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assays > processSequence > parameterValues are not being parsed by the ENA endpoint #73

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bedroesb opened this issue Nov 7, 2024 · 0 comments

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bedroesb commented Nov 7, 2024

              {
                "@id": "#parameter/349",
                "parameterName": {
                  "annotationValue": "library_construction_protocol",
                  "termAccession": "",
                  "termSource": ""
                }
              },
              {
                "@id": "#parameter/351",
                "parameterName": {
                  "annotationValue": "design_description",
                  "termAccession": "",
                  "termSource": ""
                }
              },
              {
                "@id": "#parameter/352",
                "parameterName": {
                  "annotationValue": "library source",
                  "termAccession": "",
                  "termSource": ""
                }
              },

Is not present in the submitted xML:

SUBMISSION>
repository-services-isa_sra-1         |     <ACTIONS>
repository-services-isa_sra-1         |       <ACTION>
repository-services-isa_sra-1         |         <ADD/>
repository-services-isa_sra-1         |       </ACTION>
repository-services-isa_sra-1         |     </ACTIONS>
repository-services-isa_sra-1         |   </SUBMISSION>
repository-services-isa_sra-1         |   <STUDY_SET>
repository-services-isa_sra-1         |     <STUDY alias="Arabidopsis thaliana-0.27327375948287413">
repository-services-isa_sra-1         |       <DESCRIPTOR>
repository-services-isa_sra-1         |         <STUDY_TITLE>Arabidopsis thaliana</STUDY_TITLE>
repository-services-isa_sra-1         |         <STUDY_DESCRIPTION>Nucleic acid sequencing and metabolomics and proteomics of Arabidopsis thaliana in specific experimental conditions to test a specific hypothesis.</STUDY_DESCRIPTION>
repository-services-isa_sra-1         |         <STUDY_ABSTRACT>Nucleic acid sequencing and metabolomics and proteomics of Arabidopsis thaliana in specific experimental conditions to test a specific hypothesis.</STUDY_ABSTRACT>
repository-services-isa_sra-1         |         <STUDY_TYPE existing_study_type="Other"/>
repository-services-isa_sra-1         |       </DESCRIPTOR>
repository-services-isa_sra-1         |       <STUDY_ATTRIBUTES>
repository-services-isa_sra-1         |         <STUDY_ATTRIBUTE>
repository-services-isa_sra-1         |           <TAG>SEEK Study ID</TAG>
repository-services-isa_sra-1         |           <VALUE>10</VALUE>
repository-services-isa_sra-1         |         </STUDY_ATTRIBUTE>
repository-services-isa_sra-1         |         <STUDY_ATTRIBUTE>
repository-services-isa_sra-1         |           <TAG>SEEK creation date</TAG>
repository-services-isa_sra-1         |           <VALUE>2022-11-03T16:20:49Z</VALUE>
repository-services-isa_sra-1         |         </STUDY_ATTRIBUTE>
repository-services-isa_sra-1         |       </STUDY_ATTRIBUTES>
repository-services-isa_sra-1         |     </STUDY>
repository-services-isa_sra-1         |   </STUDY_SET>
repository-services-isa_sra-1         |   <EXPERIMENT_SET>
repository-services-isa_sra-1         |     <EXPERIMENT alias="#other_material/332-0.27327375948287413">
repository-services-isa_sra-1         |       <TITLE>extract 1</TITLE>
repository-services-isa_sra-1         |       <STUDY_REF refname="Arabidopsis thaliana-0.27327375948287413"/>
repository-services-isa_sra-1         |       <DESIGN>
repository-services-isa_sra-1         |         <DESIGN_DESCRIPTION>ISA-Test</DESIGN_DESCRIPTION>
repository-services-isa_sra-1         |         <SAMPLE_DESCRIPTOR accession="SAMEA131434011"/>
repository-services-isa_sra-1         |         <LIBRARY_DESCRIPTOR>
repository-services-isa_sra-1         |           <LIBRARY_STRATEGY>OTHER</LIBRARY_STRATEGY>
repository-services-isa_sra-1         |           <LIBRARY_SOURCE>OTHER</LIBRARY_SOURCE>
