527
+USA: WI,http://www.wikidata.org/entity/Q1537
+USA: NE,http://www.wikidata.org/entity/Q1553
+USA: IA,http://www.wikidata.org/entity/Q1546
+USA: OK,http://www.wikidata.org/entity/Q1649
+USA: KS,http://www.wikidata.org/entity/Q1558
+USA: VT,http://www.wikidata.org/entity/Q16551
+USA: MO,http://www.wikidata.org/entity/Q1581
+USA: LA,http://www.wikidata.org/entity/Q1588
+USA: KY,http://www.wikidata.org/entity/Q1603
+USA: AR,http://www.wikidata.org/entity/Q1612
+China,http://www.wikidata.org/entity/Q148
+China: Beijing,http://www.wikidata.org/entity/Q956
+China: Hong Kong,http://www.wikidata.org/entity/Q8646
+China: Shanghai,http://www.wikidata.org/entity/Q8686
+China: Chongqing,http://www.wikidata.org/entity/Q11725
+China: Tianjin,http://www.wikidata.org/entity/Q11736
+China: Macau,http://www.wikidata.org/entity/Q14773
+China: Guangdong,http://www.wikidata.org/entity/Q15175
+China: Guangxi Zhuang Autonomous Region,http://www.wikidata.org/entity/Q15176
+China: Jiangsu,http://www.wikidata.org/entity/Q16963
+China: Zhejiang,http://www.wikidata.org/entity/Q16967
+China: Tibet Autonomous Region,http://www.wikidata.org/entity/Q17269
+China: Heilongjiang,http://www.wikidata.org/entity/Q19206
+China: Sichuan,http://www.wikidata.org/entity/Q19770
+China: Hebei,http://www.wikidata.org/entity/Q21208
+China: Xinjiang,http://www.wikidata.org/entity/Q34800
+China: Anhui,http://www.wikidata.org/entity/Q40956
+China: Inner Mongolia,http://www.wikidata.org/entity/Q41079
+China: Fujian,http://www.wikidata.org/entity/Q41705
+China: Hainan,http://www.wikidata.org/entity/Q42200
+China: Gansu,http://www.wikidata.org/entity/Q42392
+China: Yunnan,http://www.wikidata.org/entity/Q43194
+China: Shandong,http://www.wikidata.org/entity/Q43407
+China: Henan,http://www.wikidata.org/entity/Q43684
+China: Liaoning,http://www.wikidata.org/entity/Q43934
+China: Jilin,http://www.wikidata.org/entity/Q45208
+China: Hunan,http://www.wikidata.org/entity/Q45761
+China: Hubei,http://www.wikidata.org/entity/Q46862
+China: Qinghai,http://www.wikidata.org/entity/Q45833
+China: Shanxi,http://www.wikidata.org/entity/Q46913
+China: Shaanxi,http://www.wikidata.org/entity/Q47974
+China: Guizhou,http://www.wikidata.org/entity/Q47097
+China: Jiangxi,http://www.wikidata.org/entity/Q57052
+China: Ningxia Hui Autonomous Region,http://www.wikidata.org/entity/Q57448
+30.59 N 114.3 E,http://www.wikidata.org/entity/Q11746
+Sri Lanka,http://www.wikidata.org/entity/Q854
+Syria,http://www.wikidata.org/entity/Q858
+Tajikistan,http://www.wikidata.org/entity/Q863
+Canada,http://www.wikidata.org/entity/Q16
+Thailand,http://www.wikidata.org/entity/Q869
+Japan,http://www.wikidata.org/entity/Q17
+Turkmenistan,http://www.wikidata.org/entity/Q874
+Norway,http://www.wikidata.org/entity/Q20
+Ireland,http://www.wikidata.org/entity/Q27
+United Arab Emirates,http://www.wikidata.org/entity/Q878
+Vietnam,http://www.wikidata.org/entity/Q881
+United States of America,http://www.wikidata.org/entity/Q30
+South Korea,http://www.wikidata.org/entity/Q884
+Denmark,http://www.wikidata.org/entity/Q35
