feat: add otu schema support

virtool · Jul 16, 2024 · 4050c40 · 4050c40
1 parent 8441d10
commit 4050c40
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diff --git a/tests/__snapshots__/test_add.ambr b/tests/__snapshots__/test_add.ambr
@@ -1,27 +1,198 @@
 # serializer version: 1
-# name: TestCreateOTU.test_autofill
+# name: TestCreateOTU.test_empty_success
   dict({
     'acronym': '',
     'excluded_accessions': list([
     ]),
     'legacy_id': None,
-    'molecule': None,
     'name': 'Cabbage leaf curl Jamaica virus',
-    'schema': list([
+    'schema': None,
+    'taxid': 345184,
+  })
+# ---
+# name: TestCreateOTU.test_otu_autoschema[1278205-accessions0]
+  dict({
+    'acronym': '',
+    'excluded_accessions': list([
+    ]),
+    'isolates': list([
+      dict({
+        'legacy_id': None,
+        'name': dict({
+          'type': isolate,
+          'value': '4706174',
+        }),
+        'sequences': list([
+          dict({
+            'accession': 'NC_020160',
+            'definition': 'Dahlia latent viroid, complete sequence',
+            'legacy_id': None,
+            'segment': '',
+            'sequence': 'CAGGTCTTCTAAGGGTTCCTGTGGTGCCTCCCTCCAAGGCCGCGTAGGGAAAGAAAAAGTGAAAGAAAGTGTACCTGAAGAGAGAGAGACTCTCTGAGGAGCCCCGGGGCAACTCCGAGAGTGCTGCGGCAGGAGGAGCCGGGGGCGGAGGTTGTCTCGCTCTTGAGAGCTCCGCTCCTTGTAGCTTTGAGACTACCGCCCTTTTGCTTCCTTCTCGCTGGCTGACTCGAGGACGCGACCGGTGGTACACCAAGAGGTCTCCACCTCCTAGGGTACTTTTTTCTAACACCGATTCCGTACCGAGCGCCGGAGAGTGAAGCGCCCAGGGCTCCAAAGAAGCCC',
+          }),
+        ]),
+      }),
     ]),
+    'legacy_id': None,
+    'name': 'Dahlia latent viroid',
+    'schema': dict({
+      'molecule': dict({
+        'strandedness': 'single',
+        'topology': 'linear',
+        'type': 'RNA',
+      }),
+      'multipartite': False,
+      'segments': list([
+        dict({
+          'length': 342,
+          'name': 'Dahlia latent viroid',
+          'required': True,
+        }),
+      ]),
+    }),
+    'taxid': 1278205,
+  })
+# ---
+# name: TestCreateOTU.test_otu_autoschema[345184-accessions1]
+  dict({
+    'acronym': '',
+    'excluded_accessions': list([
+    ]),
+    'isolates': list([
+      dict({
+        'legacy_id': None,
+        'name': dict({
+          'type': isolate,
+          'value': 'CUc-3',
+        }),
+        'sequences': list([
+          dict({
+            'accession': 'DQ178610',
+            'definition': 'Cabbage leaf curl Jamaica virus clone 1910 Cu3-A8 segment DNA-A, complete sequence',
+            'legacy_id': None,