repository-services-isa_sra-1         |           <LIBRARY_SELECTION>RT-PCR</LIBRARY_SELECTION>
repository-services-isa_sra-1         |           <LIBRARY_LAYOUT>
repository-services-isa_sra-1         |             <SINGLE/>
repository-services-isa_sra-1         |           </LIBRARY_LAYOUT>
repository-services-isa_sra-1         |         </LIBRARY_DESCRIPTOR>
repository-services-isa_sra-1         |       </DESIGN>
repository-services-isa_sra-1         |       <PLATFORM>
repository-services-isa_sra-1         |         <OXFORD_NANOPORE>
repository-services-isa_sra-1         |           <INSTRUMENT_MODEL>MinION</INSTRUMENT_MODEL>
repository-services-isa_sra-1         |         </OXFORD_NANOPORE>
repository-services-isa_sra-1         |       </PLATFORM>
repository-services-isa_sra-1         |     </EXPERIMENT>
repository-services-isa_sra-1         |     <EXPERIMENT alias="#other_material/333-0.27327375948287413">
repository-services-isa_sra-1         |       <TITLE>library 1</TITLE>
repository-services-isa_sra-1         |       <STUDY_REF refname="Arabidopsis thaliana-0.27327375948287413"/>
repository-services-isa_sra-1         |       <DESIGN>
repository-services-isa_sra-1         |         <DESIGN_DESCRIPTION>ISA-Test</DESIGN_DESCRIPTION>
repository-services-isa_sra-1         |         <SAMPLE_DESCRIPTOR accession="SAMEA131434011"/>
repository-services-isa_sra-1         |         <LIBRARY_DESCRIPTOR>
repository-services-isa_sra-1         |           <LIBRARY_STRATEGY>OTHER</LIBRARY_STRATEGY>
repository-services-isa_sra-1         |           <LIBRARY_SOURCE>OTHER</LIBRARY_SOURCE>
repository-services-isa_sra-1         |           <LIBRARY_SELECTION>RT-PCR</LIBRARY_SELECTION>
repository-services-isa_sra-1         |           <LIBRARY_LAYOUT>
repository-services-isa_sra-1         |             <SINGLE/>
repository-services-isa_sra-1         |           </LIBRARY_LAYOUT>
repository-services-isa_sra-1         |         </LIBRARY_DESCRIPTOR>
repository-services-isa_sra-1         |       </DESIGN>
repository-services-isa_sra-1         |       <PLATFORM>
repository-services-isa_sra-1         |         <OXFORD_NANOPORE>
repository-services-isa_sra-1         |           <INSTRUMENT_MODEL>MinION</INSTRUMENT_MODEL>
repository-services-isa_sra-1         |         </OXFORD_NANOPORE>
repository-services-isa_sra-1         |       </PLATFORM>
repository-services-isa_sra-1         |     </EXPERIMENT>
repository-services-isa_sra-1         |   </EXPERIMENT_SET>
repository-services-isa_sra-1         |   <RUN_SET>
repository-services-isa_sra-1         |     <RUN alias="#assay/18_20_21-0.27327375948287413">
repository-services-isa_sra-1         |       <TITLE>#assay/18_20_21</TITLE>
repository-services-isa_sra-1         |       <EXPERIMENT_REF refname="#other_material/333"/>
repository-services-isa_sra-1         |       <DATA_BLOCK>
repository-services-isa_sra-1         |         <FILES>
repository-services-isa_sra-1         |           <FILE filename="ENA_TEST2.R2.fastq.gz" filetype="fastq" checksum_method="MD5" checksum="69c903251902c1e0b75331f70e531012"/>
repository-services-isa_sra-1         |         </FILES>
repository-services-isa_sra-1         |       </DATA_BLOCK>
repository-services-isa_sra-1         |     </RUN>
repository-services-isa_sra-1         |   </RUN_SET>
repository-services-isa_sra-1         |   <PROJECT_SET>
repository-services-isa_sra-1         |     <PROJECT alias="Bob's investigation-0.27327375948287413">
repository-services-isa_sra-1         |       <TITLE>Bob's investigation</TITLE>
repository-services-isa_sra-1         |       <DESCRIPTION></DESCRIPTION>
repository-services-isa_sra-1         |       <SUBMISSION_PROJECT>
repository-services-isa_sra-1         |         <SEQUENCING_PROJECT/>
repository-services-isa_sra-1         |       </SUBMISSION_PROJECT>
repository-services-isa_sra-1         |     </PROJECT>
repository-services-isa_sra-1         |   </PROJECT_SET>
repository-services-isa_sra-1         | </WEBIN>
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