V1.2.0 Prod Update (CDCgov#60)

* Update Dev to v1.2.0 (CDCgov#59)

* Create codeql-analysis.yml (CDCgov#25)

* Create codeql.yml (CDCgov#29)

* Dthoward96 workflow correction (CDCgov#30)

* Delete .github/workflows/codeql-analysis.yml

* Delete .github/workflows/python-package-mamba.yml

* Add files via upload (CDCgov#31)

* bug fix process.py (CDCgov#32)

Missing a return for config file function and correcting a error message to print the correct df

* Create GHCR_docker.yml (CDCgov#33)

* Create GHCR_docker.yml

* Update GHCR_docker.yml

Correct changes for master branch

* FTP folder bug fix submit.py (CDCgov#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 (CDCgov#41)

automatic test builds dockerfile on pull request. This will prevent merging to master if Dockerfile fails to build correctly.

* Dthoward96 org id patch (CDCgov#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 (CDCgov#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 (CDCgov#49)

Changes requirement from only isolate to require either strain or isolate for BioSample and GenBank

* create.py duplicate strain name bug (CDCgov#50)

Fixes issue that creates duplicate strain columns when using src-strain

* Bug fix process.py (CDCgov#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 (CDCgov#53)

* Bug fix for gisaid name overwriting genbank name for fasta file

* bug fix fasta file creation (CDCgov#55)

Fix issue where it requires fasta file for non-fasta submission

* Bug fix create.py (CDCgov#56)

Correct issue where organism and collection date was being added to the comment.cmt file for genbank submissions

* Table2asn bug fixes (CDCgov#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 (CDCgov#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>

gisaid_handler.py

@@ -97,7 +97,6 @@ def submit_gisaid(organism: str, submission_dir: str, submission_name: str, conf
 	gisaid_cli = file_handler.validate_gisaid_installer(submission_dir=submission_dir, organism=organism)
 	print(f"Uploading sample files to GISAID-{organism}, as a '{submission_type}' submission. If this is not intended, interrupt immediately.", file=sys.stdout)
 	time.sleep(5)
-	sub = process_gisaid_log(log_file=os.path.join(submission_dir, "gisaid_upload_log_" + str(1) + ".txt"), submission_dir=submission_dir)
 	# Set number of attempt to 3 if erroring out occurs
 	attempts = 1
 	# Submit to GISAID

shiny/index.py

@@ -6,7 +6,7 @@
     ui.HTML(
         """
 <h2>Overview</h2>
-<p><code>seqsender</code> is a Python program that is developed to automate the process of generating necessary submission files and batch uploading them to <ins>NCBI archives</ins> (such as <strong>BioSample</strong>, <strong>SRA</strong>, and <strong>Genbank</strong>) and <ins>GISAID databases</ins> (e.g. <strong>EpiFlu</strong> and <strong>EpiCoV</strong>). Presently, the pipeline is capable of uploading <strong>Influenza A Virus</strong> (FLU) and <strong>SARS-COV-2</strong> (COV) data. However, the dynamic nature of this pipeline can allow for additional uploads of other organisms in future updates or requests.</p>
+<p><code>seqsender</code> is a Python program that is developed to automate the process of generating necessary submission files and batch uploading them to <ins>NCBI archives</ins> (such as <strong>BioSample</strong>, <strong>SRA</strong>, and <strong>Genbank</strong>) and <ins>GISAID databases</ins> (e.g. <strong>EpiFlu</strong>, <strong>EpiPox</strong>, and <strong>EpiCoV</strong>).</p>
 <h2>Public Domain Standard Notice</h2>
 <p>This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the <a href="https://creativecommons.org/publicdomain/zero/1.0/">CC0 1.0 Universal public domain dedication</a>. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.</p>
 <h2>License Standard Notice</h2>