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* Use `with` in place of plain `open`
* Use f-strings in place of `str.format()`
* Remove string interpolation from queries - provide data as query parameters
* other minor fixes
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi
* Update the request endpoint, so that it produces a vertical or horizontal
heatmap depending on the user's request.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Fix issue according to review
https://github.com/genenetwork/genenetwork3/pull/37#discussion_r714549781
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* Add missing function and module docstrings
* Remove unused imports
* Fix import order
* Rework some code sections to fix issues
* Disable some pylint errors.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update the check to look for at least 2 traits before trying to generate the
heatmap.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/api/heatmaps.py: Serialize the figure to JSON
* gn3/heatmaps.py: Return the figure object
Serialize the Plotly figure into JSON, and return that, so that it can be
used on the client to display the image.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/api/heatmaps.py: Fix bugs in data parsing
* gn3/app.py: enable CORS
* gn3/settings.py: add flask-cors configurations
* guix.scm: Add flask-cors dependency
For easier testing of the heatmaps generation feature, this commit activates
the cross-origin resource sharing for all "localhost" origins.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/api/heatmaps.py: Parse incoming data to build up correct trait names and
respond with only the computed heatmap data.
* gn3/heatmaps.py: Return only the computed data for heatmaps and clustering.
Since GN3 is supposed to handle only the data, and db-access, this commit
ensures that GN3 responds to the client with only the computed heatmap data,
and does not try to generate the heatmaps themselves.
The generation of the heatmaps will be delegated to the UI clients, such as
GeneNetwork2.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* To help with demonstrating that the code is producing the expected output,
for now, we return the path to the generated html file that displays the
interactive heatmap.
At this point, it is mostly useful in the development environment. Moving
forward, we might have to actually stream the raw html, or if we can get the
Kaleido library packaged for GNU Guix, stream the images binary data instead.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Intergrate the heatmap generation code on the /api/heatmaps/clustered
endpoint.
The endpoint should take a json query of the form:
{"traits_names": [ ... ] }
where the "traits_name" value is a list of the full names of traits.
A sample query to the endpoint could be something like the following:
curl -i -X POST "http://localhost:8080/api/heatmaps/clustered" \
-H "Accept: application/json" \
-H "Content-Type: application/json" \
-d '{
"traits_names": [
"UCLA_BXDBXH_CARTILAGE_V2::ILM103710672",
"UCLA_BXDBXH_CARTILAGE_V2::ILM2260338",
"UCLA_BXDBXH_CARTILAGE_V2::ILM3140576",
"UCLA_BXDBXH_CARTILAGE_V2::ILM5670577",
"UCLA_BXDBXH_CARTILAGE_V2::ILM2070121",
"UCLA_BXDBXH_CARTILAGE_V2::ILM103990541",
"UCLA_BXDBXH_CARTILAGE_V2::ILM1190722",
"UCLA_BXDBXH_CARTILAGE_V2::ILM6590722",
"UCLA_BXDBXH_CARTILAGE_V2::ILM4200064",
"UCLA_BXDBXH_CARTILAGE_V2::ILM3140463"
]
}'
which should respond with a json response containing the raw binary string
for the png format and possibly another for the svg format.
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