+            'segment': 'DNA-A',
+            'sequence': 'ACCGGATGGCCGCGATTTTTTGGAGTCATGCGTGGGACCACGCATTAAATGAAATCTAACCAATCACATGCCGCCTGAGAAGGTTAGATATTATGGCGTACTTAGTGCGCTGTGGGCCTATAAAAAGAAATGAAATTTCATTTTATGCTTTACTTCGAAATGCCTAAGCGGGATGCCCCGTGGCGTTCAATGGCGGGGACCTCTAAGGTGTCCCGCAATGCTAACTACTCACCTCGTGCAGGTATAACCCATAAATTTGATAAGGCCGCTGCCTGGGTTAACAGGCCCATGTACAGGAAGCCCAGGATTTATAGGATGTTTAGAAGCCCTGATGTTCCCAGAGGCTGTGAAGGCCCATGTAAGGTCCAATCTTATGAGCAGCGTCATGATATCTCACATGTTGGGAAGGTCATCTGCATTTCGGATATAACACGTGGCAATGGTATTACCCATCGTGTTGGGAAGCGTTTCTGCGTCAAGTCCGTCTACATTTTGGGCAAGATATGGATGGACGAGAATATCAAGCTCAAGAACCACACCAACAGTGTCATGTCTTGGTTGGTTAGGGACAGGAGACCTTATGGCACTCCTATGGAATTTGGGCAAGTGTTCAACATGTTCGACAACGAGCCCAGTACTGCTACTGTGAAGAACGATCTGCGTGATCGTTTTCAAGTCATGCATAAGTTCTACGCCAAGGTAACCGGTGGGCAGTATGCGAGTAACGAGCAGGCGCTGGTGAAGCGGTTCTGGAAGGTCAATAACTACGTGGTGTATAACCATCAAGAAGCAGGGAAATACGAGAATCATACGGAGAACGCTCTGTTATTGTATATGGCATGTACTCATGCCTCTAATCCTGTGTATGCGACATTGAAAATTCGGATCTATTTTTATGATTCGATAACAAATTAATAAATTTTGATTTTTATATCATGATTTTCGTGTACATGAGTTACATAGGATCTGTCCGTTGCGAAACGAACAGCTCTAATTACATGATTGATACCAATAACCCCTAGGTTATCTAAATGAGACATTACAAGGCATTTGAATCTACTTAAATATGTCGGCCCAGAAGCTCTCATCGAACTCGTCCAGACCTGGAAATTGAAGTAGGCTTTGTGGAGATCCAATGCTCTCCGTAGGTTGTGGTTGAACCGGACTTGGATGTGGTAGATCCTGGTTCTGGTGTACAACGGGTCCTCTACGCGTTGTATCTTGAAATACAGGGGATTTGGAACCTCCCAGATAAAAACGGAATTCTCTGCCTGAGCTACAGTGATGCTCTCCCCGGTGCGTGAATCCATTATCAGCGCAATTGATATGGAGGAAGATAGAACACCCGCAGTTCAAATCAATGCGTCTTCTGCGTACAGCTCTCCTTTTAGCAGTCTTGTGCTGTGCTTTGATAGAGGGGGGCTTCAAGGGTGATGAATTTCGCATTTTTGATAGTCCACGCTCTGAGTGATGCGTTTTCCTCTTTGTTGAGGAAACTTATATAACCGCTCCCCTCTCCTGGATTGCACAGCACGATTGAGGGTATGCCACCTTTAATTTGAACTGGTTTGCCGTACTTACAGTTTGATTGCCAGTCCCTTTGGGCCCCAATGAGCTCTTTCCAGTGCTTTAGCTTTAGATATTGCGGAGCTATGTCATCAATGACGTTATATTCCACATTATTTGAAAAGACCTTTGAATTAAAGTCGAGGTGCCCACTCAAATAATTATGTGGTCCTAATGCACGCGCCCACATGGTCTTGCCTGTTCGTGAATCACCTTCCACTATGATACTAATAGGTCTTTCCGGCCGCGCAGCGGCACTCCGACCAAAATAGTCATCTGCCCACTCTTGCATTTCGTCCGGGACGTTAGTAAAGGAGGAGAGGGGAAACGGAGGAGACCAAGGATCCGGAGCCTTACTGAAAATCCTATCGAGGTTACTGGATAGGTTGTGATACTGAAAAAGAAACTTCTCCGGGAGCTTTTCTTTAATGATTTTCATGGCCTCCTCCTTTGTTCCAGAGTTTAGTGCCTCGGCGGCTGCGTCGTTAGCTGTTTGCTGACCGCCTCTAGCACTTCTTCCGTCGATCTGGAACACTCCCCATTCAACTGTATCTCCGTCCTTGTCGATGTAGGACTTGACGTCGGAGCTGGATTTAGCTCCCTGTATGTTCGGATGGAAATGTGCTGACCGGGATGGGGAGACCAAGTCGAAGAATCTGTTATTCGTGCAGTTGTACTTCCCTTCGAACTGTATGAGAACGTGGATATGAGGCTCCCCATTTTCATGAAGCTCTCTGCATATTTTGATGAACTTCTTGTTCACCGGAGTGTTTATTTTTTGTAATTGGGAAAGTGCCTCTTCTTTGCTAAGAGAGCATCGTGGATACGTAAGGAAATAGTTTTTGGCTTTAACTGAGAAAGAGCCCTTTCGTGGCATATTTGTAAATATGGGTGTTCCCCCGATAGCTCTCTCGCTCAAAACTCCTATGAATTGGGGGAACTGGGGGAACTTATATAGTAGAAGTTCCTAAAGGCAAATCAACACGTGGCGGCCATCCGTTATAATATT',
