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NAL-i5K / tripal_eutils

ncbi loader via the eutils interface
GNU General Public License v3.0
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Issue 241 Allow loading multiple records #242

Closed dsenalik closed 1 year ago

dsenalik commented 1 year ago

For Issue #241 The relatively simple changes here allow loading of multiple NCBI records at the same time, by just separating them with a delimiter of comma, semicolon, or space. The preview button only previews the first record if more than one is supplied. I also added a trim() so that if the user includes a space before or after the accession, nothing unexpected happens.

dsenalik commented 1 year ago

Example of new appearance eutils_example

dsenalik commented 1 year ago

In my example above, I noticed a colon at the start of the project name. This happens if child->Name is an empty string. Fixed with commit https://github.com/NAL-i5K/tripal_eutils/pull/242/commits/fcc0466ea213726d222bcdf993f5413d734d4155

dsenalik commented 1 year ago

A rare issue now more likely to occur when loading multiple accessions is a transient error downloading from NCBI. Generally this can be fixed by just trying again. To accomplish this, wrap the download section in a retry loop and try up to three times before giving up. See commit https://github.com/NAL-i5K/tripal_eutils/pull/242/commits/6ba742e8725a23d23c0792bc795f6c53b5faa3d9

dsenalik commented 1 year ago

Another thing noticeable when loading multiple BioSamples is that SAMD type of BioSamples end up with an accession number very different from the number part of the SAMD number. Add both to the log message when different with commit https://github.com/NAL-i5K/tripal_eutils/pull/242/commits/bcc8adc555d936b43cd777036642ef7d3d56839e Example: Inserting record into Chado: biosample: 30033048 (SAMD00518119)