| Age | Commit message (Expand) | Author |
|---|
| 2021-10-25 | pep8 formatting,pylint fixes | Alexander Kabui |
| 2021-10-25 | add socket obj and emit process | Alexander Kabui |
| 2021-10-25 | fix issues serializing byte string | Alexander Kabui |
| 2021-10-25 | rename key to image_data | Alexander Kabui |
| 2021-10-25 | add function to process images | Alexander Kabui |
| 2021-10-25 | add function to capture output in real time | Alexander Kabui |
| 2021-10-25 | Implement `fetch_literature_correlations` and depedencies...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Migrate:
* `web.webqtl.correlation.CorrelationPage.getTempLiteratureTable`
* `web.webqtl.correlation.CorrelationPage.fetchLitCorrelations`
from GeneNetwork1.
The first function creates and populates a temporary table with the
literature correlations data.
The second function uses the data in the newly created temporary table to
link the trait with the correlation value.
| Frederick Muriuki Muriithi |
| 2021-10-25 | Implement `get_filename` for correlations...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Implement `get_filename` for the correlations, to be used to determine
whether to do fast or normal correlations.
This is a migration of the
`web.webqtl.correlation.CorrelationPage.getFileName` function in GN1
| Frederick Muriuki Muriithi |
| 2021-10-21 | Implement `translate_to_mouse_gene_id` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Migrate the `web.webqtl.correlation/CorrelationPage.translateToMouseGeneID`
function in GN1 to GN3.
This is a function that retrieves data from the database, and therefore uses
a system outside of our code, therefore, the function does not have a
corresponding unit test.
This kind of function will probably need to be tested at the integration or
system tests level, where we test that our code interacts correcly with any
and all external systems that it should.
| Frederick Muriuki Muriithi |
| 2021-10-21 | Implement `find_identical_traits` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement function `find_identical_traits`
* tests/unit/test_partial_correlations.py: implement tests for function
`find_identical_traits`
Migrate `web.webqtl.correlation.correlationFunction.findIdenticalTraits`
function in GN1 to here, adding in tests to ensure the migration works in a
bug-compatible version with the original.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Implement remaining `fix_samples` functionality...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement `fix_samples` function
* tests/unit/test_partial_correlations.py: implement tests for `fix_samples`
function
Implement the remaining partial migration for the
`web.webqtl.correlation.correlationFunction.fixStrain` function in GN1.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Implement `dictify_by_samples`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement `dictify_by_samples` function
* tests/unit/test_partial_correlations.py: implement tests for
`dictify_by_samples` function
Implement the `dictify_by_samples` function as a partial migration of the
`web.webqtl.correlation.correlationFunction.fixStrains` function from GN1.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Implement `control_samples` function as is in GN1...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: Implement `control_samples` function
* tests/unit/test_partial_correlations.py: add tests for `control_samples`
function
Implement the function `control_samples` and make it mostly bug-compatible
with the `web/webqtl/correlation/correlationFunction.controlStrain` function
in GN1.
This implementation in GN3 does not do any calls to the database. It will
rely on other functions to provide the data from the database to it.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Move `export_informative` function to `gn3.db.traits` module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move `export_informative` function here
* gn3/partial_correlations.py: Remove `export_informative` function
* tests/unit/db/test_traits.py: Move `export_informative` function tests here
* tests/unit/test_partial_correlations.py: Remove `export_informative`
function tests
The `export_informative` function relates more to the traits than to the
partial correlations, and could find use in more than just the partial
correlations stuff. This commit moves the function to the more
traits-specific `gn3.db.traits` module.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Move 'export_trait_data' to 'gn3.db.traits' module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move function `export_trait_data` here
* gn3/heatmaps.py: Remove function `export_trait_data`
* tests/unit/db/test_traits.py: Move function `export_trait_data` tests here
* tests/unit/test_heatmaps.py: Remove function `export_trait_data` here
Function `export_trait_data` more closely corresponds to the traits and is
used in more than just the `gn3.heatmaps` module. This commit moves the
relevant code over to the `gn3.db.traits` module and also moves the tests to
the corresponding tests modules.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Migrate `export_informative` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: Implement a mostly, bug-compatible
`export_informative` function as part of migrating the partial correlations
feature over to GN3 from GN1
* tests/unit/test_partial_correlations.py: Implement tests to ensure the code
work in a similar manner as that one in GN1.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-corre... | Frederick Muriuki Muriithi |
| 2021-10-19 | Implement remaining `fix_samples` functionality...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement `fix_samples` function
* tests/unit/test_partial_correlations.py: implement tests for `fix_samples`
function
Implement the remaining partial migration for the
`web.webqtl.correlation.correlationFunction.fixStrain` function in GN1.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Fix some linting issues | Frederick Muriuki Muriithi |
| 2021-10-19 | Allow CORS_ORIGINS to be configurable via the environment...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi
* gn3/app.py: setup CORS after all the configuration sources are loaded.
* gn3/settings.py: Parse CORS_ORIGINS from the environment variables.