+Afghanistan,http://www.wikidata.org/entity/Q889
+Bangladesh,http://www.wikidata.org/entity/Q902
+Poland,http://www.wikidata.org/entity/Q36
+Mali,http://www.wikidata.org/entity/Q912
+Italy,http://www.wikidata.org/entity/Q38
+Angola,http://www.wikidata.org/entity/Q916
+Switzerland,http://www.wikidata.org/entity/Q39
+Bhutan,http://www.wikidata.org/entity/Q917
+Austria,http://www.wikidata.org/entity/Q40
+Brunei,http://www.wikidata.org/entity/Q921
+Tanzania,http://www.wikidata.org/entity/Q924
+Turkey,http://www.wikidata.org/entity/Q43
+Philippines,http://www.wikidata.org/entity/Q928
+Portugal,http://www.wikidata.org/entity/Q45
+Uruguay,http://www.wikidata.org/entity/Q77
+Central African Republic,http://www.wikidata.org/entity/Q929
+Togo,http://www.wikidata.org/entity/Q945
+Egypt,http://www.wikidata.org/entity/Q79
+Tunisia,http://www.wikidata.org/entity/Q948
+Zambia,http://www.wikidata.org/entity/Q953
+Mexico,http://www.wikidata.org/entity/Q96
+Zimbabwe,http://www.wikidata.org/entity/Q954
+South Sudan,http://www.wikidata.org/entity/Q958
+Kenya,http://www.wikidata.org/entity/Q114
+Benin,http://www.wikidata.org/entity/Q962
+Ethiopia,http://www.wikidata.org/entity/Q115
+Botswana,http://www.wikidata.org/entity/Q963
+Ghana,http://www.wikidata.org/entity/Q117
+Burkina Faso,http://www.wikidata.org/entity/Q965
+Burundi,http://www.wikidata.org/entity/Q967
+France,http://www.wikidata.org/entity/Q142
+Comoros,http://www.wikidata.org/entity/Q970
+United Kingdom,http://www.wikidata.org/entity/Q145
+Republic of the Congo,http://www.wikidata.org/entity/Q971
+People's Republic of China,http://www.wikidata.org/entity/Q148
+Democratic Republic of the Congo,http://www.wikidata.org/entity/Q974
+Brazil,http://www.wikidata.org/entity/Q155
+Djibouti,http://www.wikidata.org/entity/Q977
+Germany,http://www.wikidata.org/entity/Q183
+Eritrea,http://www.wikidata.org/entity/Q986
+The Gambia,http://www.wikidata.org/entity/Q1005
+Latvia,http://www.wikidata.org/entity/Q211
+Czech Republic,http://www.wikidata.org/entity/Q213
+Guinea,http://www.wikidata.org/entity/Q1006
+Guinea-Bissau,http://www.wikidata.org/entity/Q1007
+Slovakia,http://www.wikidata.org/entity/Q214
+Ivory Coast,http://www.wikidata.org/entity/Q1008
+Romania,http://www.wikidata.org/entity/Q218
+Cape Verde,http://www.wikidata.org/entity/Q1011
+Cameroon,http://www.wikidata.org/entity/Q1009
+Bulgaria,http://www.wikidata.org/entity/Q219
+Lesotho,http://www.wikidata.org/entity/Q1013
+Croatia,http://www.wikidata.org/entity/Q224
+Liberia,http://www.wikidata.org/entity/Q1014
+Libya,http://www.wikidata.org/entity/Q1016
+Kazakhstan,http://www.wikidata.org/entity/Q232
+Montenegro,http://www.wikidata.org/entity/Q236
+Madagascar,http://www.wikidata.org/entity/Q1019
+Barbados,http://www.wikidata.org/entity/Q244
+Indonesia,http://www.wikidata.org/entity/Q252
+Malawi,http://www.wikidata.org/entity/Q1020
+Mauritania,http://www.wikidata.org/entity/Q1025
+South Africa,http://www.wikidata.org/entity/Q258
+Mauritius,http://www.wikidata.org/entity/Q1027
+Algeria,http://www.wikidata.org/entity/Q262
