https://github.com/cdcgov/seqsender - 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 https://github.com/CDCgov/seqsender/pull/122

Full Changelog: https://github.com/CDCgov/seqsender/compare/v1.3.3...v1.3.4

- Python
Published by dthoward96 9 months ago

https://github.com/cdcgov/seqsender - 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 https://github.com/CDCgov/seqsender/pull/119

Full Changelog: https://github.com/CDCgov/seqsender/compare/v1.3.2...v1.3.3

- Python
Published by dthoward96 about 1 year ago

https://github.com/cdcgov/seqsender - V1.3.2

V1.3.2 Release of SeqSender

Changes:

SeqSender: - SeqSender will force columns that are expected to be uppercase for "submissionlog.csv" in order to prevent error where column could become lowercase and validator would error out. - Organism", "Database", "SubmissionType", "SubmissionStatus", "SubmissionID"

What's Changed

• v1.3.2 upload log bug fix by @dthoward96 in https://github.com/CDCgov/seqsender/pull/110

Full Changelog: https://github.com/CDCgov/seqsender/compare/v1.3.1...v1.3.2

- Python
Published by dthoward96 over 1 year ago

https://github.com/cdcgov/seqsender - V1.3.1

V1.3.1 Release of SeqSender

Changes:

SeqSender: - Fixes a bug where how the database submission options were selected would cause SeqSender to be unable to find the validation schema for the config file resulting in a error. - Example: When selecting databases via "-bsgn" would not cause an error but "-b -s -g -n", which is a valid submission option would cause the identifiers used to identify the correct file to swap resulting in SeqSender to be unable to find the correct file.

What's Changed

• Update test data by @dthoward96 in https://github.com/CDCgov/seqsender/pull/108
• v1.3.1 Bug Fix by @dthoward96 in https://github.com/CDCgov/seqsender/pull/109

Full Changelog: https://github.com/CDCgov/seqsender/compare/v1.3.0...v1.3.1

- Python
Published by dthoward96 over 1 year ago

https://github.com/cdcgov/seqsender - V1.3.0

V1.2.7 Release of SeqSender

Changes:

SeqSender metadata options updated per: https://www.chcoc.gov/content/initial-guidance-regarding-president-trump%E2%80%99s-executive-order-defending-women

BioSample: - SeqSender field for "gender_restroom" has been removed from metadata templates/validation.

GISAID: - SeqSender field "gs-gender" has been changed to "gs-sex". - SeqSender field "gs-HostGender" has been changed to "gs-HostSex". - Automation for validating metadata has been updated to these new field names.

What's Changed

• fix version number by @dthoward96 in https://github.com/CDCgov/seqsender/pull/106
• v1.3.0 Update by @dthoward96 in https://github.com/CDCgov/seqsender/pull/107

Full Changelog: https://github.com/CDCgov/seqsender/compare/v1.2.7...v1.3.0

- Python
Published by dthoward96 over 1 year ago

https://github.com/cdcgov/seqsender - V1.2.7 Release

V1.2.7 Release of SeqSender

Changes:

GISAID: - Add's support for epiRSV and add's metadata template for epiRSV to submission wizard.

What's Changed

• V1.2.7 by @dthoward96 in https://github.com/CDCgov/seqsender/pull/104

Full Changelog: https://github.com/CDCgov/seqsender/compare/v1.2.6...v1.2.7

- Python
Published by dthoward96 over 1 year ago

https://github.com/cdcgov/seqsender - V1.2.6 Release

V1.2.6 Release of SeqSender

Changes:

• NCBI:
  • GenBank:
  • As part of recent changes to GenBank, some fields are now required, have been renamed, or deprecated and can no longer be used for submission. Please be sure to update your submissions accordingly.
  • "src-Host" and "src-Isolate" are now required fields.
  • "src-Country" has been renamed to "src-geolocname". As per changes required by the INSDC. The field now is capable of holding additional location information. Additional region or locality information must be after the country, ocean, or major sea name and separated by a ':'. For example: USA: Riverview Park, Ripkentown, MD. For all available country names: http://www.insdc.org/documents/country-qualifier-vocabulary.
  • Deprecated Columns: "src-Authority", "src-Biotype", "src-Biovar", "src-Chemovar", "src-Forma", "src-Formaspecialis", "src-Identifiedby", "src-Pathovar", "src-Pop_variant", "src-Serogroup", "src-Subclone", "src-Subtype", "src-Substrain", "src-Type"
  • BioSample:
  • Resolves NCBI submission bug for BioSample xml not validating against schema, missing descriptor. Metadata field for biosample submissions bs-sample_title is now a required field to resolve this issue.

What's Changed

• V1.2.6 Update by @dthoward96 in https://github.com/CDCgov/seqsender/pull/101
• v1.2.6 update by @dthoward96 in https://github.com/CDCgov/seqsender/pull/102

Full Changelog: https://github.com/CDCgov/seqsender/compare/v1.2.5...v1.2.6

- Python
Published by dthoward96 over 1 year ago

https://github.com/cdcgov/seqsender - V1.2.5 Release

V1.2.5 Release of SeqSender

Changes:

• NCBI/GISAID:
  • Validation of config file username/password now allows more special characters.

