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manuleramanulera
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Remap file ids in migration to v0.4.0 (#58)
* remap file ids * include example with files for when tests run
1 parent 6f55510 commit 83e09e2

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Lines changed: 351 additions & 0 deletions

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‎src/data/examples/cloning_strategy_with_files.json‎

Lines changed: 63 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,63 @@
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{
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"sequences": [
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{
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"id": 1,
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"type": "TextFileSequence",
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"sequence_file_format": "genbank",
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"overhang_crick_3prime": 0,
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"overhang_watson_3prime": 0,
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"file_content": "LOCUS name 2026 bp DNA linear SYN 27-JAN-2025\nDEFINITION description.\nACCESSION name\nVERSION name\nKEYWORDS .\nSOURCE \n ORGANISM .\n .\nFEATURES Location/Qualifiers\n gene 1..338\n /label=\"prl103\"\n /locus_tag=\"SPOM_SPNCRNA.1708\"\n /gene_synonym=\"prl3; SPNCRNA.5498\"\n /db_xref=\"GeneID:90818481\"\n /db_xref=\"PomBase:SPNCRNA.1708\"\n ncRNA 1..338\n /label=\"prl103\"\n /ncRNA_class=\"lncRNA\"\n /locus_tag=\"SPOM_SPNCRNA.1708\"\n /gene_synonym=\"prl3; SPNCRNA.5498\"\n /product=\"Pdc2-Repressed lncRNA, antisense to Mat1-Mi\"\n /transcript_id=\"NR_191361.1\"\n /db_xref=\"GeneID:90818481\"\n /db_xref=\"PomBase:SPNCRNA.1708\"\n gene complement(210..338)\n /label=\"mat1-Mi\"\n /locus_tag=\"SPOM_SPBC23G7.17C\"\n /gene_synonym=\"mat1-Mm; matMi; matMm\"\n /db_xref=\"GeneID:3361261\"\n /db_xref=\"PomBase:SPBC23G7.17c\"\n mRNA complement(210..338)\n /label=\"mat1-Mi\"\n /locus_tag=\"SPOM_SPBC23G7.17C\"\n /gene_synonym=\"mat1-Mm; matMi; matMm\"\n /product=\"M-specific transcription factor Mi\"\n /transcript_id=\"NM_001021772.1\"\n /db_xref=\"GeneID:3361261\"\n /db_xref=\"PomBase:SPBC23G7.17c\"\n CDS complement(210..338)\n /label=\"mat1-Mi\"\n /locus_tag=\"SPOM_SPBC23G7.17C\"\n /gene_synonym=\"mat1-Mm; matMi; matMm\"\n gene 473..1018\n /label=\"mat1-Mc\"\n /locus_tag=\"SPOM_SPBC23G7.09\"\n /gene_synonym=\"mat1Mc; matMc\"\n /db_xref=\"GeneID:2539619\"\n /db_xref=\"PomBase:SPBC23G7.09\"\n mRNA 473..1018\n /label=\"mat1-Mc\"\n /locus_tag=\"SPOM_SPBC23G7.09\"\n /gene_synonym=\"mat1Mc; matMc\"\n /product=\"M-specific transcription factor Mc\"\n /transcript_id=\"NM_001021773.3\"\n /db_xref=\"GeneID:2539619\"\n /db_xref=\"PomBase:SPBC23G7.09\"\n CDS 473..1018\n /label=\"mat1-Mc\"\n /locus_tag=\"SPOM_SPBC23G7.09\"\n /gene_synonym=\"mat1Mc; matMc\"\n primer_bind 1279..1298\n /label=\"Msmt0-RF-Fw\"\n /note=\"sequence: ATACATGGATTTTACTGCCC\"\n primer_bind complement(1510..1529)\n /label=\"smt0-RF-Rv\"\n /note=\"sequence: ATGGTTGAGGAAGTGGAACG\"\nORIGIN\n 1 tagtgggtta gccgtgaaag gaaaagagag tgagaagaag ggtaggaaaa gaagagagag\n 61 tagttgaagg aaaaatattg gaagaggtag tatttttctg tatgcatatg catatgcatt\n 121 tgtatagcat acaaccttta atttaatagc catacaacct aatagccaga