+Morocco,http://www.wikidata.org/entity/Q1028
+Mozambique,http://www.wikidata.org/entity/Q1029
+Uzbekistan,http://www.wikidata.org/entity/Q265
+Namibia,http://www.wikidata.org/entity/Q1030
+Chile,http://www.wikidata.org/entity/Q298
+Niger,http://www.wikidata.org/entity/Q1032
+Singapore,http://www.wikidata.org/entity/Q334
+Nigeria,http://www.wikidata.org/entity/Q1033
+Bahrain,http://www.wikidata.org/entity/Q398
+Uganda,http://www.wikidata.org/entity/Q1036
+Australia,http://www.wikidata.org/entity/Q408
+Rwanda,http://www.wikidata.org/entity/Q1037
+Argentina,http://www.wikidata.org/entity/Q414
+São Tomé and Príncipe,http://www.wikidata.org/entity/Q1039
+Peru,http://www.wikidata.org/entity/Q419
+Senegal,http://www.wikidata.org/entity/Q1041
+Seychelles,http://www.wikidata.org/entity/Q1042
+North Korea,http://www.wikidata.org/entity/Q423
+Sierra Leone,http://www.wikidata.org/entity/Q1044
+Cambodia,http://www.wikidata.org/entity/Q424
+Sudan,http://www.wikidata.org/entity/Q1049
+Somalia,http://www.wikidata.org/entity/Q1045
+Eswatini,http://www.wikidata.org/entity/Q1050
+East Timor,http://www.wikidata.org/entity/Q574
+Chad,http://www.wikidata.org/entity/Q657
+New Zealand,http://www.wikidata.org/entity/Q664
+Kingdom of the Netherlands,http://www.wikidata.org/entity/Q29999
+India,http://www.wikidata.org/entity/Q668
+Tuvalu,http://www.wikidata.org/entity/Q672
+Samoa,http://www.wikidata.org/entity/Q683
+Solomon Islands,http://www.wikidata.org/entity/Q685
+Vanuatu,http://www.wikidata.org/entity/Q686
+Papua New Guinea,http://www.wikidata.org/entity/Q691
+Palau,http://www.wikidata.org/entity/Q695
+Nauru,http://www.wikidata.org/entity/Q697
+Federated States of Micronesia,http://www.wikidata.org/entity/Q702
+Marshall Islands,http://www.wikidata.org/entity/Q709
+Kiribati,http://www.wikidata.org/entity/Q710
+Mongolia,http://www.wikidata.org/entity/Q711
+Fiji,http://www.wikidata.org/entity/Q712
+Venezuela,http://www.wikidata.org/entity/Q717
+Paraguay,http://www.wikidata.org/entity/Q733
+Guyana,http://www.wikidata.org/entity/Q734
+Ecuador,http://www.wikidata.org/entity/Q736
+Colombia,http://www.wikidata.org/entity/Q739
+Bolivia,http://www.wikidata.org/entity/Q750
+Trinidad and Tobago,http://www.wikidata.org/entity/Q754
+Saint Vincent and the Grenadines,http://www.wikidata.org/entity/Q757
+Saint Lucia,http://www.wikidata.org/entity/Q760
+Saint Kitts and Nevis,http://www.wikidata.org/entity/Q763
+Jamaica,http://www.wikidata.org/entity/Q766
+Grenada,http://www.wikidata.org/entity/Q769
+Guatemala,http://www.wikidata.org/entity/Q774
+The Bahamas,http://www.wikidata.org/entity/Q778
+Antigua and Barbuda,http://www.wikidata.org/entity/Q781
+Honduras,http://www.wikidata.org/entity/Q783
+Dominica,http://www.wikidata.org/entity/Q784
+Dominican Republic,http://www.wikidata.org/entity/Q786
+Haiti,http://www.wikidata.org/entity/Q790
+El Salvador,http://www.wikidata.org/entity/Q792
+Iran,http://www.wikidata.org/entity/Q794
+Iraq,http://www.wikidata.org/entity/Q796
+Costa Rica,http://www.wikidata.org/entity/Q800
+Israel,http://www.wikidata.org/entity/Q801
