| Age | Commit message (Expand) | Author |
|---|
| 2022-01-10 | Convert keys to string...* Some traits have a name composed of all numerals, which leads to the names
being interpreted as numbers. This commit forces them to string to avoid
subtle bugs where the code fails.
| Frederick Muriuki Muriithi |
| 2022-01-10 | Fix error in query: Replace '=' with 'IN' | Frederick Muriuki Muriithi |
| 2022-01-10 | Rework database functions to fetch multiple items...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* In an attempt to optimise the performance of the partial correlations
feature, this commit reworks some database access functions to fetch
multiple items from the database, per query, unlike their original forms
which would fetch a single item per query.
This reduces queries to the database, and should hopefully improve the
responsiveness of the partial correlations feature.
| Frederick Muriuki Muriithi |
| 2022-01-05 | Merge branch 'main' into fix/check-for-duplicates-before-deletions-or-insertions | BonfaceKilz |
| 2022-01-04 | traits.py: Don't use "value" to check if a record exists...The problem with using the "value" record is that it's a floating point
number. See
<https://www.bonfacemunyoki.com/post/2021-10-21-comparing-floating-point-numbers/>
on why comparing floating point numbers can be an issue.
| BonfaceKilz |
| 2022-01-04 | traits.py: Return early during an insert if the give record exists...Sometimes, a user will try to insert data twice, on in some instances, 2
different users will attempt the same inserts of the same records separately.
In such cases, ignore the insert, and return early.
| BonfaceKilz |
| 2022-01-04 | traits.py Delete a record only if it exists...In the case when the user tries to delete the same data twice, prior to this
commit, an error was being generated. This commit remedies this by checking
if a record exists prior to deleting it.
| BonfaceKilz |
| 2021-12-23 | db: Assist mypy with explicit type declaration....* gn3/db/datasets.py (dataset_metadata): Assist mypy by explicitly declaring
type of return dictionary.
| Arun Isaac |
| 2021-12-23 | db: Fix sparql_query return type....* gn3/db/datasets.py: Import List from typing.
(sparql_query): Set return type to List[Dict[str, Any]].
| Arun Isaac |
| 2021-12-23 | db: Fix wrong continued indentation....* gn3/db/datasets.py (dataset_metadata): Fix wrong continued indentation.
| Arun Isaac |
| 2021-12-14 | linting: Fix obvious linting issues | Frederick Muriuki Muriithi |
| 2021-12-14 | Fix bug: expects int, gets object - Fixed. | Frederick Muriuki Muriithi |
| 2021-12-14 | mypy: ignore some imports and errors...* Ignore some missing library stubs
* Ignore some typing errors
* Fix obvious typing errors
| Frederick Muriuki Muriithi |
| 2021-12-14 | Set explicit formatting for sequences in queries...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* the mysqlclient is sometimes finicky with the format specifiers, especially
in the `WHERE ... IN ...` clauses where a sequence of values is
provided. This commit explicitly sets the format specifiers for such clauses
so as to avoid sporadic failures due to differences in the form of data from
one query to the next.
| Frederick Muriuki Muriithi |
| 2021-12-13 | Fix errors with query...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Use the correct format string paradigm: put f before opening quote.
* Provide missing space just before 'FROM' clause
| Frederick Muriuki Muriithi |
| 2021-12-10 | Fix parameters...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Provide parameters as a dict of items (which works for MySQL), rather than
as keywork arguments (as works in PostgreSQL).
| Frederick Muriuki Muriithi |
| 2021-12-09 | Prevent error on no result. Fix indexing...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* If the dataset name is not found, don't cause an exception, instead, return
the provided search name.
* Use the correct inner object
| Frederick Muriuki Muriithi |
| 2021-12-09 | Provide clearer error message...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* To help with debugging error conditions, provide the original name to help
with figuring out why the error was raised
| Frederick Muriuki Muriithi |
| 2021-12-06 | Merge branch 'main' of github.com:genenetwork/genenetwork3 | Frederick Muriuki Muriithi |
| 2021-12-02 | Implement dataset metadata API endpoint....* guix.scm: Import (gnu packages rdf).
(genenetwork3)[propagated-inputs]: Add python-sparqlwrapper.
* gn3/settings.py (SPARQL_ENDPOINT): New variable.
* gn3/api/general.py: Import datasets from gn3.db.
(dataset_metadata): New API endpoint.
* gn3/db/datasets.py: Import re, Template from string, Dict and Optional from
typing, JSON and SPARQLWrapper from SPARQLWrapper, SPARQL_ENDPOINT from
gn3.settings.
