Pre hackathon - Githubissues

Preparations for the BioHackathon:

Implementation of the password manager

Example response BioSamples Submission:

{'targetRepository': 'biosamples', 'accessions': [{'id': 'SAMEA131432416'}, {'id': 'SAMEA131432417'}]}

Example response ENA submission (I don't have a valid ISA JSON):

{'targetRepository': 'ena.embl', 'errors': [{'type': 'INVALID_METADATA', 'message': "Failed to validate experiment xml, error: Expected element 'LIBRARY_STRATEGY' before the end of the content in element LIBRARY_DESCRIPTOR"}, {'type': 'INVALID_METADATA', 'message': "Failed to validate experiment xml, error: Expected element 'LIBRARY_STRATEGY' before the end of the content in element LIBRARY_DESCRIPTOR"}, {'type': 'INVALID_METADATA', 'message': "Failed to validate experiment xml, error: Expected element 'LIBRARY_STRATEGY' before the end of the content in element LIBRARY_DESCRIPTOR"}], 'info': [], 'accessions': []}

From the ENA service logs:

isa_sra-1         | <?xml version="1.0" encoding="UTF-8"?>
isa_sra-1         | 
isa_sra-1         | <WEBIN>
isa_sra-1         |   <SUBMISSION>
isa_sra-1         |     <ACTIONS>
isa_sra-1         |       <ACTION>
isa_sra-1         |         <ADD/>
isa_sra-1         |       </ACTION>
isa_sra-1         |     </ACTIONS>
isa_sra-1         |   </SUBMISSION>
isa_sra-1         |   <STUDY_SET>
isa_sra-1         |     <STUDY alias="Simple ENA use-case-0.8911644804211576">
isa_sra-1         |       <DESCRIPTOR>
isa_sra-1         |         <STUDY_TITLE>Simple ENA use-case</STUDY_TITLE>
isa_sra-1         |         <STUDY_DESCRIPTION></STUDY_DESCRIPTION>
isa_sra-1         |         <STUDY_ABSTRACT></STUDY_ABSTRACT>
isa_sra-1         |         <STUDY_TYPE existing_study_type="Other"/>
isa_sra-1         |       </DESCRIPTOR>
isa_sra-1         |       <STUDY_ATTRIBUTES>
isa_sra-1         |         <STUDY_ATTRIBUTE>
isa_sra-1         |           <TAG>ena_sample_alias_prefix</TAG>
isa_sra-1         |           <VALUE>https://datahub.elixir-belgium.org/samples/</VALUE>
isa_sra-1         |         </STUDY_ATTRIBUTE>
isa_sra-1         |         <STUDY_ATTRIBUTE>
isa_sra-1         |           <TAG>SEEK Study ID</TAG>
isa_sra-1         |           <VALUE>3</VALUE>
isa_sra-1         |         </STUDY_ATTRIBUTE>
isa_sra-1         |         <STUDY_ATTRIBUTE>
isa_sra-1         |           <TAG>SEEK creation date</TAG>
isa_sra-1         |           <VALUE>2024-02-16T13:02:09Z</VALUE>
isa_sra-1         |         </STUDY_ATTRIBUTE>
isa_sra-1         |       </STUDY_ATTRIBUTES>
isa_sra-1         |     </STUDY>
isa_sra-1         |   </STUDY_SET>
isa_sra-1         |   <EXPERIMENT_SET>
isa_sra-1         |     <EXPERIMENT alias="#other_material/5-0.8911644804211576">
isa_sra-1         |       <TITLE>Mouse library 1</TITLE>
isa_sra-1         |       <STUDY_REF refname="Simple ENA use-case-0.8911644804211576"/>
isa_sra-1         |       <DESIGN>
isa_sra-1         |         <DESIGN_DESCRIPTION>ISA-Test</DESIGN_DESCRIPTION>
isa_sra-1         |         <SAMPLE_DESCRIPTOR/>
