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add responses for private data
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@Vkale1
Vkale1 committed Dec 27, 2024
1 parent 4e8d108 commit 677001c
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40 changes: 40 additions & 0 deletions tests/fixtures/responses/private_run_from_assembly.xml
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<?xml version="1.0" encoding="UTF-8"?>
<ANALYSIS_SET>
<ANALYSIS alias="webin-genome-ERR4918394_62952e961c26f0859b4ebdd83d93e4e7" center_name="UNIVERSITY OF COPENHAGEN" accession="ERZ2626953">
<IDENTIFIERS>
<PRIMARY_ID>ERZ2626953</PRIMARY_ID>
<SUBMITTER_ID namespace="UNIVERSITY OF COPENHAGEN">webin-genome-ERR4918394_62952e961c26f0859b4ebdd83d93e4e7</SUBMITTER_ID>
</IDENTIFIERS>
<TITLE>Genome assembly: ERR4918394_62952e961c26f0859b4ebdd83d93e4e7</TITLE>
<STUDY_REF accession="ERP125469">
<IDENTIFIERS>
<PRIMARY_ID>ERP125469</PRIMARY_ID>
<SECONDARY_ID>PRJEB41657</SECONDARY_ID>
</IDENTIFIERS>
</STUDY_REF>
<SAMPLE_REF accession="ERS5444411">
<IDENTIFIERS>
<PRIMARY_ID>ERS5444411</PRIMARY_ID>
</IDENTIFIERS>
</SAMPLE_REF>
<RUN_REF accession="ERR4918394">
<IDENTIFIERS>
<PRIMARY_ID>ERR4918394</PRIMARY_ID>
</IDENTIFIERS>
</RUN_REF>
<ANALYSIS_TYPE>
<SEQUENCE_ASSEMBLY>
<NAME>ERR4918394_62952e961c26f0859b4ebdd83d93e4e7</NAME>
<TYPE>primary metagenome</TYPE>
<PARTIAL>false</PARTIAL>
<COVERAGE>17.0</COVERAGE>
<PROGRAM>metaSPAdes v3.14.1</PROGRAM>
<PLATFORM>DNBSEQ-G400</PLATFORM>
<MOL_TYPE>genomic DNA</MOL_TYPE>
</SEQUENCE_ASSEMBLY>
</ANALYSIS_TYPE>
<FILES>
<FILE checksum="62952e961c26f0859b4ebdd83d93e4e7" checksum_method="MD5" filename="ERZ262/ERZ2626953/ERR4918394.fasta.gz" filetype="fasta"/>
</FILES>
</ANALYSIS>
</ANALYSIS_SET>
159 changes: 159 additions & 0 deletions tests/fixtures/responses/private_sample.xml
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<?xml version="1.0" encoding="UTF-8"?>
<SAMPLE_SET>
<SAMPLE alias="SA01_02C1a_metaG" center_name="UNIVERSITY OF COPENHAGEN" accession="ERS5444411">
<IDENTIFIERS>
<PRIMARY_ID>ERS5444411</PRIMARY_ID>
<SUBMITTER_ID namespace="UNIVERSITY OF COPENHAGEN">SA01_02C1a_metaG</SUBMITTER_ID>
</IDENTIFIERS>
<TITLE>SA01.02C1a</TITLE>
<SAMPLE_NAME>
<TAXON_ID>1602388</TAXON_ID>
<SCIENTIFIC_NAME>fish gut metagenome</SCIENTIFIC_NAME>
</SAMPLE_NAME>
<DESCRIPTION>Salmon metagenomic DNA data from Distal gut content; animal SA01.02 from tank SA01 with treatment Tiger</DESCRIPTION>
<SAMPLE_ATTRIBUTES>
<SAMPLE_ATTRIBUTE>
<TAG>adapters</TAG>
<VALUE>AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA;GAACGACATGGCTACGATCCGACTT</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>collection date</TAG>
<VALUE>2019-06-11</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>geographic location (country and/or sea)</TAG>
<VALUE>Norway</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>geographic location (latitude)</TAG>
<VALUE>66.079905</VALUE>
<UNITS>DD</UNITS>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>geographic location (longitude)</TAG>
<VALUE>12.587848</VALUE>
<UNITS>DD</UNITS>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>geographic location (region and locality)</TAG>
<VALUE>Dønna; Nordland county</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>host body site</TAG>
<VALUE>Distal gut content</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>host common name</TAG>
<VALUE>Atlantic salmon</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>host diet</TAG>
<VALUE>Fermented algae meal (added in in oil coating)</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>host diet treatment</TAG>
<VALUE>Tiger: SA Control</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>host disease status</TAG>
<VALUE>Wounded:-</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>host scientific name</TAG>
<VALUE>Salmo salar</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>host subject id</TAG>
<VALUE>SA01.02</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>host taxid</TAG>
<VALUE>8030</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>host total mass</TAG>
<VALUE>290.4</VALUE>
<UNITS>g</UNITS>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>nucleic acid extraction</TAG>
<VALUE>D-rex protocol</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>pcr primers</TAG>
<VALUE>N/A</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>project name</TAG>
