V1.2.0 Update #58
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V1.2.0 Update #58
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removing test yml
dthoward96
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Aug 6, 2024
* Create codeql-analysis.yml (#25) * Create codeql.yml (#29) * Dthoward96 workflow correction (#30) * Delete .github/workflows/codeql-analysis.yml * Delete .github/workflows/python-package-mamba.yml * Add files via upload (#31) * bug fix process.py (#32) Missing a return for config file function and correcting a error message to print the correct df * Create GHCR_docker.yml (#33) * Create GHCR_docker.yml * Update GHCR_docker.yml Correct changes for master branch * FTP folder bug fix submit.py (#34) Some FTP accounts have the folder structure /submit/Production/ instead of /Production/. This fix automatically corrects for this difference in folder structure. * update template metadata required fields + check submitting databases are valid * Update process.py removed the gs-sequence_name specified for flu * Create docker_test_build.yml (#41) automatic test builds dockerfile on pull request. This will prevent merging to master if Dockerfile fails to build correctly. * Dthoward96 org id patch (#42) * Update cov_config.yaml remove org_id from examples * Update flu_config.yaml remove org_id from examples * Update create.py remove org_id from xml creation * Dthoward96 bugfix (#45) * Update report.py Bug fix to allow for other submit folders in FTP of ncbi * Update process.py bug fix for capitalization of folder name * Add files via upload (#49) Changes requirement from only isolate to require either strain or isolate for BioSample and GenBank * create.py duplicate strain name bug (#50) Fixes issue that creates duplicate strain columns when using src-strain * Bug fix process.py (#51) Bug fix for upload log. When only one database was submitted it, it would convert the database name into a list and error out. * Bug fix for gisaid name overwriting genbank name for fasta file (#53) * Bug fix for gisaid name overwriting genbank name for fasta file * bug fix fasta file creation (#55) Fix issue where it requires fasta file for non-fasta submission * Bug fix create.py (#56) Correct issue where organism and collection date was being added to the comment.cmt file for genbank submissions * Table2asn bug fixes (#57) * Table2asn bug fixes Resolve issue with table2asn not allowing multiple sequences in the fasta file and for the table2asn sendmail function not properly grabbing the sqn file. * Update submit.py * V1.2.0 Update (#58) * Version updates * Env update * Delete .github/workflows/python-package-mamba.yml removing test yml * pandera schema update * Delete gisaid_cli/poxCLI directory * bug fixes * Delete FLU_test directory * Delete OTHER_species directory * Delete POX_species directory * mypy validation added * mypy integration * Shiny Update * Seqsender v1.2.0 website updates * Update README.md * Update README.md * shiny website updates * Seqsender shiny updates * V1.2.0 Prod Update --------- Co-authored-by: rchau88 <[email protected]> Co-authored-by: snu3 <[email protected]>
dthoward96
added a commit
that referenced
this pull request
Aug 6, 2024
* Update Dev to v1.2.0 (#59) * Create codeql-analysis.yml (#25) * Create codeql.yml (#29) * Dthoward96 workflow correction (#30) * Delete .github/workflows/codeql-analysis.yml * Delete .github/workflows/python-package-mamba.yml * Add files via upload (#31) * bug fix process.py (#32) Missing a return for config file function and correcting a error message to print the correct df * Create GHCR_docker.yml (#33) * Create GHCR_docker.yml * Update GHCR_docker.yml Correct changes for master branch * FTP folder bug fix submit.py (#34) Some FTP accounts have the folder structure /submit/Production/ instead of /Production/. This fix automatically corrects for this difference in folder structure. * update template metadata required fields + check submitting databases are valid * Update process.py removed the gs-sequence_name specified for flu * Create docker_test_build.yml (#41) automatic test builds dockerfile on pull request. This will prevent merging to master if Dockerfile fails to build correctly. * Dthoward96 org id patch (#42) * Update cov_config.yaml remove org_id from examples * Update flu_config.yaml remove org_id from examples * Update create.py remove org_id from xml creation * Dthoward96 bugfix (#45) * Update report.py Bug fix to allow for other submit folders in FTP of ncbi * Update process.py bug fix for capitalization of folder name * Add files via upload (#49) Changes requirement from only isolate to require either strain or isolate for BioSample and GenBank * create.py duplicate strain name bug (#50) Fixes issue that creates duplicate strain columns when using src-strain * Bug fix process.py (#51) Bug fix for upload log. When only one database was submitted it, it would convert the database name into a list and error out. * Bug fix for gisaid name overwriting genbank name for fasta file (#53) * Bug fix for gisaid name overwriting genbank name for fasta file * bug fix fasta file creation (#55) Fix issue where it requires fasta file for non-fasta submission * Bug fix create.py (#56) Correct issue where organism and collection date was being added to the comment.cmt file for genbank submissions * Table2asn bug fixes (#57) * Table2asn bug fixes Resolve issue with table2asn not allowing multiple sequences in the fasta file and for the table2asn sendmail function not properly grabbing the sqn file. * Update submit.py * V1.2.0 Update (#58) * Version updates * Env update * Delete .github/workflows/python-package-mamba.yml removing test yml * pandera schema update * Delete gisaid_cli/poxCLI directory * bug fixes * Delete FLU_test directory * Delete OTHER_species directory * Delete POX_species directory * mypy validation added * mypy integration * Shiny Update * Seqsender v1.2.0 website updates * Update README.md * Update README.md * shiny website updates * Seqsender shiny updates * V1.2.0 Prod Update --------- Co-authored-by: rchau88 <[email protected]> Co-authored-by: snu3 <[email protected]> * V1.2.0 Prod Update --------- Co-authored-by: rchau88 <[email protected]> Co-authored-by: snu3 <[email protected]>
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V1.2.0 Update of SeqSender:
Note: When upgrading to V1.2.0, some files have changed. Before upgrading your current version, finish processing any of your current submissions before completing the update. To see the new changes, use the "Submission Wizard" in the updated documentation to generate a new config file and to view the updated metadata fields required for submitting samples with SeqSender.
Updates: