Merge branch 'master' of github.com:arvados/bh20-seq-resource

7 files changed, 421 insertions, 36 deletions

diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv
index 20e8a9b..6b43137 100644
--- a/scripts/dict_ontology_standardization/ncbi_countries.csv
+++ b/scripts/dict_ontology_standardization/ncbi_countries.csv
@@ -39,6 +39,7 @@ Chad,http://www.wikidata.org/entity/Q657
 Chile,http://www.wikidata.org/entity/Q298
 China,http://www.wikidata.org/entity/Q148
 China: Anhui,http://www.wikidata.org/entity/Q40956
+"China: Anhui, Fuyang":http://www.wikidata.org/entity/Q360584
 China: Beijing,http://www.wikidata.org/entity/Q956
 China: Chongqing,http://www.wikidata.org/entity/Q11725
 China: Fujian,http://www.wikidata.org/entity/Q41705
@@ -48,6 +49,7 @@ China: Guangdong,http://www.wikidata.org/entity/Q15175
 China: Guangxi Zhuang Autonomous Region,http://www.wikidata.org/entity/Q15176
 China: Guangzhou,http://www.wikidata.org/entity/Q16572
 China: Guizhou,http://www.wikidata.org/entity/Q47097
+China: Hangzhou,http://www.wikidata.org/entity/Q4970
 China: Hainan,http://www.wikidata.org/entity/Q42200
 China: Hebei,http://www.wikidata.org/entity/Q21208
 China: Heilongjiang,http://www.wikidata.org/entity/Q19206
@@ -109,6 +111,7 @@ France,http://www.wikidata.org/entity/Q142
 Gabon,http://www.wikidata.org/entity/Q1000
 Georgia,http://www.wikidata.org/entity/Q230
 Germany,http://www.wikidata.org/entity/Q183
+Germany: Dusseldorf,https://www.wikidata.org/wiki/Q1718
 Ghana,http://www.wikidata.org/entity/Q117
 Greece,http://www.wikidata.org/entity/Q41
 Grenada,http://www.wikidata.org/entity/Q769
@@ -123,6 +126,7 @@ Iceland,http://www.wikidata.org/entity/Q189
 Icelandic Commonwealth,http://www.wikidata.org/entity/Q62389
 India,http://www.wikidata.org/entity/Q668
 India: Kerala State,http://www.wikidata.org/entity/Q1186
+India: Rajkot,http://www.wikidata.org/entity/Q1815245
 Indonesia,http://www.wikidata.org/entity/Q252
 Iran,http://www.wikidata.org/entity/Q794
 Iran: Qum,http://www.wikidata.org/entity/Q131664
@@ -172,6 +176,7 @@ Mozambique,http://www.wikidata.org/entity/Q1029
 Myanmar,http://www.wikidata.org/entity/Q836
 Namibia,http://www.wikidata.org/entity/Q1030
 Nauru,http://www.wikidata.org/entity/Q697
+Netherlands: Milheeze,https://www.wikidata.org/wiki/Q3314115
 Nepal,http://www.wikidata.org/entity/Q837
 New Zealand,http://www.wikidata.org/entity/Q664
 Nicaragua,http://www.wikidata.org/entity/Q811
@@ -263,6 +268,7 @@ USA: CA,http://www.wikidata.org/entity/Q99
 "USA: CA, San Diego County",http://www.wikidata.org/entity/Q108143
 USA: CO,http://www.wikidata.org/entity/Q1261
 USA: CT,http://www.wikidata.org/entity/Q779
+USA: DC,http://www.wikidata.org/entity/Q3551781
 USA: DE,http://www.wikidata.org/entity/Q1393
 USA: FL,http://www.wikidata.org/entity/Q812
 USA: GA,http://www.wikidata.org/entity/Q1428
@@ -293,6 +299,7 @@ USA: NM,http://www.wikidata.org/entity/Q1522
 USA: North Carolina,http://www.wikidata.org/entity/Q1454
 USA: NV,http://www.wikidata.org/entity/Q1227
 USA: NY,http://www.wikidata.org/entity/Q1384
+USA: New York,http://www.wikidata.org/entity/Q1384
 USA: OH,http://www.wikidata.org/entity/Q1397
 USA: OK,http://www.wikidata.org/entity/Q1649
 USA: OR,http://www.wikidata.org/entity/Q824
@@ -321,4 +328,4 @@ Viet Nam: Ho Chi Minh city,http://www.wikidata.org/entity/Q1854
 Vietnam,http://www.wikidata.org/entity/Q881
 Yemen,http://www.wikidata.org/entity/Q805
 Zambia,http://www.wikidata.org/entity/Q953
-Zimbabwe,http://www.wikidata.org/entity/Q954
+Zimbabwe,http://www.wikidata.org/entity/Q954
\ No newline at end of file
diff --git a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
index f5aeaae..7fa67f8 100644
--- a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
+++ b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
@@ -1,5 +1,6 @@
 nasopharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155831
 nasopharyngeal exudate,http://purl.obolibrary.org/obo/NCIT_C155831
+nasopharyngeal,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
diff --git a/scripts/docker/Dockerfile b/scripts/docker/Dockerfile
new file mode 100644
index 0000000..5bd38dd
--- /dev/null
+++ b/scripts/docker/Dockerfile
@@ -0,0 +1,10 @@
+FROM debian:10
+
+RUN apt-get update && \
+    apt-get -yq --no-install-recommends -o Acquire::Retries=6 install \
+    python3 python3-pip python3-setuptools python3-dev python-pycurl \
+    clustalw python3-biopython libcurl4-openssl-dev build-essential \
+    libssl-dev && \
+    apt-get clean
+
+RUN pip3 install bh20-seq-uploader
\ No newline at end of file
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 5257bd1..6f046ea 100755
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -7,6 +7,8 @@ import xml.etree.ElementTree as ET
 import json
 import os
 
