| Age | Commit message (Expand) | Author |
|---|
| 2022-03-08 | Create database connections within context managers...Use the `with` context manager to open database connections, so as to ensure
that those connections are closed once the call is completed. This hopefully
avoids the 'too many connections' error
| Frederick Muriuki Muriithi |
| 2022-02-21 | Fix a myriad of linter issues...* 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
| Frederick Muriuki Muriithi |
| 2021-10-19 | Enable vertical and horizontal heatmaps...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.
| Frederick Muriuki Muriithi |
| 2021-09-27 | Remove unnecessary variable....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
| Frederick Muriuki Muriithi |
| 2021-09-22 | Fix pylint errors...* Add missing function and module docstrings
* Remove unused imports
* Fix import order
* Rework some code sections to fix issues
* Disable some pylint errors.
| Frederick Muriuki Muriithi |
| 2021-09-22 | Update check: Heatmaps need at least 2 items...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.
| Frederick Muriuki Muriithi |
| 2021-09-22 | Return serialized plotly figure...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.
| Frederick Muriuki Muriithi |
| 2021-09-20 | Enable Cross-Origin Resource Sharing...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.
| Frederick Muriuki Muriithi |
| 2021-09-20 | Return only the data...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.
| Frederick Muriuki Muriithi |
| 2021-09-17 | Return path to generated filename for now...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.
| Frederick Muriuki Muriithi |
| 2021-09-16 | Intergrate the heatmap generation with the API...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.
| Frederick Muriuki Muriithi |