+          }),
+          dict({
+            'accession': 'DQ178611',
+            'definition': 'Cabbage leaf curl Jamaica virus clone 1966 Cu3-B8 segment DNA-B, complete sequence',
+            'legacy_id': None,
+            'segment': 'DNA-B',
+            'sequence': 'ACCGGATGGCCGCAAATTTTTTGGCGTCCTGGTGCTGGGGACCATCTCCCGGCCCCCCTTGGCGCACTATCTCTCATCTTTCGACGTGGCGCGTCGATGAGCGTTGGCTAACGCTTATCTCGGTGTTAGACCTTTAATTTGAATTTCGAAATAATTGGTCGTATATATCTATCTTGACCGGTCTTTGTGACGACAAAGCTTCTGACACATTGTACGATATATTGAGCGTGGTCCAATTATATTTTCTCTGCGGAGTTAGACTATCGCTTATTGTTATTCATCTTGTCTATATAATGGACGATAGGTTAATAATTTAAATCGTCTTTGACAATAACATTTAAATAACAAATCATTTTGTAGAGGAGCTGAGAATAATGTATCCTACAAAGTTTAGGCGTGGGACTTCTTACTCTCATAGACGATTTGTTTCACGTAATCCCTCTTTTAAGCGTGGAACTTTGGTTAGACGCACTGATGGGAAACGTCGTAAAGGCCCATCAAGCAAAGCCCATGATGAGCCTAAAATGAAATTACAACGCATACATGAAAATCAATATGGGCCTGAATTTGTCATGACCCACAACTCAGCTCTTTCAACATTCATTAATTTCCCGGTACTTGGGAAGATCGAACCTAACCGAAGCAGGTCGTATATTAAGTTGAATCGTTTATTATTTAAGGGAACCGTTAAGATTGAGCGTGTGCACGCTGATGTGAACATGGACGGAGTAAGTTCGAAGATAGAAGGTGTGTTCTCTCTTGTTATTGTTATGGATCGCAAGCCACATTTGAGTTCCGCTGGAGGTTTGCATACATTTGATGAAATATTTGGTGCAAGAATCCACAGCCATGGTAACTTAGCTATTACACCCGGTTTGAAAGATCGTTATTACGTGCTCCATGTTTTCAAACGCGTATTGTCTGTGGAGAAAGACACTTTGATGGTGGATCTTGAAGGATCGACCATGATATCTAATAGGCGTTATAACTGTTGGGCCTCGTTTAACGATCTTGAACATGACTCATGTAACGGTGTTTATGCGAATATAAGCAAAAATGCCATTTTAGTTTACTATTGTTGGATGTCCGATGCTATGTCTAAGGCATCGACCTTTGTATCTTACGATCTTGATTATTTAGGTTAATCCTGAATAAAATGGCGTTAAGATTGAATATATACATAAAAAATAAAAACAAGCAATTTTATTGCAATGACTTTGGTTGTGTAGGATTACAATTATTGTTAATACATTCCTGGACCGTCGTCCTAACTAGCTCGCTTAATTGGGCCACTGACATCGTTATGGTTGATTGGGCCCTCTGTAATCCAGCTTGTGATGCTGAATCCCCGGGGTCTAATGCGCTAGTTCCTAGCTGGTTGAGTTCTCTATATGGATGTAGCGCATTCTCCACTTCTGATTCAGTTTGTGGGTTTGTAAGCCCAATAGTGCTCCTTGAAGCCCATGAATCACCTGGTTGTAATTCAATTGGGCCTGTTAGTCCAATTCTTGACAATGATCTGGACCTCAACGTTTTCCTCTCCCATTTTCCGTAGTCCACATGGGAGAAATCAACATCTCTATGTGAAAATTGTTTGGAGTGAATTTTCACTGTTGGTGCCCGGAAGGGTATATCCACTGAATGTTTAGCTGTTGACAATTTCAATTTCCCTTTAAACTTGGCAAAATGTGTTCGTTGATGCACATTTGTGTCGCTAACCCTGTAATAGAGTTTCCACGGAATAGGGTCTTTTAGCGAGAAGAATGAAGATGAAAAATAGTGGAGATCTATGTTGCATCTTAAGGGAAATGTCCAAGACGCCTGTAAGGATTCATCGTCAGTCATCCTCTTATCATGGATCTCTACAATCACCGTCCCGGTTGCGTTAATTGGTACTTGCTGTCTATATTCGATGACGCAATGGTCGATTTTCATACAGCTACGATTAAGCCTTGCTGTAAATTGCGCTGCAGTTGAAGGGAATTGCAGTACTATTTCAGTAAGATCATGACATAGCTGATATTCGTCTCTATGAGACTCTATGTAATTAAACGCATTTGGAGCATTTGCTAGCTGAGAATCCATCTATAGAAATCTGCCCGCGCAGCGGCAGAGGCTTCAATAATATCTGGGTTCAAGAATAATTGTGTTGAAGAACACAACAATGAAACGACTTGTTTCACAAGGAGGAAGAGAGAATATCTGGGCTTGTTAACAAGAAGAAAATAATGATATTTTAAAGGAATGATGAATATGTTATGTTATTCCGATAACATGAGTATAATAATCTAAGTCCACCTTGTTTATATAGAGAGTGATTTTCCAGAAGTTGGAAACGCCTTGAATTTCATTTTAGTGGCATTATTGTAAATATGGGTGTTCCCCCGATAGCGCTCTCGCTCAAAACTCCTATGAATTGGGGGAACTGGGGGAACTTATATAGTAGAAGTTCCTAAAGGCAAATCAACACGTGGCGGCCATCCGTTATAGTATT',