+Yemen,http://www.wikidata.org/entity/Q805
+Jordan,http://www.wikidata.org/entity/Q810
+Nicaragua,http://www.wikidata.org/entity/Q811
+Kyrgyzstan,http://www.wikidata.org/entity/Q813
+Laos,http://www.wikidata.org/entity/Q819
+Lebanon,http://www.wikidata.org/entity/Q822
+Maldives,http://www.wikidata.org/entity/Q826
+Malaysia,http://www.wikidata.org/entity/Q833
+Myanmar,http://www.wikidata.org/entity/Q836
+Nepal,http://www.wikidata.org/entity/Q837
+Oman,http://www.wikidata.org/entity/Q842
+Pakistan,http://www.wikidata.org/entity/Q843
+Qatar,http://www.wikidata.org/entity/Q846
+Saudi Arabia,http://www.wikidata.org/entity/Q851 \ No newline at end of file
diff --git a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
new file mode 100644
index 0000000..3ec7e09
--- /dev/null
+++ b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
@@ -0,0 +1,15 @@
+Illumian NextSeq 500,http://www.ebi.ac.uk/efo/EFO_0009173
+Illumina NextSeq 500,http://www.ebi.ac.uk/efo/EFO_0009173
+Nanopore MinION,http://www.ebi.ac.uk/efo/EFO_0008632
+Oxford Nanopore MinION,http://www.ebi.ac.uk/efo/EFO_0008632
+ONT (Oxford Nanopore Technologies),http://www.ebi.ac.uk/efo/EFO_0008632
+Oxford Nanopore technologies MinION,http://www.ebi.ac.uk/efo/EFO_0008632
+MinION Oxford Nanopore,http://www.ebi.ac.uk/efo/EFO_0008632
+Illumina MiSeq,http://www.ebi.ac.uk/efo/EFO_0004205
+Illumina,http://purl.obolibrary.org/obo/OBI_0000759
+Oxford Nanopore technology,http://purl.obolibrary.org/obo/NCIT_C146818
+Oxford Nanopore Technologies,http://purl.obolibrary.org/obo/NCIT_C146818
+Oxford Nanopore,http://purl.obolibrary.org/obo/NCIT_C146818
+IonTorrent,http://purl.obolibrary.org/obo/NCIT_C125894
+Ion Torrent X5Plus,http://purl.obolibrary.org/obo/NCIT_C125894
+Sanger dideoxy sequencing,http://purl.obolibrary.org/obo/NCIT_C19641
diff --git a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
new file mode 100644
index 0000000..fcd6c94
--- /dev/null
+++ b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
@@ -0,0 +1,22 @@
+nasopharyngeal swab, http://purl.obolibrary.org/obo/NCIT_C155831
+nasopharyngeal exudate,http://purl.obolibrary.org/obo/NCIT_C155831
+respiratory swab,http://purl.obolibrary.org/obo/NCIT_C155831
+naso-pharyngeal exudate,http://purl.obolibrary.org/obo/NCIT_C155831
+nasopharyngeal aspirate,http://purl.obolibrary.org/obo/NCIT_C155831
+nasal swab specimen,http://purl.obolibrary.org/obo/NCIT_C155831
+pharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155831
+respiratory secretion,http://purl.obolibrary.org/obo/NCIT_C155831
+mid-nasal swab,http://purl.obolibrary.org/obo/NCIT_C155831
+nasopharyngeal (throat) washings,http://purl.obolibrary.org/obo/NCIT_C155831
+oropharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155835
+throat swab,http://purl.obolibrary.org/obo/NCIT_C155835
+oro-pharyngeal,http://purl.obolibrary.org/obo/NCIT_C155835
+buccal swab,http://purl.obolibrary.org/obo/NCIT_C155835
+throat washing,http://purl.obolibrary.org/obo/NCIT_C155835
+Throat Swab,http://purl.obolibrary.org/obo/NCIT_C155835
