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Fix connection to NCBI for get_species_taxids at ORG #653

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jennaj opened this issue Nov 8, 2023 · 1 comment
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Fix connection to NCBI for get_species_taxids at ORG #653

jennaj opened this issue Nov 8, 2023 · 1 comment
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@jennaj
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jennaj commented Nov 8, 2023

toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/get_species_taxids/2.10.1+galaxy2

Connection fails but produces a green dataset with taxon id, red error with taxon name. Same error message.
500 Can't connect to eutils.ncbi.nlm.nih.gov:443 (Bad hostname) No do_post output returned from 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=txid91347%5Borgn%5D&retmax=0&usehistory=y&edirect_os=linux&edirect=13.9&tool=edir

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@jennaj
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jennaj commented Nov 17, 2023

Fixed. Both name and taxids queries successful toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/get_species_taxids/2.10.1+galaxy2

Wrapper bug at both servers in toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/get_species_taxids/2.14.1+galaxy0

The name query is being sent as a taxids query, and fails with this. Seems the "name versus taxid" toggle has problems? Ticket galaxyproject/tools-iuc#5643

/data/jwd05e/main/064/491/64491173/tool_script.sh: line 27: [: too many arguments
Taxonomy ID not found

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