DDBJ study ids (DRP123456) do not map correctly

[awalsh17]

Description of the bug

When the input list includes DRP****** ids or PRJDB***** ids, the sra_ids_to_runid.py script fails with error or returns the incorrect data (for a different ID).
It appears that the efetch query fails in cls._id_to_srx(identifier)

You can take for example the id mentioned in the script: DRP004793 will return the incorrect results - a different study is returned. It returns the information for SRP000742. Here is the query and result:

curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?id=004793&db=sra&rettype=runinfo&retmode=text"

Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,LibrarySource,LibraryLayout,InsertSize,InsertDev,Platform,Model,SRAStudy,BioProject,Study_Pubmed_id,ProjectID,Sample,BioSample,SampleType,TaxID,ScientificName,SampleName,g1k_pop_code,source,g1k_analysis_group,Subject_ID,Sex,Disease,Tumor,Affection_Status,Analyte_Type,Histological_Type,Body_Site,CenterName,Submission,dbgap_study_accession,Consent,RunHash,ReadHash
SRR016082,2009-06-12 17:55:38,2014-05-26 05:26:24,5832504,209970144,0,36,1149,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR000/016/SRR016082/SRR016082.sralite.1,SRX004537,Cryptosporidium_nref,FL-cDNA,cDNA,TRANSCRIPTOMIC,SINGLE,0,0,ILLUMINA,Illumina Genome Analyzer,SRP000742,PRJDA33427,,33427,SRS002838,SAMN00004429,simple,5807,Cryptosporidium parvum,Cryptosporidium_nref,,,,,,,no,,,,,UT-MGS,SRA002056,,public,C39D154DF2031E73C9578A3317C42931,4166465432361F26049099FFC7742B15

I am not sure the best solution other than doing eutils esearch for example, term=DRP004793, and using the returned ids.

curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term=DRP004793"

<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD esearch 20060628//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20060628/esearch.dtd">
<eSearchResult><Count>645</Count><RetMax>20</RetMax><RetStart>0</RetStart><IdList>
<Id>7938219</Id>
<Id>7938218</Id>
<Id>7507857</Id>
<Id>7507856</Id>
<Id>7507855</Id>
<Id>7507854</Id>
<Id>7507853</Id>
<Id>7507852</Id>
<Id>7507851</Id>
<Id>7507850</Id>
<Id>7507849</Id>
<Id>7507848</Id>
<Id>7507847</Id>
<Id>7507846</Id>
<Id>7507845</Id>
<Id>7507844</Id>
<Id>7507843</Id>
<Id>7507842</Id>
<Id>7507841</Id>
<Id>7507840</Id>
</IdList><TranslationSet/><TranslationStack>   <TermSet>    <Term>DRP004793[All Fields]</Term>    <Field>All Fields</Field>    <Count>645</Count>    <Explode>N</Explode>   </TermSet>   <OP>GROUP</OP>  </TranslationStack><QueryTranslation>DRP004793[All Fields]</QueryTranslation></eSearchResult>

Command used and terminal output

nextflow run main.nf --input 'input.txt'

This will fail to return results from DRP004793.

just running the sra_ids_to_runinfo.py directly with input.txt gives this error:

Traceback (most recent call last):
  File "bin/sra_ids_to_runinfo.py", line 498, in <module>
    sys.exit(main())
             ^^^^^^
  File "/bin/sra_ids_to_runinfo.py", line 494, in main
    fetch_sra_runinfo(args.file_in, args.file_out, ena_metadata_fields)
  File "bin/sra_ids_to_runinfo.py", line 470, in fetch_sra_runinfo
    ids = DatabaseResolver.expand_identifier(db_id)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "bin/sra_ids_to_runinfo.py", line 223, in expand_identifier
    return cls._id_to_srx(identifier)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "bin/sra_ids_to_runinfo.py", line 241, in _id_to_srx
    cls._content_check(response, identifier)
  File "bin/sra_ids_to_runinfo.py", line 232, in _content_check
    if response.status == 204:
       ^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'status'

Relevant files

input.txt:

SRP102769
DRP004793

System information

This would happen on any system - have tested locally, awsbatch, docker, linux, macOS.
Version of nf-core/fetchngs: 1.12.0