+throat (oropharyngeal) swab,http://purl.obolibrary.org/obo/NCIT_C155835
+bronchoalveolar lavage fluid,http://purl.obolibrary.org/obo/NCIT_C13195
+swab,http://purl.obolibrary.org/obo/NCIT_C13195
+oral swab,http://purl.obolibrary.org/obo/NCIT_C13195
+bronchoalveolar lavage,http://purl.obolibrary.org/obo/NCIT_C13195
+sputum,http://purl.obolibrary.org/obo/NCIT_C13278
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 0cc1a57..a7c9dc2 100644
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -1,15 +1,19 @@
from Bio import Entrez
-Entrez.email = 'your_email_to_be_polite'
+Entrez.email = 'andresguarahino@gmail.com'
import xml.etree.ElementTree as ET
import yaml
import os
-path_ncbi_virus_accession = 'sequences.acc'
+from datetime import date
+today = date.today().strftime("%Y%m%d")
+
+dir_metadata_today = 'metadata_from_nuccore_{}'.format(today)
+dir_fasta_and_yaml_today = 'fasta_and_yaml_{}'.format(today)
-date = '20200414'
-path_seq_fasta = 'seq_from_nuccore.{}.fasta'.format(date)
-path_metadata_xml = 'metadata_from_nuccore.{}.xml'.format(date)
+dir_dict_ontology_standardization = 'dict_ontology_standardization/'
+
+path_ncbi_virus_accession = 'sequences.acc'
# Take all the ids
id_set = set()
@@ -19,9 +23,15 @@ 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))
@@ -34,108 +44,168 @@ id_set.update(tmp_list)
print(term_list + ['NCBI Virus'], len(id_set))
-if not os.path.exists(path_metadata_xml):
- # TO_DO: to check if I already have the records?
-
- with open(path_metadata_xml, 'w') as fw:
- fw.write(
- Entrez.efetch(db='nuccore', id=list(id_set), retmode='xml').read()
- )
-
+def chunks(lst, n):
+ for i in range(0, len(lst), n):
+ yield lst[i:i + n]
-tree = ET.parse(path_metadata_xml)
-GBSet = tree.getroot()
+num_ids_for_request = 100
+if not os.path.exists(dir_metadata_today):
+ os.makedirs(dir_metadata_today)
+
+ for i, id_x_list in enumerate(chunks(list(id_set), num_ids_for_request)):
+ path_metadata_xxx_xml = os.path.join(dir_metadata_today, 'metadata_{}.xml'.format(i))
+ print('Requesting {} ids --> {}'.format(len(id_x_list), path_metadata_xml))
+
+ with open(path_metadata_xxx_xml, 'w') as fw:
+ fw.write(
+ Entrez.efetch(db='nuccore', id=id_x_list, retmode='xml').read()
+ )
+
+
+term_to_uri_dict = {}
+
+for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_xxx_csv) for name_xxx_csv in os.listdir(dir_dict_ontology_standardization) if name_xxx_csv.endswith('.csv')]:
+ print('Read {}'.format(path_dict_xxx_csv))
+
+ with open(path_dict_xxx_csv) as f:
+ for line in f:
+ term, uri = line.strip('\n').split(',')
+
+ term_to_uri_dict[term] = uri
species_to_taxid_dict = {
'Homo sapiens': 9606
}
-for GBSeq in GBSet:
- accession_version = GBSeq.find('GBSeq_accession-version').text
-
- GBSeq_sequence = GBSeq.find('GBSeq_sequence')
- if GBSeq_sequence is None:
- print(accession_version, ' - sequence not found')
- continue
+if os.path.exists(dir_fasta_and_yaml_today):
+ os.makedirs(dir_fasta_and_yaml_today)
- # A general default-empty yaml could be read from the definitive one
- info_for_yaml_dict = {
- 'id': 'placeholder',