Enable the CORS_ORIGINS configuration to be set in the environment variables
to give the application some flexibility when launching.
| 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 |
| 2021-10-19 | Enable vertical orientation of heatmaps...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi
* Update the code to enable the generation of the heatmap in both the
horizontal and vertical orientations.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Swap axis labels...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi
* Switch the axis labels to make them less confusing for the user.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Add typing. Simplify arguments....Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi
* Add type-hints to the functions
* Merge the axis data and labels to simpler dict arguments to reduce number of
parameters to the function.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Remove file I/O statements...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi
* Remove file I/O from the function. If file I/O is needed, it will be
provided outside of this function.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Implement `dictify_by_samples`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement `dictify_by_samples` function
* tests/unit/test_partial_correlations.py: implement tests for
`dictify_by_samples` function
Implement the `dictify_by_samples` function as a partial migration of the
`web.webqtl.correlation.correlationFunction.fixStrains` function from GN1.
| Frederick Muriuki Muriithi |
| 2021-10-18 | Implement `control_samples` function as is in GN1...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: Implement `control_samples` function
* tests/unit/test_partial_correlations.py: add tests for `control_samples`
function
Implement the function `control_samples` and make it mostly bug-compatible
with the `web/webqtl/correlation/correlationFunction.controlStrain` function
in GN1.
This implementation in GN3 does not do any calls to the database. It will
rely on other functions to provide the data from the database to it.
| Frederick Muriuki Muriithi |
| 2021-10-18 | Move `export_informative` function to `gn3.db.traits` module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move `export_informative` function here
* gn3/partial_correlations.py: Remove `export_informative` function
* tests/unit/db/test_traits.py: Move `export_informative` function tests here
* tests/unit/test_partial_correlations.py: Remove `export_informative`
function tests
The `export_informative` function relates more to the traits than to the
partial correlations, and could find use in more than just the partial
correlations stuff. This commit moves the function to the more
traits-specific `gn3.db.traits` module.
| Frederick Muriuki Muriithi |
| 2021-10-18 | Move 'export_trait_data' to 'gn3.db.traits' module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move function `export_trait_data` here
* gn3/heatmaps.py: Remove function `export_trait_data`
* tests/unit/db/test_traits.py: Move function `export_trait_data` tests here
* tests/unit/test_heatmaps.py: Remove function `export_trait_data` here
Function `export_trait_data` more closely corresponds to the traits and is
used in more than just the `gn3.heatmaps` module. This commit moves the
relevant code over to the `gn3.db.traits` module and also moves the tests to
the corresponding tests modules.
| Frederick Muriuki Muriithi |
| 2021-10-18 | Migrate `export_informative` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: Implement a mostly, bug-compatible
`export_informative` function as part of migrating the partial correlations
feature over to GN3 from GN1
* tests/unit/test_partial_correlations.py: Implement tests to ensure the code
work in a similar manner as that one in GN1.
| Frederick Muriuki Muriithi |
| 2021-10-12 | Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into bug/f... | zsloan |
| 2021-09-28 | Provide loci names to heatmap...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Provide the loci names to the heatmaps so that hovering over the heatmap
cells displays the associated locus name.
| Frederick Muriuki Muriithi |
| 2021-09-28 | Retrieve loci names ordered by chromosomes...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/heatmaps.py: implement function
* tests/unit/test_heatmaps.py: add test
Add a function to retrieve the loci names from the traits, ordered by
chromosomes, in alphabetical order.
This is useful to provide the user with more information on hovering over
the heatmap cells: each cell will now display the locus name, trait name and
value associated with it.
| Frederick Muriuki Muriithi |
| 2021-09-28 | Approximate single-spectrum colour scale in GN1...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* To provide a somewhat similar experience to GeneNetwork1, this commit
approximates the single-spectrum colour scale in GeneNetwork1 for the
heatmaps in GeneNetwork3.
Work to get the multiple-spectrum colour sc(ales/hemes) will be done in
other commits, since that might require digging even deeper into Plotly's
guts to figure out.
| Frederick Muriuki Muriithi |
| 2021-09-27 | add file not found exception | Alexander Kabui |
| 2021-09-27 | return str error for exception | Alexander Kabui |
| 2021-09-27 | fix merge conflicts | Alexander Kabui |
| 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 |
| 2021-09-27 | Narrow the exception and add comments...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Only catch the `FileExistsError` allowing any other exception to pass
through. This tries to conform a little to the review at
https://github.com/genenetwork/genenetwork3/pull/37#discussion_r714552696
| Frederick Muriuki Muriithi |
| 2021-09-27 | Update terminology: `riset` to `group`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update terminology to use the appropriate domain terminology according to
Zachary's direction at
https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926041744
| Frederick Muriuki Muriithi |
| 2021-09-27 | Update terminology: `strain` to `sample`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update the terminology used: use `sample` in place of `strain` according to
Zachary's direction at
https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926043306
| Frederick Muriuki Muriithi |
| 2021-09-23 | minor fixes for endpoint | Alexander Kabui |
| 2021-09-23 | Return r error if returncode!=0 | Alexander Kabui |
| 2021-09-23 | read generated files from r and return output | Alexander Kabui |
| 2021-09-22 | Fix more pylint errors | Frederick Muriuki Muriithi |
| 2021-09-22 | Fix typing issues...* Ignore some errors
* Update typing definitions for some portions of code
* Add missing imports
| 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 |
| 2021-09-22 | jsonify results | Alexander Kabui |