<VALUE>HoloFood Salmon - Metagenomic DNA</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>reference host genome for decontamination</TAG>
<VALUE>GCA_000000000.0</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>sample storage buffer</TAG>
<VALUE>Shield</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>sample storage container</TAG>
<VALUE>2ml E-matrix</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>sample storage location</TAG>
<VALUE>UCPH</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>sample storage temperature</TAG>
<VALUE>-20</VALUE>
<UNITS>°C</UNITS>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>sample volume or weight for DNA extraction</TAG>
<VALUE>0.2</VALUE>
<UNITS>mL</UNITS>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>sequencing method</TAG>
<VALUE>MGISEQ-2000</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>trial timepoint</TAG>
<VALUE>0</VALUE>
<UNITS>days</UNITS>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>host storage container temperature</TAG>
<VALUE>12.76</VALUE>
<UNITS>°C</UNITS>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>host storage container pH</TAG>
<VALUE>7.05</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>host gutted mass</TAG>
<VALUE>246.6</VALUE>
<UNITS>g</UNITS>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>host length</TAG>
<VALUE>29.5</VALUE>
<UNITS>cm</UNITS>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>host diet treatment concentration</TAG>
<VALUE>0</VALUE>
<UNITS>% mass</UNITS>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>host storage container</TAG>
<VALUE>LetSea Tank: Tiger</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>ENA-CHECKLIST</TAG>
<VALUE>ERC000052</VALUE>
</SAMPLE_ATTRIBUTE>
</SAMPLE_ATTRIBUTES>
</SAMPLE>
</SAMPLE_SET>
16 changes: 16 additions & 0 deletions tests/fixtures/responses/private_study.xml
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<?xml version="1.0" encoding="UTF-8"?>
<STUDY_SET>
<STUDY accession="ERP125469" alias="ena-STUDY-UNIVERSITY OF COPENHAGEN-02-12-2020-08:09:52:762-111" center_name="UNIVERSITY OF COPENHAGEN">
<IDENTIFIERS>
<PRIMARY_ID>ERP125469</PRIMARY_ID>
<SUBMITTER_ID namespace="UNIVERSITY OF COPENHAGEN">ena-STUDY-UNIVERSITY OF COPENHAGEN-02-12-2020-08:09:52:762-111</SUBMITTER_ID>
</IDENTIFIERS>
<DESCRIPTOR>
<STUDY_TITLE>HoloFood Salmon Trial A+B Gut Metagenome</STUDY_TITLE>
<STUDY_ABSTRACT>Metagenomic raw reads, assemblies, and bins derived from HoloFood salmon gut samples from trial A and B. The samples in this project contributed to the salmon MAG catalogue (project: PRJEB55376 [ERP140265]).</STUDY_ABSTRACT>
<STUDY_DESCRIPTION>Metagenomic raw reads, assemblies, and bins derived from HoloFood salmon gut samples from trial A and B. The samples in this project contributed to the salmon MAG catalogue (project: PRJEB55376 [ERP140265]).</STUDY_DESCRIPTION>
<CENTER_PROJECT_NAME>HoloFood Salmon Trial A+B Gut Metagenome</CENTER_PROJECT_NAME>
<STUDY_TYPE existing_study_type="Other"/>
</DESCRIPTOR>
</STUDY>
</STUDY_SET>
25 changes: 25 additions & 0 deletions tests/fixtures/responses/public_run_from_assembly.xml
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<ANALYSIS_SET>
<ANALYSIS accession="ERZ2626953" alias="webin-genome-ERR4918394_62952e961c26f0859b4ebdd83d93e4e7" center_name="UNIVERSITY OF COPENHAGEN">
<IDENTIFIERS>
<PRIMARY_ID>ERZ2626953</PRIMARY_ID>
<SUBMITTER_ID namespace="UNIVERSITY OF COPENHAGEN">webin-genome-ERR4918394_62952e961c26f0859b4ebdd83d93e4e7</SUBMITTER_ID>
</IDENTIFIERS>
<TITLE>Genome assembly: ERR4918394_62952e961c26f0859b4ebdd83d93e4e7</TITLE>
<STUDY_REF accession="ERP125469">
<IDENTIFIERS>
<PRIMARY_ID>ERP125469</PRIMARY_ID>
<SECONDARY_ID>PRJEB41657</SECONDARY_ID>
</IDENTIFIERS>
</STUDY_REF>
<SAMPLE_REF accession="ERS5444411">
<IDENTIFIERS>
<PRIMARY_ID>ERS5444411</PRIMARY_ID>
<EXTERNAL_ID namespace="BioSample">SAMEA7687881</EXTERNAL_ID>
</IDENTIFIERS>
</SAMPLE_REF>
<RUN_REF accession="ERR4918394">
<IDENTIFIERS>
<PRIMARY_ID>ERR4918394</PRIMARY_ID>
</IDENTIFIERS>
</RUN_REF>
<ANALYSIS_TYPE>
2 changes: 1 addition & 1 deletion tests/fixtures/responses/public_study.json
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"study_accession": "PRJEB41657",
"study_description": "Metagenomic raw reads, assemblies, and bins derived from HoloFood salmon gut samples from trial A and B. The samples in this project contributed to the salmon MAG catalogue (project: PRJEB55376 [ERP140265])."
}
]
]

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