- 'host': {},
- 'sample': {},
- 'virus': {},
- 'technology': {},
- 'submitter': {}
- }
-
+ for path_metadata_xxx_xml in [os.path.join(dir_metadata_today, name_metadata_xxx_xml) for name_metadata_xxx_xml in os.listdir(dir_metadata_today) if name_metadata_xxx_xml.endswith('.xml')]:
+ tree = ET.parse(path_metadata_xxx_xml)
+ GBSet = tree.getroot()
- info_for_yaml_dict['sample']['sample_id'] = accession_version
- info_for_yaml_dict['submitter']['authors'] = ';'.join([x.text for x in GBSeq.iter('GBAuthor')])
+ for GBSeq in GBSet:
+ accession_version = GBSeq.find('GBSeq_accession-version').text
-
- GBSeq_comment = GBSeq.find('GBSeq_comment')
- if GBSeq_comment is not None and 'Assembly-Data' in GBSeq_comment.text:
- GBSeq_comment_text = GBSeq_comment.text.split('##Assembly-Data-START## ; ')[1].split(' ; ##Assembly-Data-END##')[0]
-
- for info_to_check, field_in_yaml in zip(
- ['Assembly Method', 'Coverage', 'Sequencing Technology'],
- ['sequence_assembly_method', 'sequencing_coverage', 'sample_sequencing_technology']
- ):
- if info_to_check in GBSeq_comment_text:
- info_for_yaml_dict['technology'][field_in_yaml] = GBSeq_comment_text.split('{} :: '.format(info_to_check))[1].split(' ;')[0]
-
-
- for GBFeature in GBSeq.iter('GBFeature'):
- if GBFeature.find('GBFeature_key').text != 'source':
- continue
-
- for GBQualifier in GBFeature.iter('GBQualifier'):
- GBQualifier_value = GBQualifier.find('GBQualifier_value')
- if GBQualifier_value is None:
+ GBSeq_sequence = GBSeq.find('GBSeq_sequence')
+ if GBSeq_sequence is None:
+ print(accession_version, ' - sequence not found')
continue
- GBQualifier_value_text = GBQualifier_value.text
-
- GBQualifier_name_text = GBQualifier.find('GBQualifier_name').text
-
- if GBQualifier_name_text == 'host':
- GBQualifier_value_text_list = GBQualifier_value_text.split('; ')
-
- info_for_yaml_dict['host']['host_common_name'] = GBQualifier_value_text_list[0]
-
- if GBQualifier_value_text_list[0] in species_to_taxid_dict:
- info_for_yaml_dict['host']['host_species'] = species_to_taxid_dict[GBQualifier_value_text_list[0]]
-
- if len(GBQualifier_value_text_list) > 1:
- if GBQualifier_value_text_list[1] in ['male', 'female']:
- info_for_yaml_dict['host']['host_sex'] = GBQualifier_value_text_list[1]
- else:
- info_for_yaml_dict['host']['host_health_status'] = GBQualifier_value_text_list[1]
-
- if 'age' in GBQualifier_value_text:
- info_for_yaml_dict['host']['host_age'] = int(GBQualifier_value_text_list[2].split('age ')[1])
- info_for_yaml_dict['host']['host_age_unit'] = 'year'
- elif GBQualifier_name_text == 'collected_by':
- if any([x in GBQualifier_value_text.lower() for x in ['institute', 'hospital', 'city', 'center']]):
- info_for_yaml_dict['sample']['collecting_institution'] = GBQualifier_value_text
- else:
- info_for_yaml_dict['sample']['collector_name'] = GBQualifier_value_text
- elif GBQualifier_name_text == 'isolation_source':
- info_for_yaml_dict['sample']['specimen_source'] = GBQualifier_value_text
- elif GBQualifier_name_text == 'collection_date':
- # TO_DO: which format we will use?