+from dateutil import parser
+
 num_ids_for_request = 100
 
 dir_metadata = 'metadata_from_nuccore'
@@ -37,20 +39,19 @@ if not os.path.exists(dir_metadata):
         tmp_list = [x.split('.')[0] for x in tmp_list]
 
         print(term, len(tmp_list))
-        tmp_list=tmp_list
-    #    tmp_list = tmp_list[0:2] # restricting to small run
+        #tmp_list = tmp_list[0:2] # restricting to small run
 
         id_set.update([x.split('.')[0] for x in tmp_list])
 
     print(term_list, len(id_set))
 
-    with open(path_ncbi_virus_accession) as f:
-        tmp_list = [line.strip('\n') for line in f]
-
-    print('NCBI Virus', len(tmp_list))
-    id_set.update(tmp_list)
-
-    print(term_list + ['NCBI Virus'], len(id_set))
+    if os.path.exists(path_ncbi_virus_accession):
+        with open(path_ncbi_virus_accession) as f:
+            tmp_list = [line.strip('\n') for line in f]
+        print('NCBI Virus', len(tmp_list))
+        id_set.update(tmp_list)
+        term_list.append('NCBI Virus')
+        print(term_list, len(id_set))
 
     for i, id_x_list in enumerate(chunks(list(id_set), num_ids_for_request)):
         path_metadata_xxx_xml = os.path.join(dir_metadata, 'metadata_{}.xml'.format(i))
@@ -86,7 +87,7 @@ if not os.path.exists(dir_fasta_and_yaml):
     os.makedirs(dir_fasta_and_yaml)
 
 missing_value_list = []
-    
+
 for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) for name_metadata_xxx_xml in os.listdir(dir_metadata) if name_metadata_xxx_xml.endswith('.xml')]:
     tree = ET.parse(path_metadata_xxx_xml)
     GBSet = tree.getroot()
@@ -110,23 +111,23 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
             'submitter': {}
         }
 
