Fix ncbi_manifest ETL

• Only get index data from sra manifest
• Move country_region and continent from summary location node to sample node
• Fix file extension
• Submit virus sequence contig taxonomy data

Add Bayes model workflow, X-ray notebooks, fix CTP ETL

Release Notes

For: uc-cdis/covid19-tools

Notes since tag: 4.4.5

Notes to tag/commit: 4.5.0

Generated: 2020-12-07

Improvements

• Fix CTP ETL N/A handling, update to new URL, improve error handling (#153)
• Modify text for DarkCovid Jupyter notebook (#151)
• Modify text of DarkNet Binary Jupyter notebook. (#150)
• Notebook is reviewed by Kyle and Gina (#146)

New Features

• Add Bayes model Mariner workflow as an ETL that can be run on a cronjob
  (#142)
• Add two notebooks -- binary classification and three classes classification
  by Covid DarkNet using x-ray datasets (#146)

Dependency Updates

• Peregrine.py python code for data query and download (#146)

ETL for NCBI

Feat/ncbi manifest (#147)

* feat(ncbi_manifest): add ncbi_manifest module

* fixup

* chore(log): more log

* chore(code): rename funtion

* feat(update_release): update the last release date

* fixup

* chore(logs): more logs

* feat(retry): retry logic

* feat(retry): retry

* chore(logs): more logs

* fix(exception): handle TimeoutError

* fixup

* fixup

* fix(session): use single session only

* feat(session): use single session only

* fix(continent): fix continent enum value

* fixup

* feat(last_submission): update project last submission

* fix(indent): fix indent

* chore(refactor): refactor and fix indent error

* chore(code): refactor

* fix(doc): fix readme

* fixup

Improve Simulation Graph Readability

Use every other week as date label, not every week.

4.4.3

Release Notes

For: uc-cdis/covid19-tools

Notes since tag: 4.4.2

Notes to tag/commit: 4.4.3

Generated: 2020-11-10

Bug Fixes

• Fix occasional JHU_TO_S3 ETL failures because of missing data (#139)

Move fields to socio demographic

Move fields to socio demographic

4.4.1

Release Notes

For: uc-cdis/covid19-tools

Notes since tag: 4.4.0

Notes to tag/commit: 4.4.1

Generated: 2020-11-04

Bug Fixes

• Change base image to our hosted base image (#138)
• JHU ETL: fix failure when encountering an empty row in the input data (#136)

4.4.0

Release Notes

For: uc-cdis/covid19-tools

Notes since tag: 4.3.0

Notes to tag/commit: 4.4.0

Generated: 2020-11-03

Bug Fixes

• Fix JHU ETL failures due to timeouts (#135)
• Fix IDPH ETL failures due to timeouts (#134)
• Adds header to PUT requests to indexd on updating indexd records (#130)

New Features

• Add ATLAS ETL (#131)
• ETL for submiting NCBI metadata (#128)
• clinical_notes in imaging_file will now contain the name of the folder - basically the category to which the file is related (#129)

US/Canada recovered counts

Release Notes

For: uc-cdis/covid19-tools

Notes since tag: 4.2.2

Notes to tag/commit: 4.3.0

Generated: 2020-10-13

New Features

• Make global country recovered counts available for US and Canada (#127)

Improvements

• When the original global count provided in the dataset is greater than the
  aggregated count we calculated, use the original (#127)

4.2.2

Add more enum values