+          }),
+        ]),
+      }),
+    ]),
+    'legacy_id': None,
+    'name': 'Cabbage leaf curl Jamaica virus',
+    'schema': dict({
+      'molecule': dict({
+        'strandedness': 'double',
+        'topology': 'circular',
+        'type': 'DNA',
+      }),
+      'multipartite': True,
+      'segments': list([
+        dict({
+          'length': 2575,
+          'name': 'DNA-A',
+          'required': True,
+        }),
+        dict({
+          'length': 2494,
+          'name': 'DNA-B',
+          'required': True,
+        }),
+      ]),
+    }),
     'taxid': 345184,
   })
 # ---
-# name: TestCreateOTU.test_empty_success
+# name: TestCreateOTUCommands.test_autofill
   dict({
     'acronym': '',
     'excluded_accessions': list([
     ]),
     'legacy_id': None,
-    'molecule': None,
     'name': 'Cabbage leaf curl Jamaica virus',
-    'schema': list([
+    'schema': dict({
+      'molecule': dict({
+        'strandedness': 'double',
+        'topology': 'circular',
+        'type': 'DNA',
+      }),
+      'multipartite': True,
+      'segments': list([
+        dict({
+          'length': 2575,
+          'name': 'DNA-A',
+          'required': True,
+        }),
+        dict({
+          'length': 2494,
+          'name': 'DNA-B',
+          'required': True,
+        }),
+      ]),
+    }),
+    'taxid': 345184,
+  })
+# ---
+# name: TestCreateOTUCommands.test_autofill_with_schema
+  OTUSchema(molecule=Molecule(strandedness='double', type='DNA', topology='circular'), segments=[Segment(name='DNA-A', required=True, length=2575), Segment(name='DNA-B', required=True, length=2494)], multipartite=True)
+# ---
+# name: TestCreateOTUCommands.test_autoschema[1278205-accessions0]
+  dict({
+    'acronym': '',
+    'excluded_accessions': list([
     ]),
+    'legacy_id': None,
+    'name': 'Dahlia latent viroid',
+    'schema': dict({
+      'molecule': dict({
+        'strandedness': 'single',
+        'topology': 'linear',
+        'type': 'RNA',
+      }),
+      'multipartite': False,
+      'segments': list([
+        dict({
+          'length': 342,
+          'name': 'Dahlia latent viroid',
+          'required': True,
+        }),