-        
+
         info_for_yaml_dict['sample']['sample_id'] = accession_version
-        info_for_yaml_dict['sample']['source_database_accession'] = accession_version
-        
-        
+        info_for_yaml_dict['sample']['source_database_accession'] = ["http://identifiers.org/insdc/"+accession_version+"#sequence"] #accession is turned into resolvable URL/URI now
+
+
         # submitter info
         GBSeq_references = GBSeq.find('GBSeq_references')
         if GBSeq_references is not None:
-            info_for_yaml_dict['submitter']['authors'] = ';'.join([x.text for x in GBSeq_references.iter('GBAuthor')])
-            
+            info_for_yaml_dict['submitter']['authors'] = ["{}".format(x.text) for x in GBSeq_references.iter('GBAuthor')]
+
             GBReference = GBSeq_references.find('GBReference')
             if GBReference is not None:
                 GBReference_journal = GBReference.find('GBReference_journal')
-                
+
                 if GBReference_journal is not None and GBReference_journal.text != 'Unpublished':
                     if 'Submitted' in GBReference_journal.text:
-                        info_for_yaml_dict['submitter']['submitter_name'] = GBReference_journal.text.split(') ')[1].split(',')[0].strip()
+                        info_for_yaml_dict['submitter']['submitter_name'] = ["{}".format(GBReference_journal.text.split(') ')[1].split(',')[0].strip())]
                         info_for_yaml_dict['submitter']['submitter_address'] = ','.join(GBReference_journal.text.split(') ')[1].split(',')[1:]).strip()
                     else:
                         info_for_yaml_dict['submitter']['additional_submitter_information'] = GBReference_journal.text
@@ -146,8 +147,9 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
                     if field_in_yaml == 'sequencing_coverage':
                         # A regular expression would be better!
                         try:
-                            info_for_yaml_dict['technology'][field_in_yaml] = float(
-                                tech_info_to_parse.strip('(average)').strip("reads/nt").strip('(average for 6 sequences)').replace(',', '.').strip(' xX>'))
+                            info_for_yaml_dict['technology'][field_in_yaml] = [
+                                float(tech_info_to_parse.strip('(average)').strip("reads/nt").strip('(average for 6 sequences)').replace(',', '.').strip(' xX>'))
+                            ]
                         except ValueError:
                             print(accession_version, "Couldn't make sense of Coverage '%s'" % tech_info_to_parse)
                             pass
@@ -162,8 +164,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
 
                             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
+                        info_for_yaml_dict['technology']['sample_sequencing_technology'] = [x for x in new_seq_tec_list]
                     else:
                         info_for_yaml_dict['technology'][field_in_yaml] = tech_info_to_parse
 
@@ -199,7 +200,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
 
                         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'
+                            info_for_yaml_dict['host']['host_age_unit'] = 'http://purl.obolibrary.org/obo/UO_0000036'
                 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
@@ -208,24 +209,46 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
                 elif GBQualifier_name_text == 'isolation_source':
                     if GBQualifier_value_text.upper() in term_to_uri_dict:
                         GBQualifier_value_text = GBQualifier_value_text.upper() # For example, in case of 'usa: wa'
-                    
+
                     if GBQualifier_value_text in term_to_uri_dict:
-                        info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict[GBQualifier_value_text]
+                        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', 'np/op']:
-                            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']
-                        elif GBQualifier_value_text in ['nasopharyngeal swab/throat 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['throat swab']
+                            info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['oropharyngeal swab']]
+                        elif GBQualifier_value_text in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab']:
+                            info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['throat swab']]
                         elif GBQualifier_value_text in ['nasopharyngeal aspirate/throat swab']:
-                            info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict['nasopharyngeal aspirate']
-                            info_for_yaml_dict['sample']['specimen_source2'] = term_to_uri_dict['throat swab']
+                            info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal aspirate'], term_to_uri_dict['throat swab']]
                         else:
                             missing_value_list.append('\t'.join([accession_version, '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
+                    date_to_write = GBQualifier_value_text
+                    
+                    if len(GBQualifier_value_text.split('-')) == 1:
+                        if int(GBQualifier_value_text) < 2020:
+                            date_to_write = "15 12 {}".format(GBQualifier_value_text)
+                        else:
+                            date_to_write = "15 01 {}".format(GBQualifier_value_text)
+
+                        if 'additional_collection_information' in info_for_yaml_dict['sample']:
+                            info_for_yaml_dict['sample']['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
+                        else:
+                            info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
+                    elif len(GBQualifier_value_text.split('-')) == 2:
+                        date_to_write += '-15'
+                        
+                        if 'additional_collection_information' in info_for_yaml_dict['sample']:
+                            info_for_yaml_dict['sample']['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
+                        else:
+                            info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
+                    elif len(GBQualifier_value_text.split('-')) == 3:
+                        GBQualifier_value_text_list = GBQualifier_value_text.split('-')
+
+                        if GBQualifier_value_text_list[1].isalpha():
+                            date_to_write = GBQualifier_value_text_list[1] + ' ' + GBQualifier_value_text_list[0] + ' ' + GBQualifier_value_text_list[2]
+
+                    info_for_yaml_dict['sample']['collection_date'] = date_to_write
                 elif GBQualifier_name_text in ['lat_lon', 'country']:
                     if GBQualifier_value_text == 'Hong Kong':
                         GBQualifier_value_text = 'China: Hong Kong'
@@ -237,7 +260,10 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
 