aacgccttcc\n 181 caatttactg aaccctgctt atatgtagtt tataattgtt gtgtcttttt tttacgttta\n 241 agttgtaatt tgatgttaga atttattaca atggatgcaa gttttaactc aatttgatca\n 301 cataggattt gaattgtaaa aaggtcttct gctgacatta ttagtatgta ttgtgcttta\n 361 gattaaatta ttgtgtttta gtgtattttg ttcctttgtt tttgggtttc tttgttctgt\n 421 aagtagttaa ataccctcca cactctacac ctaccttgca ctcacaacta caatggactc\n 481 acaccaagaa ttatcagcgg gttcccctat ttcctacgac tttttagatc cagactggtg\n 541 ttttaaaaga taccttacaa aggatgctct tcattcaatt gaaactggca aaggtgctgc\n 601 ttactttgtt cctgatggct ttactcctat actcattcct aactcacaaa gctacctgtt\n 661 ggatgggaat tctgcacaac tgccaagacc tcaaccaata tccttcacat tggatcaatg\n 721 taaagttccc ggctatattt tgaagagttt acggaaagac actacgtcta ctgaacgtac\n 781 tccgagaccc cctaatgctt ttatattata caggaaggaa aaacatgcta cattattaaa\n 841 gtctaaccct tccatcaata attcacaagt ttccaagctg gttggagaga tgtggagaaa\n 901 cgaatcaaag gaagtacgta tgcgatattt taagatgtct gagttttata aagcacaaca\n 961 tcagaaaatg taccctggtt ataagtacca gcctagaaag aataaagtta aaagataata\n 1021 atggtaatat ttatggtatt taataaagaa ttttgaaatt gatttaaata tgcttcttag\n 1081 agttacattc actgaagatt ataatgtaat attttgtgta ccccatttgc gttgagttat\n 1141 tctatagtaa ttattgtgtg ttctattaac gatgtattgc gatttatatc tgttatgcta\n 1201 acataacgta gttctaagca ctgtaatgcc atactgtttt agagggtgat gcttcctaaa\n 1261 atctccttac ataaagtaat acatggattt tactgccctg attctatcga aatatgctgt\n 1321 tttttttatt cgtttttatt tattttcaat aatttttttg taatataaat gtatagccat\n 1381 acatcttgaa ctccttacac caatacttca tatccattag ccattttcct ttataaacat\n 1441 atattaaacc tcatcccaaa tgcatctacc cactctttac attcacatcc ctattccttt\n 1501 aatatcttac gttccacttc ctcaaccata gagcattctt tataaatcac tttaatatgc\n 1561 tttacttcca cacactactg ctaccattgc cttgcacagt actcccctta ctcacacacc\n 1621 ttcaatcaca ctcctatctc catacaggac ccaacatgta ttaaacatta tccccctaca\n 1681 ccattttccc tcatcatcca atatgtttct actattatca cacaccgtct ctacctcccg\n 1741 ccaattttaa ctgtcttcat ttccacctac aactctctat ccacactttc tcaccctata\n 1801 aacatttaat acactcctac aatataccat cccatcctat tatcatatat actcctcctt\n 1861 ctcagatcac atcctctcca actccattca cacatctttt tctttacaca ccctcaccca\n 1921 cgctctccat acctcacgca aaccaatata cacataccca actcacacta aaaaattaaa\n 1981 ttttacctat ctattaaaga tatttaccct gtgttgtacc taatcc\n//"
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}
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],
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"sources": [
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{
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"id": 1,
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"type": "UploadedFileSource",
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"output_name": null,
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"database_id": null,
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"input": [],
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"sequence_file_format": "genbank",
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"file_name": "final_product.gb",
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"index_in_file": 0,
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"circularize": false,
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"coordinates": null
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}
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],
