Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Tkakar/cat 1091 add kaggle2 logic #3669

Merged
merged 6 commits into from
Jan 21, 2025
Merged

Tkakar/cat 1091 add kaggle2 logic #3669

Show file tree
Hide file tree
Changes from 5 commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
0f57e41
Updated logic for epic visualization
tkakar Jan 9, 2025
d454013
Added changelog and bumped portal-viz release
tkakar Jan 16, 2025
f398e0e
Merge branch 'main' into tkakar/cat-1091-add-kaggle2-logic
tkakar Jan 16, 2025
538b8e3
Added changes to requirement.txt
tkakar Jan 16, 2025
b8de7ef
Minor comment edits
tkakar Jan 16, 2025
7b0ed91
Updated comment command for req.in
tkakar Jan 17, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG-update-epic-seg-logic.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
- Updated logic to access the builder for EPIC Segmentation masks using the epic vitessce-hint.
4 changes: 2 additions & 2 deletions context/app/routes_browse.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -117,8 +117,8 @@ def details_vitessce(type, uuid):
marker = request.args.get('marker') or None
parent = client.get_entity(parent_uuid) if parent_uuid else None
epic_uuid = None
if 'segmentation_mask' in entity.get('vitessce-hints') and entity.get(
'status') != 'Error' and entity.get("pipeline") == "Segmentation Mask":
if 'epic' in entity.get('vitessce-hints') and entity.get(
'status') != 'Error':
epic_uuid = uuid
if parent is None:
ancestors = entity.get('immediate_ancestor_ids')
Expand Down
4 changes: 1 addition & 3 deletions context/requirements.in
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,4 @@
# Update requirements.txt if this file changes:
# pip install pip-tools
# pip-compile --allow-unsafe --generate-hashes --output-file=context/requirements.txt context/requirements.in
Flask>=3.1.0
Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I removed these as they seem to be needed for the pre-uv era and was causing errors.

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Good call, the correct command should now be uv pip compile context/requirements.in --universal --output-file context/requirements.txt

Flask[async]>=3.1.0
globus-sdk>=3.9.0
Expand All @@ -16,7 +14,7 @@ hubmap-commons>=2.1.18
boto3==1.28.17

# Plain "git+https://github.com/..." references can't be hashed, so we point to a release zip instead.
https://github.com/hubmapconsortium/portal-visualization/archive/refs/tags/0.3.6.zip
https://github.com/hubmapconsortium/portal-visualization/archive/refs/tags/0.3.8.zip

# Security warning for older versions;
# Can be removed when commons drops prov dependency.
Expand Down
26 changes: 20 additions & 6 deletions context/requirements.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
# This file was autogenerated by uv via the following command:
# pip install pip tools
# uv pip compile context/requirements.in --universal --output-file context/requirements.txt
aiobotocore==2.5.4
# via s3fs
Expand Down Expand Up @@ -147,6 +148,8 @@ kiwisolver==1.4.4
# via matplotlib
lazy-loader==0.3
# via scikit-image
legacy-api-wrap==1.4.1
# via scanpy
llvmlite==0.40.1
# via
# numba
Expand Down Expand Up @@ -234,7 +237,14 @@ packaging==23.1
# scanpy
# scikit-image
# statsmodels
pandas==1.4.1
pandas==2.1.0 ; python_full_version >= '3.12'
# via
# anndata
# scanpy
# seaborn
# statsmodels
# vitessce
pandas==2.2.3 ; python_full_version < '3.12'
# via
# anndata
# scanpy
Expand All @@ -256,7 +266,7 @@ pillow==11.0.0
# scikit-image
platformdirs==2.5.1
# via black
portal-visualization @ https://github.com/hubmapconsortium/portal-visualization/archive/refs/tags/0.3.6.zip
portal-visualization @ https://github.com/hubmapconsortium/portal-visualization/archive/refs/tags/0.3.8.zip
# via -r context/requirements.in
propcache==0.2.0
# via yarl
Expand All @@ -271,7 +281,9 @@ pycparser==2.21 ; platform_python_implementation != 'PyPy'
pyjwt==2.4.0
# via globus-sdk
pynndescent==0.5.10
# via umap-learn
# via
# scanpy
# umap-learn
pyparsing==3.0.7
# via
# matplotlib
Expand Down Expand Up @@ -320,7 +332,7 @@ s3fs==2023.6.0
# via fsspec
s3transfer==0.6.2
# via boto3
scanpy==1.9.3
scanpy==1.10.4
# via vitessce
scikit-image==0.21.0
# via ome-zarr
Expand All @@ -339,7 +351,7 @@ scipy==1.8.0
# statsmodels
# umap-learn
# vitessce
seaborn==0.12.2
seaborn==0.13.2
# via scanpy
session-info==1.0.0
# via scanpy
Expand Down Expand Up @@ -388,14 +400,16 @@ typing-extensions==4.1.1
# asgiref
# black
# python-datauri
tzdata==2024.2
# via pandas
umap-learn==0.5.3
# via scanpy
urllib3==1.26.17
# via
# botocore
# distributed
# requests
vitessce==3.4.0
vitessce==3.5.0
# via portal-visualization
werkzeug==3.1.3
# via flask
Expand Down
Loading