Age | Commit message (Expand) | Author |
2021-10-25 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-corre... | Frederick Muriuki Muriithi |
2021-10-25 | mypy:Incompatible types in assignment fix | Alexander Kabui |
2021-10-25 | mypy fix for none stdout | Alexander Kabui |
2021-10-25 | pylint and pep8 formatting | Alexander Kabui |
2021-10-25 | fix unittests | Alexander Kabui |
2021-10-25 | minor fixes for sript enable annotations | Alexander Kabui |
2021-10-25 | add flask-socketio input to gn3 | Alexander Kabui |
2021-10-25 | minor modification for emitting data:add namespaces | Alexander Kabui |
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 | script modification : add debug statements | 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 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-corre... | 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 |
2021-10-21 | Document tests better...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Document the issues better to help with understanding what each test checks
for.
| 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 | Disable pylint issue...* Disable minor pylint issue.
| 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 | Disable pylint issue...* Disable minor pylint issue.
| 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 |
2021-10-14 | Fixed when model is set to account for situations with no covariates | zsloan |
2021-10-14 | Incorporated Danny's code for calculating QTL main effects into rqtl_wrapper.R | zsloan |
2021-10-12 | Merge pull request #40 from zsloan/bug/fix_rqtl_covariates...Bug/fix rqtl covariates | zsloan |
2021-10-12 | Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into bug/f... | zsloan |
2021-10-06 | guix.scm: Add python-flask-cors and python-plotly dependencies | BonfaceKilz |
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 |