(sparql_query, dataset_metadata): New functions.
| Arun Isaac |
| 2021-11-29 | Merge branch 'main' into partial-correlations | Muriithi Frederick Muriuki |
| 2021-11-29 | Fix linting errors...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2021-11-29 | Provide entry-point function for the partial correlations...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Provide the entry-point function to the partial correlation feature. This is
the function that ochestrates the fetching of the data, and processing it
for output by the API endpoint (to be implemented).
| Frederick Muriuki Muriithi |
| 2021-11-29 | Fix bugs in data...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Process the db_name and db_type values.
* Return data correctly
| Frederick Muriuki Muriithi |
| 2021-11-29 | Update return type...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Return the complete filename when found, or the boolean value False, when it
is not found.
| Frederick Muriuki Muriithi |
| 2021-11-29 | Return only values...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Return the values from the database, not the tuples.
| Frederick Muriuki Muriithi |
| 2021-11-29 | Update typing notations on functions...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2021-11-29 | Fix query parametrisation...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Pass parameters to the query the way the MySQL driver expects.
| Frederick Muriuki Muriithi |
| 2021-11-29 | Retrieve the species name given the group...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Migrate the `web.webqtl.dbFunction.webqtlDatabaseFunction.retrieveSpecies`
in GeneNetwork1 to `gn3.db.species.species_name` in GeneNetwork3 to enable
the retrieval of the species name, given the group name (formerly RISet).
| Frederick Muriuki Muriithi |
| 2021-11-29 | db: traits: Support additions and deletions from csv file | BonfaceKilz |
| 2021-11-29 | db: traits: Remove trailing ".0" in int values | BonfaceKilz |
| 2021-11-29 | db: traits: Remove "\n\n" when generating csv file...In excel, "\n\n" is replaced with ",,,," during upload.
| BonfaceKilz |
| 2021-11-25 | db: traits: Support additions and deletions from csv file | BonfaceKilz |
| 2021-11-24 | db: traits: Remove trailing ".0" in int values | BonfaceKilz |
| 2021-11-23 | db: traits: Remove "\n\n" when generating csv file...In excel, "\n\n" is replaced with ",,,," during upload.
| BonfaceKilz |
| 2021-11-23 | Fix a myriad of linting errors...* Fix linting errors like:
- Unused variables
- Undeclared variable errors (mostly caused by typos, and wrong names)
- Missing documentation strings for functions
etc.
| Frederick Muriuki Muriithi |
| 2021-11-23 | Update documentation for functions...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Document functions for posterity.
| Frederick Muriuki Muriithi |
| 2021-11-22 | Add test to query builders...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Add some tests for the query builders to ensure that the queries are built
up correctly.
| Frederick Muriuki Muriithi |
| 2021-11-22 | Migrate `web.webqtl.correlation.CorrelationPage.fetchAllDatabaseData` 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.fetchAllDatabaseData` function from
GN1 to GN3.
| Frederick Muriuki Muriithi |
| 2021-11-22 | Make the DB connection argument the first...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* To make the code more composable down the line, make the database connection
argument the first argument for functions that access the database, since
they will always require the connection.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Add some condition checking functions...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Add the `check_for_literature_info` and
`check_symbol_for_tissue_correlation` functions to check for the presence of
specific data.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Fix linting and typing errors...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2021-11-04 | Rework sorting: remove `compare_tissue_correlation_absolute_values`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/correlations.py: Remove the
`compare_tissue_correlation_absolute_values` function which is no longer
needed.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Complete `build_temporary_tissue_correlations_table`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: Remove comments after updating
usage of the function at call point
* gn3/db/correlations.py: Complete the implementation of the
`build_temporary_tissue_correlations_table` function
| Frederick Muriuki Muriithi |
| 2021-11-04 | Move `correlations_of_all_tissue_traits`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: new
function (`correlations_of_all_tissue_traits`).
* gn3/db/correlations.py: delete
function (`correlations_of_all_tissue_traits`).
Move the function to `gn3.computations.partial_correlations` module and
comment out the db-access code.
Rework it to receive, as arguments, the data it previously fetched from the
database, and add comments on future rework to get the function working
again.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Add missing comma...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2021-11-04 | Move the function to computations module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* The function `batch_computed_tissue_correlation` is a pure computations
function with no expressions accessing the database, as far as I can tell,
therefore, this commit moves the function over to the
gn3.computations.partial_correlations module that holds the pure computation
functions.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Remove if clauses: replace with dict...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Remove the if clauses to simplify the code flow: use a dictionary of queries
and select the appropriate query from the dictionary instead.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Stub out `batch_computed_tissue_correlation` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Stub out `batch_computed_tissue_correlation` function to be used in
implementing the function down the line.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Complete `correlations_of_all_tissue_traits`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Complete the implementation of the `correlations_of_all_tissue_traits`
function by providing a call to a non-implemented function.
| Frederick Muriuki Muriithi |
