Dthoward96 bugfix #45
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Bug fix to allow for other submit folders in FTP of ncbi
bug fix for capitalization of folder name
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 <110563969+rchau88@users.noreply.github.com> Co-authored-by: snu3 <snu3@cdc.gov>
dthoward96
added a commit
that referenced
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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 <110563969+rchau88@users.noreply.github.com> Co-authored-by: snu3 <snu3@cdc.gov> * V1.2.0 Prod Update --------- Co-authored-by: rchau88 <110563969+rchau88@users.noreply.github.com> Co-authored-by: snu3 <snu3@cdc.gov>
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