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"primers": [],
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"description": "",
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"files": [
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{
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"type": "SequencingFile",
31+
"sequence_id": 1,
32+
"file_name": "BZO902_13409020_13409020.ab1",
33+
"file_type": "Sequencing file",
34+
"alignment": [
35+
"tagtgggttagccgtgaaaggaaaagagagtgagaagaagggtaggaaaagaagagagagtagttgaaggaaaaatattggaagaggtagtatttttctgtatgcatatgcatatgcatttgtatagcatacaacctttaatttaatagccatacaacctaatagccagaaacgccttcccaatttactgaaccctgcttatatgtagtttataattgttgtgtcttttttttacgtttaagttgtaatttgatgttagaatttattacaatggatgcaagttttaactcaatttgatcacataggatttgaattgtaaaaaggtcttctgctgacattattagtatgtattgtgctttagattaaattattgtgttttagtgtattttgttcctttgtttttgggtttctttgttctgtaagtagttaaataccctccacactctacacctaccttgcactcacaactacaatggactcacaccaagaattatcagcgggttcccctatttcctacgactttttagatccagactggtgttttaaaagataccttacaaaggatgctcttcattcaattgaaactggcaaaggtgctgcttactttgttcctgatggctttactcctatactcattcctaactcacaaagctacctgttggatgggaattctgcacaactgccaagacctcaaccaatatccttcacattggatcaatgtaaagttcccggctatattttgaagagtttacggaaagacactacgtctactgaacgtactccgagaccccctaatgcttttatattatacaggaaggaaaaacatgctacattattaaagtctaacccttccatcaataattcacaagtttccaagctggttggagagatgtggagaaacgaatcaaaggaagtacgtatgcgatattttaagatgtctgagttttataaagcacaacatcagaaaatgtaccctggttataagtaccagcctagaaagaataaagttaaaagataataatggtaatatttatggtatttaataaagaattttgaaattgatttaaatatgcttcttagagttacattcactgaagattataatgtaatattttgtgtaccccatttgcgttgagttattctatagtaattattgtgtgttctattaacgatgtattgcgatttatatctgttatgctaacataacgtagttctaagcactgtaatgccatactgttttagagggtgatgcttcctaaaatctccttacataaagtaatacatggattttactgccctgattctatcgaaatatgctgttttttttattcgtttttatttattttcaataatttttttgtaatataaatgtatag---------ccatacatcttgaactccttacaccaatacttcatatccattagccattttcctttataaacatatattaaacctcatcccaaatgcatctacccactctttacattcacatccctattcctttaatatcttacgttccacttcctcaaccatagagcattctttataaatcactttaatatgctttacttccacacactactgctaccattgccttgcacagtactccccttactcacacaccttcaatcacactcctatctccatacaggacccaacatgtattaaacattatccccctacaccattttccctcatcatccaatatgtttctactattatcacacaccgtctctacctcccgccaattttaactgtcttcatttccacctacaactctctatccacactttctcaccctataaacatttaatacactcctacaatataccatcccatcctattatcatatatactcctccttctcagatcacatcctctccaactccattcacacatctttttctttacacaccctcacccacgctctccatacctcacgcaaaccaatatacacatacccaactcacactaaaaaattaaattttacctatctattaaagatatttaccctgtgttgtacctaatcc",
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"---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttgttcta----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aggcactgtaatgccatactgttttagagggtgatgcttcctaaaatctccttacataaagtaatacatggattttactgccctgattctatcgaaatatgctgttttttttattcgtttttatttattttcaataatttttttgtaatataaatgtatagtctttctccccatacatcttgaactccttacaccaatacttcatatccattagccattttcctttataaacatatattaaacctcatcccaaatgcatctacccactctttacattcacatccctattcctttaatatcttacgttccacttcctcaaccatagagcattctttataaatcactttaattagctt------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------acttcccccccggg------------------------------------------------------------------------------------------------------------------------------------------------"
37+
]
38+
},
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{
40+
"type": "SequencingFile",
41+
"sequence_id": 1,
42+
"file_name": "BZO903_13409037_13409037.ab1",
43+
"file_type": "Sequencing file",
44+
"alignment": [
45+
"tagtgggttagccgtgaaaggaaaagagagtgagaagaagggtaggaaaagaagagagagtagttgaaggaaaaatattggaagaggtagtatttttctgtatgcatatgcatatgcatttgtatagcatacaacctttaatttaatagccatacaacctaatagccagaaacgccttcccaatttactgaaccctgcttatatgtagtttataattgttgtgtcttttttttacgtttaagttgtaatttgatgttagaatttattacaatggatgcaagttttaactcaatttgatcacataggatttgaattgtaaaaaggtcttctgctgacattattagtatgtattgtgctttagattaaattattgtgttttagtgtattttgttcctttgtttttgggtttctttgttctgtaagtagttaaataccctccacactctacacctaccttgcactcacaactacaatggactcacaccaagaattatcagcgggttcccctatttcctacgactttttagatccagactggtgttttaaaagataccttacaaaggatgctcttcattcaattgaaactggcaaaggtgctgcttactttgttcctgatggctttactcctatactcattcctaactcacaaagctacctgttggatgggaattctgcacaactgccaagacctcaaccaatatccttcacattggatcaatgtaaagttcccggctatattttgaagagtttacggaaagacactacgtctactgaacgtactccgagaccccctaatgcttttatattatacaggaaggaaaaacatgctacattattaaagtctaacccttccatcaataattcacaagtttccaagctggttggagagatgtggagaaacgaatcaaaggaagtacgtatgcgatattttaagatgtctgagttttataaagcacaacatcagaaaatgtaccctggttataagtaccagcctagaaagaataaagttaaaagataataatggtaatatttatggtatttaataaagaattttgaaattgatttaaatatgcttcttagagttacattcactgaagattataatgtaatattttgtgtaccccatttgcgttgagttattctatagtaattattgtgtgttctattaacgatgtattgcgatttatatctgttatgctaacataacgtagttctaagcactgtaatgccatactgttttagagggtgatgcttcctaaaatctccttacataaagtaatacatggattttactgccctgattctatcgaaatatgctgttttttttattcgtttttatttattttcaataatttttttgtaatataaatgtatag---------ccatacatcttgaactccttacaccaatacttcatatccattagccattttcctttataaacatatattaaacctcatcccaaatgcatctacccactctttacattcacatccctattcctttaatatcttacgttccacttcctcaaccatagagcattctttataaatcactttaatatgctttacttccacacactactgctaccattgccttgcacagtactccccttactcacacaccttcaatcacactcctatctccatacaggacccaacatgtattaaacattatccccctacaccattttccctcatcatccaatatgtttctactattatcacacaccgtctctacctcccgccaattttaactgtcttcatttccacctacaactctctatccacactttctcaccctataaacatttaatacactcctacaatataccatcccatcctattatcatatatactcctccttctcagatcacatcctctccaactccattcacacatctttttctttacacaccctcacccacgctctccatacctcacgcaaaccaatatacacatacccaactcacactaaaaaattaaattttacctatctattaaagatatttaccctgtgttgtacctaatcc",
46+
"---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttgttcta----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aggccctgtaatgccatactgttttagagggtgatgcttcctaaaatctccttacataaagtaatacatggattttactgccctgattctatcgaaatatgctgttttttttattcgtttttatttattttcaataatttttttgtaatataaatgtatagtctttctccccatacatcttgaactccttacaccaatacttcatatccattagccattttcctttataaacatatattaaacctcatcccaaatgcatctacccactctttacattcacatccctattcctttaatatcttacgttccacttcctcaaccatagagcattctttataaatcactttaatatgctt------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------attccccctcggg-------------------------------------------------------------------------------------------------------------------------------------------------"
47+
]
48+
},
49+
{
50+
"type": "SequencingFile",
51+
"sequence_id": 1,
52+
"file_name": "BZO904_13409044_13409044.ab1",
53+
"file_type": "Sequencing file",
54+
"alignment": [
55+
