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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/sequences.acc396
-rw-r--r--setup.py2
9 files changed, 607 insertions, 195 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/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
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+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
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-MT326133
-MT325563
-MT326164
-MT326166
-MT326167
+MT324681
+MT324682
+MT324683
+MT328032
+MT328035
MT325569
MT326097
MT326106
@@ -177,146 +290,83 @@ MT326101
MT326099
MT326098
MT326094
-MT326093
-MT326092
-MT326091
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-MT326085
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-MT325576
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MT039874
MT077125
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MT322397
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MT322399
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MT322400
MT322401
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MT322404
MT322405
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MT322408
MT322409
MT322410
MT322411
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MT322415
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MT322417
MT322418
MT322419
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MT322421
MT322422
MT322423
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MT320891
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MT308692
MT308693
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MT308698
MT308699
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MT308703
MT308704
MT308694
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MT308697
MT308700
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MT308702
MT304476
MT304474
MT304475
MT293547
MT304477
-MT304483
-MT300186
MT304478
MT304479
-MT304480
MT304481
MT304482
MT304484
@@ -324,9 +374,12 @@ MT304485
MT304486
MT304487
MT304488
+MT304491
+MT304480
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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
-MN938389
-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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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={
generated by cgit v1.2.3 (git 2.45.2) at 2024-11-08 17:01:56 +0000