- info_for_yaml_dict['sample']['collection_date'] = GBQualifier_value_text
- elif GBQualifier_name_text in ['lat_lon', 'country']:
- info_for_yaml_dict['sample']['collection_location'] = GBQualifier_value_text
- elif GBQualifier_name_text == 'note':
- info_for_yaml_dict['sample']['additional_collection_information'] = GBQualifier_value_text
- elif GBQualifier_name_text == 'isolate':
- info_for_yaml_dict['virus']['virus_strain'] = GBQualifier_value_text
- elif GBQualifier_name_text == 'db_xref':
- info_for_yaml_dict['virus']['virus_species'] = int(GBQualifier_value_text.split('taxon:')[1])
-
- with open('{}.fasta'.format(accession_version), 'w') as fw:
- fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper()))
- with open('{}.yaml'.format(accession_version), 'w') as fw:
- yaml.dump(info_for_yaml_dict, fw, default_flow_style=False)
+
+ # A general default-empty yaml could be read from the definitive one
+ info_for_yaml_dict = {
+ 'id': 'placeholder',
+ 'host': {},
+ 'sample': {},
+ 'virus': {},
+ 'technology': {},
+ 'submitter': {}
+ }
+
+
+ info_for_yaml_dict['sample']['sample_id'] = accession_version
+ info_for_yaml_dict['submitter']['authors'] = ';'.join([x.text for x in GBSeq.iter('GBAuthor')])
+
+
+ GBSeq_comment = GBSeq.find('GBSeq_comment')
+ if GBSeq_comment is not None and 'Assembly-Data' in GBSeq_comment.text:
+ GBSeq_comment_text = GBSeq_comment.text.split('##Assembly-Data-START## ; ')[1].split(' ; ##Assembly-Data-END##')[0]
+
+ for info_to_check, field_in_yaml in zip(
+ ['Assembly Method', 'Coverage', 'Sequencing Technology'],
+ ['sequence_assembly_method', 'sequencing_coverage', 'sample_sequencing_technology']
+ ):
+ if info_to_check in GBSeq_comment_text:
+ tech_info_to_parse = GBSeq_comment_text.split('{} :: '.format(info_to_check))[1].split(' ;')[0]
+
+ if field_in_yaml == 'sequencing_coverage':
+ # A regular expression would be better!