"tagtgggttagccgtgaaaggaaaagagagtgagaagaagggtaggaaaagaagagagagtagttgaaggaaaaatattggaagaggtagtatttttctgtatgcatatgcatatgcatttgtatagcatacaacctttaatttaatagccatacaacctaatagccagaaacgccttcccaatttactgaaccctgcttatatgtagtttataattgttgtgtcttttttttacgtttaagttgtaatttgatgttagaatttattacaatggatgcaagttttaactcaatttgatcacataggatttgaattgtaaaaaggtcttctgctgacattattagtatgtattgtgctttagattaaattattgtgttttagtgtattttgttcctttgtttttgggtttctttgttctgtaagtagttaaataccctccacactctacacctaccttgcactcacaactacaatggactcacaccaagaattatcagcgggttcccctatttcctacgactttttagatccagactggtgttttaaaagataccttacaaaggatgctcttcattcaattgaaactggcaaaggtgctgcttactttgttcctgatggctttactcctatactcattcctaactcacaaagctacctgttggatgggaattctgcacaactgccaagacctcaaccaatatccttcacattggatcaatgtaaagttcccggctatattttgaagagtttacggaaagacactacgtctactgaacgtactccgagaccccctaatgcttttatattatacaggaaggaaaaacatgctacattattaaagtctaacccttccatcaataattcacaagtttccaagctggttggagagatgtggagaaacgaatcaaaggaagtacgtatgcgatattttaagatgtctgagttttataaagcacaacatcagaaaatgtaccctggttataagtaccagcctagaaagaataaagttaaaagataataatggtaatatttatggtatttaataaagaattttgaaattgatttaaatatgcttcttagagttacattcactgaagattataatgtaatattttgtgtaccccatttgcgttgagttattctatagtaattattgtgtgttctattaacgatgtattgcgatttatatctgttatgctaacataacgtagttctaagcactgtaatgccatactgttttagagggtgatgcttcctaaaatctccttacataaagtaatacatggattttactgccctgattctatcgaaatatgctgttttttttattcgtttttatttattttcaataatttttttgtaatataaatgtatag---------ccatacatcttgaactccttacaccaatacttcatatccattagccattttcctttataaacatatattaaacctcatcccaaatgcatctacccactctttacattcacatccctattcctttaatatcttacgttccacttcctcaaccatagagcattctttataaatcactttaatatgctttacttccacacactactgctaccattgccttgcacagtactccccttactcacacaccttcaatcacactcctatctccatacaggacccaacatgtattaaacattatccccctacaccattttccctcatcatccaatatgtttctactattatcacacaccgtctctacctcccgccaattttaactgtcttcatttccacctacaactctctatccacactttctcaccctataaacatttaatacactcctacaatataccatcccatcctattatcatatatactcctccttctcagatcacatcctctccaactccattcacacatctttttctttacacaccctcacccacgctctccatacctcacgcaaaccaatatacacatacccaactcacactaaaaaattaaattttacctatctattaaagatatttaccctgtgttgtacctaatcc",
56+
"-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gtttgttcta----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aggccatgtaatgccatactgttttagagggtgatgcttcctaaaatctccttacataaagtaatacatggattttactgccctgattctatcgaaatatgctgttttttttattcgtttttatttattttcaataatttttttgtaatataaatgtatagtctttctccccatacatcttgaactccttacaccaatacttcatatccattagccattttcctttataaacatatattaaacctcatcccaaatgcatctacccactctttacattcacatccctattcctttaatatcttacgttccacttcctcaaccatagagcattctttataaatcactttaattagctt------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------acttcccccccggg------------------------------------------------------------------------------------------------------------------------------------------------"
57+
]
58+
}
59+
],
60+
"schema_version": "0.4.0",
61+
"backend_version": null,
62+
"frontend_version": null
63+
}

‎src/opencloning_linkml/migrations/transformations/v0_2_9_to_v_0_4_0.py‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -104,6 +104,10 @@ def migrate_0_2_9_to_0_4_0(data: dict) -> dict:
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for sequence in old_dict["sequences"]:
105105
sequence["id"] = sequence_id_map[sequence["id"]]
106106

107+
if "files" in old_dict and old_dict["files"] is not None:
108+
for file in old_dict["files"]:
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file["sequence_id"] = sequence_id_map[file["sequence_id"]]
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107111
# Ids of primers cannot clash with sequences anymore
108112
latest_id = len(sorted_sources)
109113
for i, primer in enumerate(old_dict["primers"]):

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