V1.1.0 #117

DougManuel · 2021-03-12T22:54:45Z

Addresses: #59, #84, #90, #92, #93, #96, #97, #99, #102, #103, #104, #113, #114, #116.

Also see changelog.

Before merging to main:

@hswerdfe volunteered to clean-up merge conflict with CSV.
update changelog.
check ERD and SQL reflects model.

@DougManuel

@DougManuel noticed some typos on a quick scan. Also in the ERD - Sample table has a typo which has 'ID' instead of 'sampleID'

Ontario Template based on ODM v1.0. Includes some validation rules

…rated using snakecase Sentence for english and deepl.com for french.

…ter information not being auto generated.

…and the content

added in tables to help generate metadata

README.md

vipileggi · 2021-03-13T12:57:28Z

README.md

+  - New `porpVar`: Proportion of variant in sample.
+  - `SiteMeasure` table, `type` variable
+    - `wwBOD5c`, 5 day biochemical oxygen demand
+    - `wwPtot`, Total phosphates


MECP lab typically measures total phosphorous (TP) wwTP; but this is fine also but not too common from my experience.

README.md

…ater into dev

DougManuel · 2021-03-15T14:10:31Z

There are a few open issues. I am not sure if they just need to be closed or still work to do.

#101, #106, #112, #113.

…ater into dev

vipileggi and others added 30 commits January 31, 2021 17:58

Update metadata.md

1e6e71b

@DougManuel noticed some typos on a quick scan. Also in the ERD - Sample table has a typo which has 'ID' instead of 'sampleID'

Add files via upload

5dd7007

Ontario Template based on ODM v1.0. Includes some validation rules

added in tables to help generate metadata

15345c6

made R script to generate SQL code that will make a DB

2ea56b5

sql generator now adds comments, and works to create a blank sqlite db

9281d09

removed special charaters from csv files

ec36aa2

sql db genorator now includes table desciptions as comments.

67367f6

sql db generator now add forgin keys to sql statments

6faec57

all variables now have english and french labels, that were auto gene…

398bb7a

…rated using snakecase Sentence for english and deepl.com for french.

plural tables

8e8c46d

added auto generated markdown file.

0dcb853

metadata file generated from template file, with some header and foo…

ca58aed

…ter information not being auto generated.

add labels in en and fr to the tables table.

e0dd1b8

I think this fixed the issue with the push failure

bc86aa4

Removed one of the template files for the metadata, kept one of them …

3767ab2

…and the content

fix bug in metadata generation.

c562088

[feature] add comment header for metadata_template.md

82ef9f6

[feature] include instructions to generate metadata_template.md

3b8b0aa

added naming conventions section

633c5f7

added naming conventions section

e9267cc

added naming conventions section

534936b

Merge pull request #96 from Big-Life-Lab/dev_hswerdfe

fcdfbb7

added in tables to help generate metadata

[feature] Variant reporting #59

1e1c872

[feature] additional category for variant reporting #59

9c70234

[bug] typos from 1e6e71b

f6a9bbf

[feature] update changelog for v1.1.0.

0b3fa3f

[bug] update variable names with lowercase first character

c7d9112

[feature] addition of organization to Reporter table

de8f188

[feature] addition of organization to Reporter table #97

133f1f5

Merge remote-tracking branch 'origin/dev' into dev

b500365

NielsNicolai added 2 commits March 10, 2021 14:17

Solves quotation error

811894c

Solves quoatation error II

05b4155

DougManuel requested review from hswerdfe, jeandavidt, NielsNicolai and vipileggi March 12, 2021 22:54