                     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
+                    if 'additional_collection_information' in info_for_yaml_dict['sample']:
+                        info_for_yaml_dict['sample']['additional_collection_information'] += '; ' + GBQualifier_value_text
+                    else:
+                        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':
@@ -254,7 +280,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
         with open(os.path.join(dir_fasta_and_yaml, '{}.yaml'.format(accession_version)), 'w') as fw:
             json.dump(info_for_yaml_dict, fw, indent=2)
 
-        
+
 if len(missing_value_list) > 0:
     with open('missing_terms.tsv', 'w') as fw:
         fw.write('\n'.join(missing_value_list))
diff --git a/scripts/import.cwl b/scripts/import.cwl
new file mode 100644
index 0000000..d84516b
--- /dev/null
+++ b/scripts/import.cwl
@@ -0,0 +1,30 @@
+cwlVersion: v1.1
+class: CommandLineTool
+baseCommand: python3
+inputs:
+  scripts:
+    type: File
+    default:
+      class: File
+      location: import_to_arvados.py
+    inputBinding: {position: 1}
+  importScript:
+    type: File
+    default:
+      class: File
+      location: from_genbank_to_fasta_and_yaml.py
+    inputBinding: {position: 2}
+  dict:
+    type: Directory
+    default:
+      class: Directory
+      location: dict_ontology_standardization
+    inputBinding: {position: 3}
+outputs: []
+requirements:
+  DockerRequirement:
+    dockerPull: bh20-seq-uploader/import
+  NetworkAccess:
+    networkAccess: true
+  WorkReuse:
+    enableReuse: false
diff --git a/scripts/import_to_arvados.py b/scripts/import_to_arvados.py
new file mode 100644
index 0000000..78cd13d
--- /dev/null
+++ b/scripts/import_to_arvados.py
@@ -0,0 +1,14 @@
+import os
+import subprocess
+import glob
+import sys
+
+os.chdir(os.environ["TMPDIR"])
+os.symlink(sys.argv[2], "dict_ontology_standardization")
+subprocess.run(sys.argv[1])
+
+os.chdir("fasta_and_yaml")
+fasta_files = glob.glob("*.fasta")
+
+for f in fasta_files:
+    subprocess.run(["bh20-seq-uploader", f, "%s.yaml" %f[:-6]])
diff --git a/scripts/sequences.acc b/scripts/sequences.acc
index a99c4e6..697d868 100644
--- a/scripts/sequences.acc
+++ b/scripts/sequences.acc
@@ -1,4 +1,299 @@
 NC_045512
+MT394528
+MT394529
+MT394530
+MT394531
+MT394864
+MT396241
+MT396242
+MT396243
+MT396244
+MT396245
+MT396246
+MT396247
+MT396248
+MT396266
+MT380726
+MT380727
+MT380728
+MT380729
+MT380730
+MT380731
+MT380732
+MT380733
+MT380734
+MT385414
+MT385415
+MT385416
+MT385417
+MT385418
+MT385419
+MT385420
+MT385421
+MT385422
+MT385423
+MT385424
+MT385425
+MT385426
+MT385427
+MT385428
+MT385429
+MT385430
+MT385431
+MT385432
+MT385433
+MT385434
+MT385435
+MT385436
+MT385437
+MT385438
+MT385439
+MT385440
+MT385441
+MT385442
+MT385443
+MT385444
+MT385445
+MT385446
+MT385447
+MT385448
+MT385449
+MT385450
+MT385451
+MT385452
+MT385453
+MT385454
+MT385455
+MT385456
+MT385457
+MT385458
+MT385459
+MT385460
+MT385461
+MT385462
+MT385463
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+MT385465
+MT385466
+MT385467
+MT385468
+MT385469
+MT385470
+MT385471
+MT385472
+MT385473
+MT385474
+MT385475
+MT385476
+MT385477
+MT385478
+MT385479
+MT385480
+MT385481
+MT385482
+MT385483
+MT385484
+MT385485
+MT385486
+MT385487
+MT385488
+MT385489
+MT385490
+MT385491
+MT385492
+MT385493
+MT385494
+MT385495
+MT385496
+MT385497
+MT186683
+MT252677
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+MT252685
+MT252686
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+MT252690
+MT252691
+MT252692
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+MT252694
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+MT252696
+MT252697
+MT252698
+MT252699
+MT252700
+MT252701
+MT252702
+MT252703
+MT252704
+MT252705
+MT252706
+MT252707
+MT252708
+MT252709
+MT252710
+MT252711
+MT252712
+MT252713
+MT252715
+MT252716
+MT252717
+MT252719
+MT252721
+MT252723
+MT252725
+MT252726
+MT252728
+MT252729
+MT252730
+MT252733
+MT252734
+MT252735
+MT252736
+MT252737
+MT252738
+MT252739
+MT252740
+MT252741
+MT252742
+MT252745
+MT252746
+MT252747
+MT252748
+MT252749
+MT252756
+MT252757
+MT252758
+MT252761
+MT252763
+MT252764
+MT252765
+MT252766
+MT252767
+MT252768
+MT252769
+MT252770
+MT252771
+MT252772
+MT252773
+MT252774
+MT252775
+MT252778
+MT252779
+MT252780
+MT252781
+MT252782
+MT252783
+MT252784
+MT252785
+MT252787
+MT252788
+MT252792
+MT252793
+MT252794
+MT252795
+MT252797
+MT252798
+MT252799
+MT252800
+MT252801
+MT252802
+MT252803
+MT252804
+MT252805
+MT252806
+MT252807
+MT252808
+MT252809
+MT252810
+MT252811
+MT252821
+MT252822
+MT252823
+MT252824
+MT339043
+MT365033
+MT374101
+MT374102
+MT374103
+MT374104
+MT374105
+MT374106
+MT374107
+MT374108
+MT374109
+MT374110
+MT374111
+MT374112
+MT374113
+MT374114
+MT374115
+MT374116
+MT375428
+MT375429
+MT375430
+MT375431
+MT375432
+MT375433
+MT375434
+MT375435
+MT375436
+MT375437
+MT375438
+MT375439
+MT375440
+MT375441
+MT375442
+MT375443
+MT375444
+MT375445
+MT375446
+MT375447
+MT375448
+MT375449
+MT375450
+MT375451
+MT375452
+MT375453
+MT375454
+MT375455
+MT375456
+MT375457
+MT375458
+MT375459
+MT375460
+MT375461
+MT375462
+MT375463
+MT375464
+MT375465
+MT375466
+MT375467
+MT375468
+MT375469
+MT375470
+MT375471
+MT375472
+MT375473
+MT375474
+MT375475
+MT375476
+MT375477
+MT375478
+MT375479
+MT375480
+MT375481
+MT375482
+MT375483
 MT370516
 MT370517
 MT370518
@@ -225,6 +520,8 @@ MT372480
 MT372481
 MT372482
 MT372483
+7BV2_P
+7BV2_T
 LC542976
 LC542809
 MT114412