What's Changed

• V1.2.5 Update by @dthoward96 in https://github.com/CDCgov/seqsender/pull/99

Full Changelog: https://github.com/CDCgov/seqsender/compare/v1.2.4...v1.2.5

- Python
Published by dthoward96 over 1 year ago

https://github.com/cdcgov/seqsender - V1.2.4 Release

V1.2.4 Release of SeqSender

Changes:

GenBank: - Fixes bug where if submitting only to GenBank/GenBank is final database processing, "submission_status" command does not see flag correctly for processing submission and ignores updating status.

What's Changed

• V1.2.4 Update by @dthoward96 in https://github.com/CDCgov/seqsender/pull/93

Full Changelog: https://github.com/CDCgov/seqsender/compare/v1.2.3...v1.2.4

- Python
Published by dthoward96 over 1 year ago

https://github.com/cdcgov/seqsender - v1.2.3 Release

v1.2.3 Release of SeqSender

Changes:

BioSample/SRA: - Fixes bug where if submitting only one sample to BioSample/SRA, file "submissionstatusreport.csv" is not correctly updated with accession for sample because "report.xml" is not processed correctly. - Added error handling for when "submissionstatusreport.csv" has no accessions to be updated but submission status is marked as "Processed".

What's Changed

• GitHub action test by @dthoward96 in https://github.com/CDCgov/seqsender/pull/83
• V1.2.3 Update by @dthoward96 in https://github.com/CDCgov/seqsender/pull/85

Full Changelog: https://github.com/CDCgov/seqsender/compare/v1.2.2...v1.2.3

- Python
Published by dthoward96 over 1 year ago

https://github.com/cdcgov/seqsender - V1.2.2 Release

V1.2.2 Release of SeqSender

Changes:

GISAID: - FLU GISAID submission metadata now correctly parses partial collection dates. If only year is present, it is now correctly stored in "CollectionYear" and if/when month is also present, it is stored in "CollectionMonth". If the entire "YYYY-MM-DD" collection date is present, it is stored in the "CollectionDate" field and "CollectionYear"/"CollectionMonth" are left empty, otherwise, if the entire collection date is not present, "CollectionDate" is left empty. All fields are added regardless of whether there are only partial/complete dates present. - FLU template/validation metadata has additional fields added. - SamplingStrategy - SequencingStrategy - SequencingTechnology - AssemblyMethod - Coverage - AdamantanesResistancepheno - OseltamivirResistancepheno - ZanamivirResistancepheno - PeramivirResistancepheno - OtherResistancepheno

What's Changed

• Merge pull request #72 from CDCgov/dev by @dthoward96 in https://github.com/CDCgov/seqsender/pull/76
• v1.2.1 documentation typos fixes by @dthoward96 in https://github.com/CDCgov/seqsender/pull/77
• Update issue templates by @dthoward96 in https://github.com/CDCgov/seqsender/pull/79
• update dev by @dthoward96 in https://github.com/CDCgov/seqsender/pull/81
• V1.2.2 Update by @dthoward96 in https://github.com/CDCgov/seqsender/pull/82

Full Changelog: https://github.com/CDCgov/seqsender/compare/v1.2.1...v1.2.2

- Python
Published by dthoward96 over 1 year ago

https://github.com/cdcgov/seqsender - V1.2.1 Release

V1.2.1 Release of SeqSender

Changes:

NOTE: Submission configs for NCBI databases have changed and some fields have been moved to the metadata file. Config File: Description: Title and Description: Comment have been removed from the config file and have been moved to the metadata as the fields "-title" and "-comment". BioSample metadata changes: Field "bs-description" has been replaced with the optional fields "bs-sampletitle" and "bs-sampledescription". This change eases submitting to BioSample as the "bs-description" field is not a attribute for biosample and is a descriptor field when uploading to BioSample. The Change of the fields allows for the user to have greater control over the input of these fields. Shiny documentation changes: Submission wizard bugs causing some fields to contain incorrect values for SeqSender have been resolved. Bugs with interactability of the submission wizard when selecting databases and editing the user config have been resolved. GISAID submissions: GISAID submission codebase has been overhauled to eliminate possible bugs related to submission differences between databases. With bugs related to generating GISAID submission files, interacting with epiCLI's, logging accessions being resolved. Other: Misc. bug fixes for other databases.

