Merge branch 'master' into patch-6

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
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+Barbados,http://www.wikidata.org/entity/Q244
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+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
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+Australia,http://www.wikidata.org/entity/Q408
+Rwanda,http://www.wikidata.org/entity/Q1037
+Argentina,http://www.wikidata.org/entity/Q414
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+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
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+Bolivia,http://www.wikidata.org/entity/Q750
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+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
-MT325610
-MT325612
-MT325616
-MT325617
-MT325618
-MT325622
-MT325623
-MT325600
-MT325606
-MT325611
-MT325613
-MT325615
-MT325619
-MT325620
-MT325624
-MT325625
+NC_045512
+MT334522
+MT334523
+MT334524
+MT334525
+MT334526
+MT334527
+MT334528
+MT334529
+MT334530
+MT334531
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+MT334533
+MT334534
+MT334535
+MT334536
+MT334537
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+MT334549
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+MT334551
+MT334552
+MT334553
+MT334554
+MT334556
+MT334557
+MT334558
+MT334559
+MT334560
+MT334561
+MT334562
+MT334563
+MT334564
+MT334565
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+MT334567
+MT334568
+MT334569
+MT334570
+MT334571
+MT334572
+MT334573
+MT324062
+MT324680
+MT324684
+MT325573
+MT325574
+MT325576
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+MT325578
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+MT325593
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+MT326093
+MT326092
+MT326091
+MT326090
+MT326085
+MT326084
+MT326083
+MT326082
+MT326081
+MT326080
+MT326077
+MT326067
+MT326057
+MT326024
+MT326025
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+MT326033
+MT326035
+MT326036
+MT326037
+MT326040
+MT326041
+MT326043
+MT326044
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+MT326053
+MT326055
+MT326056
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+MT326066
+MT326069
+MT326070
+MT326071
+MT326073
+MT326074
+MT326075
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+MT326089
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+MT325568
+MT325572
+MT325575
+MT325583
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+MT325636
+MT325637
+MT326095
+MT326096
+MT326103
+MT326112
+MT326113
+MT326114
+MT326115
+MT326122
+MT326131
+MT326132
+MT326133
+MT325563
+MT326164
+MT326166
+MT326167
+MT325570
+MT325579
+MT325581
+MT325582
+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
-MT325636
-MT325637
-MT326095
-MT326096
-MT326103
-MT326112
-MT326113
-MT326114
-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
-MT326091
-MT326090
-MT326085
-MT326084
-MT326083
-MT326082
-MT326081
-MT326080
-MT326077
-MT326067
-MT326057
-MT326024
-MT326025
-MT326032
-MT326033
-MT326035
-MT326036
-MT326037
-MT326040
-MT326041
-MT326043
-MT326044
-MT326046
-MT326049
-MT326050
-MT326052
-MT326053
-MT326055
-MT326056
-MT326059
-MT326062
-MT326063
-MT326066
-MT326069
-MT326070
-MT326071
-MT326073
-MT326074
-MT326075
-MT326088
-MT326089
-MT327745
-MT324062
-MT324680
-MT324684
-MT325573
-MT325574
-MT325576
-MT325577
-MT325578
-MT325580
-MT325591
-MT325592
-MT325593
-MT325595
-MT325605
-MT325627
-MT326028
-MT326029
-MT326031
-MT326048
-MT325570
-MT325579
-MT325581
-MT325582
-MT325586
-MT325594
-MT325598
-MT325626
-MT325628
-MT325633
-MT325634
-MT326030
-MT326038
-MT326058
-MT324681
-MT324682
-MT324683
-MT328032
-MT328035
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+MT325601
+MT325602
+MT325607
+MT325608
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+MT325624
+MT325625
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+MT322420
+MT322424
 MT039874
 MT077125
-MT322394
+MT322396
 MT322397
-MT322398
 MT322399
+MT322403
+MT322406
+MT322407
+MT322412
+MT322413
+MT322414
+MT322416
+MT322398
 MT322400
 MT322401
-MT322403
+MT322402
 MT322404
 MT322405
-MT322406
 MT322408
 MT322409
 MT322410
 MT322411
-MT322412
-MT322413
-MT322414
 MT322415
-MT322416
 MT322417
 MT322418
 MT322419
-MT322420
 MT322421
 MT322422
 MT322423
-MT322424
-MT322396
-MT322402
-MT322395
-MT322407
-MT320538
 MT320891
+MT320538
 MT308692
 MT308693
+MT308695
+MT308696
 MT308698
 MT308699
+MT308701
 MT308703
 MT308704
 MT308694
-MT308695
-MT308696
 MT308697
 MT308700
-MT308701
 MT308702
 MT304476
 MT304474
 MT304475
 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
-MN938389
-MN975263
-MN975268
+MN938384
+MN975262
+MN985325
+MN975264
+MN975266
 MN975267
+MN975268
 MN938388
+MN938389
 MN938390
-MN975264
-MN975265
-MN975266
-MN938386
+MN975263
 MN938385
-MN938384
-MN975262
-MN985325
+MN938386
+MN938387
+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={