isa_sra-1         |         <LIBRARY_DESCRIPTOR/>
isa_sra-1         |       </DESIGN>
isa_sra-1         |       <PLATFORM>
isa_sra-1         |         <OXFORD_NANOPORE>
isa_sra-1         |           <INSTRUMENT_MODEL>MinION</INSTRUMENT_MODEL>
isa_sra-1         |         </OXFORD_NANOPORE>
isa_sra-1         |       </PLATFORM>
isa_sra-1         |     </EXPERIMENT>
isa_sra-1         |     <EXPERIMENT alias="#other_material/6-0.8911644804211576">
isa_sra-1         |       <TITLE>Human library 1</TITLE>
isa_sra-1         |       <STUDY_REF refname="Simple ENA use-case-0.8911644804211576"/>
isa_sra-1         |       <DESIGN>
isa_sra-1         |         <DESIGN_DESCRIPTION>ISA-Test</DESIGN_DESCRIPTION>
isa_sra-1         |         <SAMPLE_DESCRIPTOR/>
isa_sra-1         |         <LIBRARY_DESCRIPTOR/>
isa_sra-1         |       </DESIGN>
isa_sra-1         |       <PLATFORM>
isa_sra-1         |         <OXFORD_NANOPORE>
isa_sra-1         |           <INSTRUMENT_MODEL>MinION</INSTRUMENT_MODEL>
isa_sra-1         |         </OXFORD_NANOPORE>
isa_sra-1         |       </PLATFORM>
isa_sra-1         |     </EXPERIMENT>
isa_sra-1         |     <EXPERIMENT alias="#other_material/7-0.8911644804211576">
isa_sra-1         |       <TITLE>Human library 2</TITLE>
isa_sra-1         |       <STUDY_REF refname="Simple ENA use-case-0.8911644804211576"/>
isa_sra-1         |       <DESIGN>
isa_sra-1         |         <DESIGN_DESCRIPTION>ISA-Test</DESIGN_DESCRIPTION>
isa_sra-1         |         <SAMPLE_DESCRIPTOR/>
isa_sra-1         |         <LIBRARY_DESCRIPTOR/>
isa_sra-1         |       </DESIGN>
isa_sra-1         |       <PLATFORM>
isa_sra-1         |         <OXFORD_NANOPORE>
isa_sra-1         |           <INSTRUMENT_MODEL>MinION</INSTRUMENT_MODEL>
isa_sra-1         |         </OXFORD_NANOPORE>
isa_sra-1         |       </PLATFORM>
isa_sra-1         |     </EXPERIMENT>
isa_sra-1         |   </EXPERIMENT_SET>
isa_sra-1         |   <RUN_SET>
isa_sra-1         |     <RUN alias="#assay/10_11-0.8911644804211576">
isa_sra-1         |       <TITLE>#assay/10_11</TITLE>
isa_sra-1         |       <EXPERIMENT_REF refname="#other_material/7"/>
isa_sra-1         |       <DATA_BLOCK>
isa_sra-1         |         <FILES>
isa_sra-1         |           <FILE filename="Raw data Human Rev" filetype="fastq" checksum_method="MD5" checksum=""/>
isa_sra-1         |         </FILES>
isa_sra-1         |       </DATA_BLOCK>
isa_sra-1         |     </RUN>
isa_sra-1         |   </RUN_SET>
isa_sra-1         |   <PROJECT_SET>
isa_sra-1         |     <PROJECT alias="ISA Compliant Test investigation 1-0.8911644804211576">
isa_sra-1         |       <TITLE>ISA Compliant Test investigation 1</TITLE>
isa_sra-1         |       <DESCRIPTION></DESCRIPTION>
isa_sra-1         |       <SUBMISSION_PROJECT>
isa_sra-1         |         <SEQUENCING_PROJECT/>
isa_sra-1         |       </SUBMISSION_PROJECT>
isa_sra-1         |     </PROJECT>
isa_sra-1         |   </PROJECT_SET>
isa_sra-1         | </WEBIN>

elixir-europe / MARS

Pre hackathon #54