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Change the NCBI Entrez search to reduce test failures #29

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peterjc opened this issue Dec 7, 2018 · 2 comments · Fixed by #30
Closed

Change the NCBI Entrez search to reduce test failures #29

peterjc opened this issue Dec 7, 2018 · 2 comments · Fixed by #30
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@peterjc
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peterjc commented Dec 7, 2018

Often the continuous integration tests are failing here:

esearch -db nucleotide -query "its1 AND Phytophthora[Organism] AND 150:800[Sequence Length]" | efetch -format fasta

Either NCBI Entrez is timing out and failing directly, or apparently it is returning with partial results, and the DB count checks are not always satisfied (currently we say we expect at least 100 taxonomy table entries).

Probably simplest to add a limit to the Entrez search string, and also a bash if statement checking the number of records saved to the FASTA file?

@peterjc peterjc added the bug Something isn't working label Dec 7, 2018
@peterjc peterjc reopened this Dec 11, 2018
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peterjc commented Dec 11, 2018

Even the reduced search can fail, this as 12:25 GMT/UTC, https://circleci.com/gh/peterjc/thapbi-pict/131

$ esearch -db nucleotide -query 'its1 AND Phytophthora[Organism] AND 150:800[Sequence Length] AND 1900:2000[Publication Date]' | efetch -format fasta
WebEnv value not found in search output - WebEnv1 
Db value not found in fetch input
Exited with code 255

peterjc added a commit that referenced this issue Feb 5, 2019
Created as follows:

$ esearch -db nucleotide -query "its1 AND Phytophthora[Organism] AND 150:800[Sequence Length] AND 1900:2000[Publication Date]" | efetch -format fasta > 20th_Century_ITS1.fasta

It has proved unreliable to generate this during the continuous
integration tests. See issue #29.
peterjc added a commit that referenced this issue Feb 5, 2019
Created as follows:

$ esearch -db nucleotide -query "its1 AND Phytophthora[Organism] AND 150:800[Sequence Length] AND 1900:2000[Publication Date]" | efetch -format fasta > 20th_Century_ITS1.fasta

It has proved unreliable to generate this during the continuous
integration tests. See issue #29.
@peterjc
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peterjc commented Feb 5, 2019

Avoiding this by checking in the sample file, done as part of #69 to get the CI tests to pass.

@peterjc peterjc closed this as completed Feb 5, 2019
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