feat: cxg conversion script updates for uns["spatial"] #7023
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Deployment Summary
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kaloster
changed the title
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #7023 +/- ##
==========================================
+ Coverage 91.93% 92.02% +0.08%
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Files 184 186 +2
Lines 15615 15852 +237
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+ Hits 14356 14588 +232
- Misses 1259 1264 +5
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. |
kaloster
commented
May 15, 2024
| @@ -8,7 +8,7 @@ RUN apt-get update && \ | |||
| apt-get upgrade -y && \ | |||
| apt install software-properties-common -y && \ | |||
| add-apt-repository ppa:deadsnakes/ppa && \ | |||
| apt-get update && apt-get install -y python3.10 python3.10-dev python3.10-venv && \ | |||
| apt-get update && apt-get install -y python3.10 python3.10-dev python3.10-venv libvips && \ | |||
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libvips is required in order to get pyvips to run
kaloster
commented
May 17, 2024
kaloster
commented
May 17, 2024
| # Cast 'in_tissue' column values as boolean to make it categorical | ||
| # https://github.com/chanzuckerberg/single-cell-explorer/issues/841 | ||
| if column_name == "in_tissue": | ||
| dtype, hints = get_dtype_and_schema_of_array(column_values.astype(bool)) |
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this is to treat the reported issue for in_tissue boolean column that sometimes stored as int. After casting it as bool it will appear as categorical in explorer
kaloster
commented
May 17, 2024
kaloster
commented
May 17, 2024
| is_valid = ( | ||
| isinstance(embedding_name, str) | ||
| and (embedding_name.startswith("X_") or embedding_name == "spatial") | ||
| and len(embedding_name) > 2 |
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valid embedding name either starts with X_ or equals to spatial
Bento007
requested changes
May 20, 2024
Bento007
approved these changes
May 21, 2024
kaloster
commented
May 21, 2024
| if embedding_name == "spatial": | ||
| embedding_name = f"{embedding_container}/{embedding_name}" | ||
| else: | ||
| embedding_name = f"{embedding_container}/{embedding_name[2:]}" |
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if "spatial" no need to strip the first 2 characters
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Reason for Change
Changes
convert_uns_to_cxg_group()handler for all uns["spatial"] actions as an additional step inmake_cxg()scriptSpatialDataProcessorclass to handlecxgconversion forunsand spatial deep zoom asset generation and uploadTesting steps
make_cxg()against a localh5ad- verify generated assets are uploaded to s3 and that the generated cxg includesunsgroup.-- datasets with fullres spatial image
-- datasets with hires only spatial image
-- datasets without spatial embedding
Notes for Reviewer
libvipshad to be added to backed and processing Docker in order to getpyvipslibrary (that generates the deep zoom tiles) to work properly