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C2c source target v1 to v2

Open vishnu-vasan opened this issue 1 year ago • 1 comments

Created the api for the C2C source target task for v2

Issue ticket number and link

Closes #xxxx (Replace xxxx with the GitHub issue number)

Checklist before requesting a review

  • [ Yes ] I have performed a self-review of my code

  • Check the correct box. Does this PR contain:

    • [ ] Breaking changes
    • [ ] New functionality
    • [ ] Major changes
    • [ ] Minor changes
    • [ ] Bug fixes

  • [ ] Proposed changes are described in the CHANGELOG.md

  • [ ] CI Tests succeed and look good!

Requirements after merging

  • [ ] Need to regenerate common/ resources

  • [ ] Need to regenerate task-specific resources. Specify: <all or ...>

vishnu-vasan avatar Feb 28 '24 12:02 vishnu-vasan

Thanks Kai, i will change them

On Tue, Apr 16, 2024 at 8:45 AM Kai Waldrant @.***> wrote:

@.**** commented on this pull request.

Make sure you use allen_brain_atlas instead of allen_mouse_brain_atlas or mouse_brain_atlas

On src/datasets/resource_test_scripts/allen_mouse_brain_atlas.sh https://github.com/openproblems-bio/openproblems-v2/pull/391#discussion_r1567380265 :

change fn toallen_brain_atlas.sh

In src/datasets/resource_test_scripts/allen_mouse_brain_atlas.sh https://github.com/openproblems-bio/openproblems-v2/pull/391#discussion_r1567381527 :

  • --seed 123 \
  • --do_subsample true \
  • --output_raw force_null \
  • --output_normalized force_null \
  • --output_hvg force_null \
  • --output_pca force_null \
  • --output_knn force_null \
  • --output_dataset '$id/dataset.h5ad' \
  • --output_meta '$id/dataset_meta.yaml' \
  • --output_state '$id/state.yaml' \
  • --publish_dir "$DATASET_DIR"

+# rm -r $DATASET_DIR/temp_* + +# run task process dataset components +src/tasks/cell_cell_communication_source_target/resources_test_scripts/mouse_brain_atlas.sh

⬇️ Suggested change

-src/tasks/cell_cell_communication_source_target/resources_test_scripts/mouse_brain_atlas.sh +src/tasks/cell_cell_communication_source_target/resources_test_scripts/allen_brain_atlas.sh

In src/tasks/cell_cell_communication_source_target/api/comp_control_method.yaml https://github.com/openproblems-bio/openproblems-v2/pull/391#discussion_r1567383237 :

    • path: /resources_test/cell_cell_communication_source_target/mouse_brain_atlas
  •  dest: resources_test/cell_cell_communication_source_target/mouse_brain_atlas

⬇️ Suggested change

    • path: /resources_test/cell_cell_communication_source_target/mouse_brain_atlas
  •  dest: resources_test/cell_cell_communication_source_target/mouse_brain_atlas
    • path: /resources_test/cell_cell_communication_source_target/allen_brain_atlas
  •  dest: resources_test/cell_cell_communication_source_target/allen_brain_atlas

In src/tasks/cell_cell_communication_source_target/api/comp_method.yaml https://github.com/openproblems-bio/openproblems-v2/pull/391#discussion_r1567384357 :

    • path: /resources_test/cell_cell_communication_source_target/mouse_brain_atlas
  •  dest: resources_test/cell_cell_communication_source_target/mouse_brain_atlas

⬇️ Suggested change

    • path: /resources_test/cell_cell_communication_source_target/mouse_brain_atlas
  •  dest: resources_test/cell_cell_communication_source_target/mouse_brain_atlas
    • path: /resources_test/cell_cell_communication_source_target/allen_brain_atlas
  •  dest: resources_test/cell_cell_communication_source_target/allen_brain_atlas

In src/tasks/cell_cell_communication_source_target/api/comp_metric.yaml https://github.com/openproblems-bio/openproblems-v2/pull/391#discussion_r1567384568 :

    • path: /resources_test/cell_cell_communication_source_target/mouse_brain_atlas
  •  dest: resources_test/cell_cell_communication_source_target/mouse_brain_atlas

⬇️ Suggested change

    • path: /resources_test/cell_cell_communication_source_target/mouse_brain_atlas
  •  dest: resources_test/cell_cell_communication_source_target/mouse_brain_atlas
    • path: /resources_test/cell_cell_communication_source_target/allen_brain_atlas
  •  dest: resources_test/cell_cell_communication_source_target/allen_brain_atlas

In src/tasks/cell_cell_communication_source_target/api/comp_process_dataset.yaml https://github.com/openproblems-bio/openproblems-v2/pull/391#discussion_r1567384760 :

    • path: /resources_test/cell_cell_communication_source_target/mouse_brain_atlas
  •  dest: resources_test/cell_cell_communication_source_target/mouse_brain_atlas

