V1.3.93

V1.3.93 Release of SeqSender

Changes:

SeqSender:

• Resolve bug for table2asn submission where if table2asn fails to validate submission is made correctly it will trap the upload log in a repeating error for missing a keyword for validation schema of the upload log. Will now attempt to rerun table2asn each time upload log is ran for table2asn submissions if table2asn fails to validate submission.

V1.3.92

V1.3.92 Release of SeqSender

Changes:

SeqSender:

• Resolve bug for table2asn submission where if "VALIDATED" is in submission ID without "EMAILED" tag for submission status would cause an error and crash.

V1.3.91

V1.3.91 Release of SeqSender

Changes:

SeqSender:

• Resolve issue where SeqSender would encounter a bug in-between BioSample and GenBank submission.

V1.3.9

V1.3.9 Release of SeqSender

Changes:

SeqSender:

• Resolves issue where NCBI ftp submission folders were not getting created correctly.

V1.3.8

V1.3.8 Release of SeqSender

Changes:

SeqSender:

• "Authors" metadata field will now detect if semi-colon is not used to separate individual users and attempt to use comma as delimiter if detected. User is now warned that comma may cause issues when it is detected to be the author field delimiter.

What's Changed

• V1.3.8 by @dthoward96 in #130

Full Changelog: v1.3.7...v1.3.8

V1.3.7

V1.3.7 Release of SeqSender

Changes:

SeqSender:
GenBank:

• Add's a toggle field "Add_Definition_Line_Accessions" to the config file for submissions to include "BioProject", "BioSample", "SRA" as fasta definition lines inside fasta file during submission in addition to the source file when linking NCBI databases.
• Fixes a bug related to table2asn submissions where "VALIDATED" flag results in a submission upload log error for a incorrect field value for GenBank submission status.

Shiny:

• Add's "Add_Definition_Line_Accessions" to the submission wizard for creating config files.
• Add's "VALIDATED" flag to shiny documentation.

V1.3.6

v1.3.6 Release of SeqSender

Changes:

SeqSender:
GenBank:

• Fixes bug related to using table2asn to submit sequences to GenBank. SeqSender would report a missing 'submission.xml' for submissions being made via table2asn when the 'submission.xml' is only for performing FTP submissions for GenBank.

V1.3.5

V1.3.5 Release of SeqSender

Changes:

SeqSender:

• Resolves table2asn errors preventing it from functioning correctly when using seqsender in docker because of missing dependencies.

What's Changed

• Dockerfile fix by @dthoward96 in #125

Full Changelog: v1.3.4...v1.3.5

V1.3.4

V1.3.4 Release of SeqSender

Changes:

SeqSender:

• Add's option to pass publication title and publication status via cmd line to prevent having to modify config file for every publication.
• Add's option to give GISAID CLI file path via config file to store CLI in separate location.
• Resolves issues and error reports when using Python 3.13

GenBank:

• Fixes bug related to submitting RSV and SeqSender rejecting it via metadata and upload log validation.
• Fixes errors related to comment file submissions for GenBank by removing "organism" and "collection_date" from comment file.

What's Changed

• v1.3.4 update by @dthoward96 in #122

Full Changelog: v1.3.3...v1.3.4

V1.3.3

V1.3.3 Release of SeqSender

Changes:

SeqSender:

• Adds a new function to test network connections with SeqSender for NCBI and GISAID.
  • python seqsender.py test_network_connection
• Add's automatic network test to SeqSender's submit command if it fails to connect to NCBI.
• Fixes a bug with the documentation site that prevented the src and cmt templates from being added to the metadata template.
• Fixes typo in genbank src template. src-comment -> gb-comment
• Adds a link back to GitHub for documentation site.

What's Changed

• V1.3.3 Update by @dthoward96 in #119

Full Changelog: v1.3.2...v1.3.3