Commits on Aug 6, 2024

1. 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>

   

   3 people authored Aug 6, 2024
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2. V1.2.0 Prod Update

   

   dthoward96 committed Aug 6, 2024
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3. Merge branch 'master' into dev

   

   dthoward96 authored Aug 6, 2024
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