+      ]),
+    }),
+    'taxid': 1278205,
+  })
+# ---
+# name: TestCreateOTUCommands.test_autoschema[345184-accessions1]
+  dict({
+    'acronym': '',
+    'excluded_accessions': list([
+    ]),
+    'legacy_id': None,
+    'name': 'Cabbage leaf curl Jamaica virus',
+    'schema': dict({
+      'molecule': dict({
+        'strandedness': 'double',
+        'topology': 'circular',
+        'type': 'DNA',
+      }),
+      'multipartite': True,
+      'segments': list([
+        dict({
+          'length': 2575,
+          'name': 'DNA-A',
+          'required': True,
+        }),
+        dict({
+          'length': 2494,
+          'name': 'DNA-B',
+          'required': True,
+        }),
+      ]),
+    }),
     'taxid': 345184,
   })
 # ---
@@ -32,10 +203,8 @@
       'excluded_accessions': list([
       ]),
       'legacy_id': None,
-      'molecule': None,
       'name': 'Cabbage leaf curl Jamaica virus',
-      'schema': list([
-      ]),
+      'schema': None,
       'taxid': 345184,
     }),
   ])

diff --git a/tests/files/src_test/00000002.json b/tests/files/src_test/00000002.json
@@ -1 +1 @@
-{"id":2,"data":{"id":"8f6fd0b9-8693-4c1b-927d-8c658fd19420","acronym":"","legacy_id":null,"molecule":null,"name":"Nanovirus-like particle","schema":[],"rep_isolate":null,"taxid":96892},"query":{"otu_id":"8f6fd0b9-8693-4c1b-927d-8c658fd19420"},"timestamp":"2024-05-22T23:54:16.279525","type":"CreateOTU"}
+{"id":2,"data":{"id":"1e8732c3-bb6c-4181-979b-36989df09978","acronym":"","legacy_id":null,"name":"Nanovirus-like particle","taxid":96892,"rep_isolate":null,"schema":null},"query":{"otu_id":"1e8732c3-bb6c-4181-979b-36989df09978"},"timestamp":"2024-07-02T22:07:21.862510","type":"CreateOTU"}
diff --git a/tests/files/src_test/00000003.json b/tests/files/src_test/00000003.json
@@ -1 +1 @@
-{"id":3,"data":{"id":"6d7cbc71-5408-4ef5-bfb0-be920b909a56","legacy_id":null,"name":{"type":"clone","value":"NOB-3"}},"query":{"otu_id":"8f6fd0b9-8693-4c1b-927d-8c658fd19420","isolate_id":"6d7cbc71-5408-4ef5-bfb0-be920b909a56"},"timestamp":"2024-05-22T23:54:16.498870","type":"CreateIsolate"}
+{"id":3,"data":{"id":"078ee644-dc52-4bb7-b847-dfe2f6b15bb8","legacy_id":null,"name":{"type":"clone","value":"NOB-3"}},"query":{"otu_id":"1e8732c3-bb6c-4181-979b-36989df09978","isolate_id":"078ee644-dc52-4bb7-b847-dfe2f6b15bb8"},"timestamp":"2024-07-02T22:07:22.082160","type":"CreateIsolate"}
diff --git a/tests/files/src_test/00000004.json b/tests/files/src_test/00000004.json
@@ -1 +1 @@