Full Changelog: https://github.com/CDCgov/seqsender/compare/v1.2.0...v1.2.1

What's Changed

• Update README.md (#61) by @dthoward96 in https://github.com/CDCgov/seqsender/pull/62
• Update README.md by @dthoward96 in https://github.com/CDCgov/seqsender/pull/63
• Update issue templates by @dthoward96 in https://github.com/CDCgov/seqsender/pull/66
• GISAID covCLI bugfixes & BioSample/SRA modifications by @erikwolfsohn in https://github.com/CDCgov/seqsender/pull/64
• Update issue templates (#66) by @dthoward96 in https://github.com/CDCgov/seqsender/pull/68
• V1.2.1. Release by @dthoward96 in https://github.com/CDCgov/seqsender/pull/69
• Dthoward96 remove cli by @dthoward96 in https://github.com/CDCgov/seqsender/pull/70
• Update dev to v1.2.1 by @dthoward96 in https://github.com/CDCgov/seqsender/pull/71
• Dev Update Readme by @dthoward96 in https://github.com/CDCgov/seqsender/pull/72

New Contributors

• @erikwolfsohn made their first contribution in https://github.com/CDCgov/seqsender/pull/64

Full Changelog: https://github.com/CDCgov/seqsender/compare/v1.2.0...v1.2.1

- Python
Published by dthoward96 over 1 year ago

https://github.com/cdcgov/seqsender - V1.2.0 Release

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: - SeqSender now supports more submission options. - All GISAID epiCLI database tools are now supported. EpiFLU, EpiCoV, EpiArbo, EpiRSV, EpiPox - All BioSample Packages are now supported. - All organisms can now be submitted to NCBI via SRA, BioSample, and GenBank via table2asn. - Now generates all supported databases, manual submission files for when submitting via GUI web portals. - NCBI database submissions can now be made with holdback dates, allowing users to upload their data to NCBI and choose when it is released to the public. - Metadata is now validated for submission errors before performing submission, including when generating files for manual submission. - Documentation has been overhauled to include detailed descriptions of all functions and interactivity. Users can now create and generate the correct config file and metadata fields needed for submitting samples via SeqSender. - Logging and output files from SeqSender are now standardized with detailed explanations of output fields in updated documentation.

What's Changed

• Final merged v1.1.0 by @dthoward96 in https://github.com/CDCgov/seqsender/pull/18
• Delete .github/workflows/codeql-analysis.yml by @dthoward96 in https://github.com/CDCgov/seqsender/pull/19
• Update README.md by @dthoward96 in https://github.com/CDCgov/seqsender/pull/21
• Create pkg_down.yaml by @dthoward96 in https://github.com/CDCgov/seqsender/pull/20
• Rename pkg_down.yaml to pkgdown.yaml by @dthoward96 in https://github.com/CDCgov/seqsender/pull/22
• Create codeql-analysis.yml by @dthoward96 in https://github.com/CDCgov/seqsender/pull/24
• Create python-package-mamba.yml by @dthoward96 in https://github.com/CDCgov/seqsender/pull/26
• Final merged by @dthoward96 in https://github.com/CDCgov/seqsender/pull/23
• remove unwanted files by @rchau88 in https://github.com/CDCgov/seqsender/pull/27
• Final merged by @rchau88 in https://github.com/CDCgov/seqsender/pull/28
• Create codeql-analysis.yml by @dthoward96 in https://github.com/CDCgov/seqsender/pull/25
• Create codeql.yml by @dthoward96 in https://github.com/CDCgov/seqsender/pull/29
• Dthoward96 workflow correction by @dthoward96 in https://github.com/CDCgov/seqsender/pull/30
• Add files via upload by @dthoward96 in https://github.com/CDCgov/seqsender/pull/31
• bug fix process.py by @dthoward96 in https://github.com/CDCgov/seqsender/pull/32
• Create GHCR_docker.yml by @dthoward96 in https://github.com/CDCgov/seqsender/pull/33
• FTP folder bug fix submit.py by @dthoward96 in https://github.com/CDCgov/seqsender/pull/34
• update template metadata with required fields for flu by @rchau88 in https://github.com/CDCgov/seqsender/pull/37
• Update process.py by @rchau88 in https://github.com/CDCgov/seqsender/pull/39
• Create dockertestbuild.yml by @dthoward96 in https://github.com/CDCgov/seqsender/pull/41
• Dthoward96 org id patch by @dthoward96 in https://github.com/CDCgov/seqsender/pull/42
• Dthoward96 bugfix by @dthoward96 in https://github.com/CDCgov/seqsender/pull/45
• add either or for strain/isolate by @dthoward96 in https://github.com/CDCgov/seqsender/pull/49
• create.py duplicate strain name bug by @dthoward96 in https://github.com/CDCgov/seqsender/pull/50
• Bug fix process.py by @dthoward96 in https://github.com/CDCgov/seqsender/pull/51
• Bug fix for gisaid name overwriting genbank name for fasta file by @dthoward96 in https://github.com/CDCgov/seqsender/pull/53
• bug fix fasta file creation by @dthoward96 in https://github.com/CDCgov/seqsender/pull/55
• Bug fix create.py by @dthoward96 in https://github.com/CDCgov/seqsender/pull/56
• Table2asn bug fixes by @dthoward96 in https://github.com/CDCgov/seqsender/pull/57
• V1.2.0 Update by @dthoward96 in https://github.com/CDCgov/seqsender/pull/58
• V1.2.0 Prod Update by @dthoward96 in https://github.com/CDCgov/seqsender/pull/60
• Update README.md by @dthoward96 in https://github.com/CDCgov/seqsender/pull/61

Full Changelog: https://github.com/CDCgov/seqsender/commits/v1.2.0

- Python
Published by dthoward96 almost 2 years ago