⬇️ Suggested change

    • path: /resources_test/cell_cell_communication_source_target/mouse_brain_atlas
  •  dest: resources_test/cell_cell_communication_source_target/mouse_brain_atlas
    • path: /resources_test/cell_cell_communication_source_target/allen_brain_atlas
  •  dest: resources_test/cell_cell_communication_source_target/allen_brain_atlas

In src/tasks/cell_cell_communication_source_target/api/file_common_dataset.yaml https://github.com/openproblems-bio/openproblems-v2/pull/391#discussion_r1567385652 :

@@ -0,0 +1,49 @@ +type: file +example: "resources_test/cell_cell_communication_source_target/mouse_brain_atlas/dataset.h5ad"

⬇️ Suggested change

-example: "resources_test/cell_cell_communication_source_target/mouse_brain_atlas/dataset.h5ad" +example: "resources_test/cell_cell_communication_source_target/allen_brain_atlas/dataset.h5ad"

In src/tasks/cell_cell_communication_source_target/api/file_prediction.yaml https://github.com/openproblems-bio/openproblems-v2/pull/391#discussion_r1567386142 :

@@ -0,0 +1,24 @@ +type: file +example: "resources_test/cell_cell_communication_source_target/mouse_brain_atlas/prediction.h5ad"

⬇️ Suggested change

-example: "resources_test/cell_cell_communication_source_target/mouse_brain_atlas/prediction.h5ad" +example: "resources_test/cell_cell_communication_source_target/allen_brain_atlas/dataset.h5ad"

In src/tasks/cell_cell_communication_source_target/api/file_score.yaml https://github.com/openproblems-bio/openproblems-v2/pull/391#discussion_r1567386338 :

@@ -0,0 +1,25 @@ +type: file +example: "resources_test/cell_cell_communication_source_target/mouse_brain_atlas/score.h5ad"

⬇️ Suggested change

-example: "resources_test/cell_cell_communication_source_target/mouse_brain_atlas/score.h5ad" +example: "resources_test/cell_cell_communication_source_target/allen_brain_atlas/dataset.h5ad"

In src/tasks/cell_cell_communication_source_target/api/file_solution.yaml https://github.com/openproblems-bio/openproblems-v2/pull/391#discussion_r1567386542 :

@@ -0,0 +1,61 @@ +type: file +example: "resources_test/cell_cell_communication_source_target/mouse_brain_atlas/solution.h5ad"

⬇️ Suggested change

-example: "resources_test/cell_cell_communication_source_target/mouse_brain_atlas/solution.h5ad" +example: "resources_test/cell_cell_communication_source_target/allen_brain_atlas/dataset.h5ad"

In src/tasks/cell_cell_communication_source_target/api/file_test.yaml https://github.com/openproblems-bio/openproblems-v2/pull/391#discussion_r1567386749 :

@@ -0,0 +1,37 @@ +type: file +example: "resources_test/cell_cell_communication_source_target/mouse_brain_atlas/test.h5ad"

⬇️ Suggested change

-example: "resources_test/cell_cell_communication_source_target/mouse_brain_atlas/test.h5ad" +example: "resources_test/cell_cell_communication_source_target/allen_brain_atlas/dataset.h5ad"

In src/tasks/cell_cell_communication_source_target/api/file_train.yaml https://github.com/openproblems-bio/openproblems-v2/pull/391#discussion_r1567386907 :

@@ -0,0 +1,37 @@ +type: file +example: "resources_test/cell_cell_communication_source_target/mouse_brain_atlas/train.h5ad"

⬇️ Suggested change

-example: "resources_test/cell_cell_communication_source_target/mouse_brain_atlas/train.h5ad" +example: "resources_test/cell_cell_communication_source_target/allen_brain_atlas/dataset.h5ad"

In src/tasks/cell_cell_communication_source_target/process_dataset/script.py https://github.com/openproblems-bio/openproblems-v2/pull/391#discussion_r1567387831 :

@@ -0,0 +1,60 @@ +import sys +import anndata as ad +# from openproblems.tasks._cell_cell_communication._common.utils import ligand_receptor_resource +import openproblems as op +import pandas as pd

+## VIASH START +par = {

  • "input": "resources_test/cell_cell_communication_source_target/mouse_brain_atlas",

⬇️ Suggested change

  • "input": "resources_test/cell_cell_communication_source_target/mouse_brain_atlas",
  • "input": "resources_test/cell_cell_communication_source_target/allen_brain_atlas",

On src/tasks/cell_cell_communication_source_target/resources_test_scripts/mouse_brain_atlas.sh https://github.com/openproblems-bio/openproblems-v2/pull/391#discussion_r1567391448 :

Change fn to allen_brain_atlas.sh

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vishnu-vasan avatar Apr 17 '24 15:04 vishnu-vasan

This work has been moved to https://github.com/openproblems-bio/task_cell_cell_communication! :) Closing this PR.

rcannood avatar Jul 02 '24 07:07 rcannood