-{"id":4,"data":{"id":"ce3ce986-a39d-4ead-9b88-d35b772b4fde","accession":"NC_005954","definition":"Okra leaf curl alphasatellite rep gene for replication associated protein, clone NOB-3","legacy_id":null,"segment":"","sequence":"ACCCCGCCTCGAGACTTTAGCCCGAGACCCTCCGTACAGTTTTTTGTGCTCTCGCTTATATTTCTGTCTTCTGCGATAGATGGCTGCAATTAAGTCACATTGGTGGTGTTTCACGGTGTTCTTCCTCTCTGCTACTGCACCTGACTTGGTGCCTCTGTTCGAAAACACTCACGTGAGTTATGCTTGTTGGCAAGAAGAGGAGTCTCCGACGACGAAACGTCGCCACCTTCAAGGATACCTGCAATTGAAGGGTCAGAGGACCCTGAACCAGGTGAAGGCCATATTTGGGGATTTGAAGCCCCATCTTGAGAAACAGCGAGCTCGTAAGACAGACGATGCTCGCGATTACTGTATGAAACCCGAAACTAGGGTTTCTGGCCCCTTTGAATTTGGGGAATACTGTCCTGCTGGTTCTCACAAACGACGACAAAGGGAACTCGTAATTCGATCTCCGGTGAGAATGGCAGAGGAAAATCCGTCCGTCTTCCGACGAGTAAAGGCAAAGATTGCTGAGGAAGAATTCCAGAAGAGCGCTCATGAGATTCAAATTTCAAATTTGAAATCTTGGCAATCGCGCCTAAAGACGCTCCTGGAGAGGGACCCAGACGACCGCACTATTCTCTGGGTTTACGGACCTAATGGTGGGGAAGGGAAATCCACTTTCGCCAGAGACCTATACAGAAGTGGGTCCTGGTTCTATACACGTGGAGGATCTGCAGATAATGTAGCTTACCAGTACATAGGATGTTTAGGCAATAATATTGTATTTGATATTCCTCGTGATAAGAAGGAGTATCTTCAGTATAGTTTAATAGAGATGTTTAAGGATAGATTAATAGTTAGTAATAAGTACGAGCCTCTTATGGCCCCTTTGCTTAATTGTATTCATGTTGTAGTTATGTCTAATTTTCTCCCAGACTTTGAGAAGATTAGTCAGGATAGAGTCCATGTAATCCCATGTATACCATGTGGTGTTTGTCTTAAACACCATAATATTAATGATAAATGTGATGATTATGTGGATTAATTATTTTTGTTTCTTGAATACAAGAAAGAATGAAATGAAAAAAAAACAAAGAAAAAACATGAGCCTTCTATTATTTTAAGATAACAGTTGCCGCGCAGCGGCATTCAAAAAAAAAATGGAAAAGAAAAATAAAATGAAAAAGAAAAATAAAATGTCTTATTAAAACGACGACGTATTGAATAAATTGATCTGGGAGTAAAATGTAAATATTGGAAACTTGCGGGCTTGCGCTATAAATATTTAAAAGTTACGGTTAAGCGGAGTAAATGTAGAAGTCTTCAGGGGTATGTGTTTGCAATTATTTTGGTCTCTCAGCTATAAATAACACGTCACGAGGCGGGTGTAGTATT"},"query":{"otu_id":"8f6fd0b9-8693-4c1b-927d-8c658fd19420","isolate_id":"6d7cbc71-5408-4ef5-bfb0-be920b909a56","sequence_id":"ce3ce986-a39d-4ead-9b88-d35b772b4fde"},"timestamp":"2024-05-22T23:54:16.499208","type":"CreateSequence"}
+{"id":4,"data":{"id":"e560682d-eb77-4d78-8017-afc3e4524c0a","accession":"NC_005954","definition":"Okra leaf curl alphasatellite rep gene for replication associated protein, clone NOB-3","legacy_id":null,"segment":"","sequence":"ACCCCGCCTCGAGACTTTAGCCCGAGACCCTCCGTACAGTTTTTTGTGCTCTCGCTTATATTTCTGTCTTCTGCGATAGATGGCTGCAATTAAGTCACATTGGTGGTGTTTCACGGTGTTCTTCCTCTCTGCTACTGCACCTGACTTGGTGCCTCTGTTCGAAAACACTCACGTGAGTTATGCTTGTTGGCAAGAAGAGGAGTCTCCGACGACGAAACGTCGCCACCTTCAAGGATACCTGCAATTGAAGGGTCAGAGGACCCTGAACCAGGTGAAGGCCATATTTGGGGATTTGAAGCCCCATCTTGAGAAACAGCGAGCTCGTAAGACAGACGATGCTCGCGATTACTGTATGAAACCCGAAACTAGGGTTTCTGGCCCCTTTGAATTTGGGGAATACTGTCCTGCTGGTTCTCACAAACGACGACAAAGGGAACTCGTAATTCGATCTCCGGTGAGAATGGCAGAGGAAAATCCGTCCGTCTTCCGACGAGTAAAGGCAAAGATTGCTGAGGAAGAATTCCAGAAGAGCGCTCATGAGATTCAAATTTCAAATTTGAAATCTTGGCAATCGCGCCTAAAGACGCTCCTGGAGAGGGACCCAGACGACCGCACTATTCTCTGGGTTTACGGACCTAATGGTGGGGAAGGGAAATCCACTTTCGCCAGAGACCTATACAGAAGTGGGTCCTGGTTCTATACACGTGGAGGATCTGCAGATAATGTAGCTTACCAGTACATAGGATGTTTAGGCAATAATATTGTATTTGATATTCCTCGTGATAAGAAGGAGTATCTTCAGTATAGTTTAATAGAGATGTTTAAGGATAGATTAATAGTTAGTAATAAGTACGAGCCTCTTATGGCCCCTTTGCTTAATTGTATTCATGTTGTAGTTATGTCTAATTTTCTCCCAGACTTTGAGAAGATTAGTCAGGATAGAGTCCATGTAATCCCATGTATACCATGTGGTGTTTGTCTTAAACACCATAATATTAATGATAAATGTGATGATTATGTGGATTAATTATTTTTGTTTCTTGAATACAAGAAAGAATGAAATGAAAAAAAAACAAAGAAAAAACATGAGCCTTCTATTATTTTAAGATAACAGTTGCCGCGCAGCGGCATTCAAAAAAAAAATGGAAAAGAAAAATAAAATGAAAAAGAAAAATAAAATGTCTTATTAAAACGACGACGTATTGAATAAATTGATCTGGGAGTAAAATGTAAATATTGGAAACTTGCGGGCTTGCGCTATAAATATTTAAAAGTTACGGTTAAGCGGAGTAAATGTAGAAGTCTTCAGGGGTATGTGTTTGCAATTATTTTGGTCTCTCAGCTATAAATAACACGTCACGAGGCGGGTGTAGTATT"},"query":{"otu_id":"1e8732c3-bb6c-4181-979b-36989df09978","isolate_id":"078ee644-dc52-4bb7-b847-dfe2f6b15bb8","sequence_id":"e560682d-eb77-4d78-8017-afc3e4524c0a"},"timestamp":"2024-07-02T22:07:22.083889","type":"CreateSequence"}
diff --git a/tests/files/src_test/00000005.json b/tests/files/src_test/00000005.json
@@ -1 +1 @@
-{"id":5,"data":{"id":"edc1156c-5751-463f-a94a-2378cc482d67","acronym":"","legacy_id":null,"molecule":null,"name":"Saccharum streak virus","schema":[],"rep_isolate":null,"taxid":683179},"query":{"otu_id":"edc1156c-5751-463f-a94a-2378cc482d67"},"timestamp":"2024-05-22T23:54:16.716583","type":"CreateOTU"}
+{"id":5,"data":{"id":"da782177-7228-40fc-b172-132c5704342b","acronym":"","legacy_id":null,"name":"Saccharum streak virus","taxid":683179,"rep_isolate":null,"schema":null},"query":{"otu_id":"da782177-7228-40fc-b172-132c5704342b"},"timestamp":"2024-07-02T22:07:22.296775","type":"CreateOTU"}
diff --git a/tests/files/src_test/00000006.json b/tests/files/src_test/00000006.json
@@ -1 +1 @@
-{"id":6,"data":{"id":"2faf986b-2167-4a52-8b32-082c6347c2e3","legacy_id":null,"name":{"type":"isolate","value":"SacSV_ZA_Emp_T1_2008"}},"query":{"otu_id":"edc1156c-5751-463f-a94a-2378cc482d67","isolate_id":"2faf986b-2167-4a52-8b32-082c6347c2e3"},"timestamp":"2024-05-22T23:54:16.923267","type":"CreateIsolate"}
+{"id":6,"data":{"id":"b505e5fa-4bee-4fc3-82c6-b4f026d54f56","legacy_id":null,"name":{"type":"isolate","value":"SacSV_ZA_Emp_T1_2008"}},"query":{"otu_id":"da782177-7228-40fc-b172-132c5704342b","isolate_id":"b505e5fa-4bee-4fc3-82c6-b4f026d54f56"},"timestamp":"2024-07-02T22:07:22.507805","type":"CreateIsolate"}