+ info_for_yaml_dict['technology'][field_in_yaml] = ';'.join(
+ [x.strip('(average)').strip("reads/nt").replace(',', '.').strip(' xX>') for x in tech_info_to_parse.split(';')]
+ )
+ elif field_in_yaml == 'sample_sequencing_technology':
+ new_seq_tec_list = []
+ for seq_tec in tech_info_to_parse.split(';'):
+ seq_tec = seq_tec.strip()
+ if seq_tec in term_to_uri_dict:
+ seq_tec = term_to_uri_dict[seq_tec]
+ else:
+ print(accession_version, 'missing technologies:', seq_tec)
+
+ new_seq_tec_list.append(seq_tec)
+
+ for n, seq_tec in enumerate(new_seq_tec_list):
+ info_for_yaml_dict['technology'][field_in_yaml + ('' if n == 0 else str(n + 1))] = seq_tec
+ else:
+ info_for_yaml_dict['technology'][field_in_yaml] = tech_info_to_parse
+
+
+ #term_to_uri_dict
+
+ for GBFeature in GBSeq.iter('GBFeature'):
+ if GBFeature.find('GBFeature_key').text != 'source':
+ continue
+
+ for GBQualifier in GBFeature.iter('GBQualifier'):
+ GBQualifier_value = GBQualifier.find('GBQualifier_value')
+ if GBQualifier_value is None:
+ continue
+ GBQualifier_value_text = GBQualifier_value.text
+
+ GBQualifier_name_text = GBQualifier.find('GBQualifier_name').text
+
+ if GBQualifier_name_text == 'host':
+ GBQualifier_value_text_list = GBQualifier_value_text.split('; ')
+
+ info_for_yaml_dict['host']['host_common_name'] = GBQualifier_value_text_list[0]
+
+ if GBQualifier_value_text_list[0] in species_to_taxid_dict:
+ info_for_yaml_dict['host']['host_species'] = species_to_taxid_dict[GBQualifier_value_text_list[0]]
+
+ if len(GBQualifier_value_text_list) > 1:
+ if GBQualifier_value_text_list[1] in ['male', 'female']:
+ info_for_yaml_dict['host']['host_sex'] = GBQualifier_value_text_list[1]
+ else:
+ info_for_yaml_dict['host']['host_health_status'] = GBQualifier_value_text_list[1]
+
+ if 'age' in GBQualifier_value_text:
+ info_for_yaml_dict['host']['host_age'] = int(GBQualifier_value_text_list[2].split('age ')[1])
+ info_for_yaml_dict['host']['host_age_unit'] = 'year'
+ elif GBQualifier_name_text == 'collected_by':
+ if any([x in GBQualifier_value_text.lower() for x in ['institute', 'hospital', 'city', 'center']]):
+ info_for_yaml_dict['sample']['collecting_institution'] = GBQualifier_value_text
+ else:
+ info_for_yaml_dict['sample']['collector_name'] = GBQualifier_value_text
+ elif GBQualifier_name_text == 'isolation_source':
+ if GBQualifier_value_text in term_to_uri_dict:
+ info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict[GBQualifier_value_text]
+ else:
+ if GBQualifier_value_text in ['NP/OP swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'np/np swab']:
+ info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict['nasopharyngeal swab']
+ info_for_yaml_dict['sample']['specimen_source2'] = term_to_uri_dict['oropharyngeal swab']
+ else:
+ print(accession_version, 'missing specimen_source:', GBQualifier_value_text)
+ elif GBQualifier_name_text == 'collection_date':
+ # TO_DO: which format we will use?
+ info_for_yaml_dict['sample']['collection_date'] = GBQualifier_value_text
+ elif GBQualifier_name_text in ['lat_lon', 'country']:
+ if GBQualifier_value_text in term_to_uri_dict:
+ GBQualifier_value_text = term_to_uri_dict[GBQualifier_value_text]
+ else:
+ print(accession_version, 'missing {}:'.format(GBQualifier_name_text), GBQualifier_value_text)
+
+ info_for_yaml_dict['sample']['collection_location'] = GBQualifier_value_text
+ elif GBQualifier_name_text == 'note':
+ info_for_yaml_dict['sample']['additional_collection_information'] = GBQualifier_value_text
+ elif GBQualifier_name_text == 'isolate':
+ info_for_yaml_dict['virus']['virus_strain'] = GBQualifier_value_text
+ elif GBQualifier_name_text == 'db_xref':
+ info_for_yaml_dict['virus']['virus_species'] = int(GBQualifier_value_text.split('taxon:')[1])
+
+ with open(os.path.join(dir_fasta_and_yaml_today, '{}.fasta'.format(accession_version)), 'w') as fw:
+ fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper()))
+
+ with open(os.path.join(dir_fasta_and_yaml_today, '{}.yaml'.format(accession_version)), 'w') as fw:
+ yaml.dump(info_for_yaml_dict, fw, default_flow_style=False)
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={
generated by cgit v1.2.3 (git 2.45.2) at 2024-11-19 04:00:17 +0000