[ci skip] Merge PR 24425
[ci skip] Merge PR 24425

Merge PR #24425, commits were: 
 * Updated entrez-direct to version 13.9

EDirect 13.9 is now public, with the following release notes:

Xtract -fasta splits long sequences into groups of 50 letters.

Xtract -select restores -in to indicate name of identifier file.

Redesigned EDirect selected by running "export USE_NEW_EDIRECT=true" to set environment variable.

New implementation also chosen by adding -newmode as the first argument to individual efetch, efilter, einfo, elink, epost, esearch, esummary, and nquire commands.

The EDirect reimplementation is still activated by running:

export USE_NEW_EDIRECT=true

It is version 14.0, and will become the default sometime later this year.

In addition to the release notes, the curl call in nquire uses the "--connect-timeout 20" flag. This eliminates the 300 second maximum data transfer limit, but doesn't hang indefinitely if the server is not responding.

Error reporting has also been improved, and einfo -help shows commands to force several error messages:

  nquire -url http://api.geonames.org/countryCode -lat 41.796 -lng "\-87.577"

  einfo -db NONE

  esearch -db pubmed -query "1233456789 [NONE]"

  elink -db pubmed -id 123456789 -related

  efetch -db pubmed -id 123456789 -format docsum

Elink and epost support a -log argument, which prints periods on the terminal as a primitive progress monitor. This was added because elink always splits large sets into groups of 500, to eliminate silent server truncation without causing sporadic server timeouts, and that could take multiple minutes to complete for a large link operation.

The history server is now synchronized between the main and backup locations, and the active server's IP address is no longer buried in the web environment string. The code that extracted that value and chose the proper location for subsequent calls is thus obsolete, and has been removed.

gregvonkuster/bioconda-recipes,zachcp/bioconda-recipes,phac-nml/bioconda-recipes,acaprez/recipes,ostrokach/bioconda-recipes,gregvonkuster/bioconda-recipes,ostrokach/bioconda-recipes,rob-p/bioconda-recipes,bioconda/bioconda-recipes,npavlovikj/bioconda-recipes,rob-p/bioconda-recipes,mdehollander/bioconda-recipes,cokelaer/bioconda-recipes,acaprez/recipes,bioconda/bioconda-recipes,acaprez/recipes,ostrokach/bioconda-recipes,ostrokach/bioconda-recipes,jfallmann/bioconda-recipes,peterjc/bioconda-recipes,bioconda/bioconda-recipes,shenwei356/bioconda-recipes,phac-nml/bioconda-recipes,bebatut/bioconda-recipes,blankenberg/bioconda-recipes,peterjc/bioconda-recipes,mdehollander/bioconda-recipes,jfallmann/bioconda-recipes,bebatut/bioconda-recipes,npavlovikj/bioconda-recipes,rob-p/bioconda-recipes,jfallmann/bioconda-recipes,phac-nml/bioconda-recipes,peterjc/bioconda-recipes,bebatut/bioconda-recipes,mdehollander/bioconda-recipes,blankenberg/bioconda-recipes,gregvonkuster/bioconda-recipes,npavlovikj/bioconda-recipes,bioconda/bioconda-recipes,npavlovikj/bioconda-recipes,peterjc/bioconda-recipes,acaprez/recipes,peterjc/bioconda-recipes,ostrokach/bioconda-recipes,mdehollander/bioconda-recipes,zachcp/bioconda-recipes,jfallmann/bioconda-recipes,phac-nml/bioconda-recipes,blankenberg/bioconda-recipes,cokelaer/bioconda-recipes,phac-nml/bioconda-recipes,zachcp/bioconda-recipes,shenwei356/bioconda-recipes,cokelaer/bioconda-recipes,zachcp/bioconda-recipes,peterjc/bioconda-recipes,blankenberg/bioconda-recipes,rob-p/bioconda-recipes,shenwei356/bioconda-recipes,shenwei356/bioconda-recipes,mdehollander/bioconda-recipes,cokelaer/bioconda-recipes,mdehollander/bioconda-recipes,bebatut/bioconda-recipes,gregvonkuster/bioconda-recipes,ostrokach/bioconda-recipes