Green Table Additions #20

puja-trivedi · 2023-10-06T14:57:25Z

No description provided.

…models into notebook_additions

satra · 2023-10-07T17:51:37Z

shouldn't this only add the yaml file? the rest should be auto generated on merge.

puja-trivedi · 2023-10-07T20:57:46Z

@satra - if you look at the workflow it is generated on "push" as well as "pull request". Although it might make more sense to change it to "merge".

name: generating other formats

on:
  push:
  pull_request:

satra · 2023-10-07T21:00:31Z

sorry i had forgotten. the conflicts misled me. yes, it would be good to test that the autogeneration works, but the actual autogeneration could happen when ready to merge, or when a label is set on the PR.

…ve orange boxes. Added that GARS objects can either point to a reference object or just store that object's id (str). Added that some orange boxes can have multiple inputs.

…models into notebook_additions

Will add back once issue is resolved.

…models into notebook_additions

djarecka · 2023-10-17T16:54:11Z

@puja-trivedi - perhaps you didn't pull the changes to autogenerated formats and that's why you have the conflicts?

Partially resolved type hints issue when inherting and importing classes from biolink. All slots except 'in_taxon' are resolved.

linkml-schema/kbmodel.yaml

pbishwakarma · 2023-11-01T18:47:16Z

linkml-schema/kbmodel.yaml

+        description: >- 
+          Histone modification marker antibodies (eg H3K27ac, H3K27me3, H3K9me3) used in conjunction with an Enriched Cell Source Barcode in order to combine multiple Enriched Cell Populations before Barcoded Cell Sample step for 10xMultiome method. 
+          Each of the Histone antibodies captures an essential part of the epigenome.
+      population: 


Should this be enrichment population?

satra · 2023-11-01T18:58:23Z

@puja-trivedi - is this the latest version of the green sheets/minimal metadata release? (and could you please fix the conflicts?)

pbishwakarma · 2023-11-01T19:21:45Z

linkml-schema/kbmodel.yaml

+        required: true
+      quantity fmol:
+        description: Amount of library pool in the tube as measured in femtamoles (fmol)
+      quantity pM:


Should this be concentration instead of quantity?

linkml-schema/kbmodel.yaml

…models into notebook_additions

satra · 2023-11-07T16:31:56Z

go for it.

…models into notebook_additions

puja-trivedi · 2023-11-08T02:05:12Z

the checks are currently failing due to a linkml issue.

Update: All checks are passing now (using the advice provided on the issue). Had to add "linkml-runtime == 1.6.0" to pyproject.toml temporarily to fix issue.

…models into notebook_additions

…is completed

…models into notebook_additions

…fix pushtobkbit

…models into notebook_additions

Puja Trivedi and others added 6 commits October 5, 2023 20:06

Modified model based off green table

7e6f9dc

Merge branch 'notebook_additions' of https://github.com/puja-trivedi/…

bd24709

…models into notebook_additions

fixed typo

359af03

removed undefined slot

ac9d78a

removed identifer because multipple are not allowed

752f3a8

generate another formats

fd158a4

Puja Trivedi and others added 7 commits October 12, 2023 15:41

Added all 3 blue boxes (digital data asset) as well as their respecti…

1b43978

…ve orange boxes. Added that GARS objects can either point to a reference object or just store that object's id (str). Added that some orange boxes can have multiple inputs.

Merge branch 'notebook_additions' of https://github.com/puja-trivedi/…

d420a9c

…models into notebook_additions

Removed any_of due to errors when generating other formats.

9804ac4

Will add back once issue is resolved.

generate another formats

4023b6c

Trying any_of for everything except in_taxon

b694019

Merge branch 'notebook_additions' of https://github.com/puja-trivedi/…

3af3dd2

…models into notebook_additions

generate another formats

724dada

Puja Trivedi and others added 2 commits October 20, 2023 13:10

Added 'subsets' to the model to help organize the classes.

5c26a4d

Partially resolved type hints issue when inherting and importing classes from biolink. All slots except 'in_taxon' are resolved.

generate another formats

f959a1a

pbishwakarma reviewed Nov 1, 2023

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pbishwakarma reviewed Nov 1, 2023

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Puja Trivedi and others added 6 commits November 1, 2023 14:46

fixing merge conflict

307e44f

Merge branch 'notebook_additions' of https://github.com/puja-trivedi/…

a0dec38

…models into notebook_additions

generate another formats

af270a1

Fixed errors caught by linter and changed nm to nM

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Merge branch 'notebook_additions' of https://github.com/puja-trivedi/…

dde508d

…models into notebook_additions

generate another formats

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Puja Trivedi added 9 commits November 7, 2023 12:41

testing out new workflow that pushes kbmodel.py to bkbit repository

f97cb9c

Merge branch 'notebook_additions' of https://github.com/puja-trivedi/…

536e4c8

…models into notebook_additions

testing out new workflow that pushes kbmodel.py to bkbit repository

1899a6c

testing out new workflow that pushes kbmodel.py to bkbit repository

80b5b47

testing out new workflow that pushes kbmodel.py to bkbit repository

c9de75f

testing out new workflow that pushes kbmodel.py to bkbit repository

cbd9d78

testing out new workflow that pushes kbmodel.py to bkbit repository

ae2722b

testing out new workflow that pushes kbmodel.py to bkbit repository

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testing out new workflow that pushes kbmodel.py to bkbit repository

736e7f1

Puja Trivedi and others added 17 commits November 7, 2023 18:20

Adding linkml_runtime=1.6.0 package to help with current linkml issue

71df609

add linkml-runtime==1.6.0 to temporarily resolve linkml issue

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generate another formats

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always run pydantic version 2

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Merge branch 'notebook_additions' of https://github.com/puja-trivedi/…

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…models into notebook_additions

changed biolink prefix

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changed biolink prefix

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changed biolink prefix name to resolve prefix mismatch error

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generate another formats

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modified pushtobkbit workflow to run only after generateotherformats …

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…is completed

Merge branch 'notebook_additions' of https://github.com/puja-trivedi/…

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…models into notebook_additions

changed entity to material sample and process to procedure

f3bd4f1

generate another formats

1d82942

Modified 'test' workflows to run on push to any branch and trying to …

fdbef80

…fix pushtobkbit

Merge branch 'notebook_additions' of https://github.com/puja-trivedi/…

01c9e9f

…models into notebook_additions

removed changes to workflows (created separate branch for these changes)

4a14153

generate another formats

e58a65a

djarecka closed this May 6, 2024

puja-trivedi deleted the notebook_additions branch November 22, 2024 19:09

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Green Table Additions #20

Green Table Additions #20

puja-trivedi commented Oct 6, 2023

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Green Table Additions #20

Green Table Additions #20

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