aboutsummaryrefslogtreecommitdiff
AgeCommit message (Collapse)Author
2024-04-10linting: Fix linting errors.Frederick Muriuki Muriithi
2024-04-10logging: Set up logging in wsgi.pyFrederick Muriuki Muriithi
Make flask use the gunicorn loggers when run under gunicorn, otherwise, use our custom logging. Putting the logging setup inside `create_app(…)` would cause each worker to override the gunicorn loggers, meaning we were not receiving the logs, especially for `debug(…)` calls.
2024-04-10Gracefully handle all `werkzeug.exceptions` errors.Frederick Muriuki Muriithi
2024-04-10Use application logger, not root logger.Frederick Muriuki Muriithi
2024-04-08Add logging for IntegrityErrorFrederick Muriuki Muriithi
2024-04-08Refactor: Make error-checking more robustFrederick Muriuki Muriithi
Rather than maintaining a dictionary of possible error-checking functions, this commit allows passing in the error-checking functions necessary for each point. This makes the code easier to extend by simply defining a new error-checking function and passing it in to the error-checking "driver".
2024-04-08Fix issues caught by integration tests.Frederick Muriuki Muriithi
2024-04-08Fix pylint and mypy errors.Frederick Muriuki Muriithi
2024-04-08bug: UI: Provide better error messaging.Frederick Muriuki Muriithi
2024-04-08bug: Handle IntegrityError: Studies cannot have same name.Frederick Muriuki Muriithi
2024-04-08bug: Check that Genotype dataset name is not duplicated.Frederick Muriuki Muriithi
2024-04-05Handle exceptions creating ProbeSet datasets.Frederick Muriuki Muriithi
2024-04-05Add explicit route for favicon to reduce noise in the logs.Frederick Muriuki Muriithi
2024-04-04Remove unused database connection.Frederick Muriuki Muriithi
2024-04-03Reduce size of data inserted per queryFrederick Muriuki Muriithi
Reduce the size of data inserted per query since MariDB allows a packet with a maximum size of 1GB. This should hopefully resolve the …OperationalError: (2006, 'Server has gone away') error.
2024-03-29Quiet linter.Frederick Muriuki Muriithi
2024-03-29Add UI to select/create tissue.Frederick Muriuki Muriithi
2024-03-22Notify user if identifiers are not consistent.Frederick Muriuki Muriithi
2024-03-22Map names in files to names in database.Frederick Muriuki Muriithi
2024-03-22Fix linting issue.Frederick Muriuki Muriithi
2024-03-21Improve channel definition documentation.Frederick Muriuki Muriithi
2024-03-20Use `url_for` to get icon.Frederick Muriuki Muriithi
2024-03-20Fix bug: correctly merge standard-error values in file to data in dbFrederick Muriuki Muriithi
`read_datavalues(…)` function returns a dict of the form: ``` { ProbeSetName01: ({…}, …), ProbeSetName02: ({…}, …), ︙ } ``` Previously, the generator would thus try to index into the keys of the datavalues, which were strings, leading to an error. This commit changes the generator to return the values of the datavalues dict as a flattened list of values.
2024-03-19Set up application logging.Frederick Muriuki Muriithi
2024-03-19Add debugging statements to track upload of R/qtl2 bundle.Frederick Muriuki Muriithi
2024-03-19Query by `Id` rather than `ProbeFreezeId`Frederick Muriuki Muriithi
Previously `ProbeFreezeId` was set as 1 more than the largest `Id` value found, which might not end up being the same as the incremented Id. This commit, thus, queries by `Id` which is more robust, and does an actual update for the `ProbeFreezeId` column to make it same value as `Id`.
2024-03-15Move defaults settings into qc_app module.Frederick Muriuki Muriithi
2024-03-14Update symbolic linkFrederick Muriuki Muriithi
The module file was changed but the link to it was not updated. This commit fixes that.
2024-03-12Build up correct path to default settingsFrederick Muriuki Muriithi
The assumption has been that the application will be started in the root of the repository, and uses that to source the default settings. It is, however, possible that the application is started in a totally different working directory, which leads to an error during startup. This commit sources the default settings relative to a know file, in this case the module __init__.py file for qc_app module.
2024-03-11Rename moduleFrederick Muriuki Muriithi
2024-03-11Fix package name: gnqc-py to gn-uploaderFrederick Muriuki Muriithi
2024-03-11Add guix-past as a channel dependencyFrederick Muriuki Muriithi
2024-03-11Make guix-bioinformatics a dependency for this channel.Frederick Muriuki Muriithi
2024-03-08Update packaging and distribution declarations.Frederick Muriuki Muriithi
2024-03-08Rename package for guixFrederick Muriuki Muriithi
2024-03-04Use `Id` rather than `ProbeFreezeId`.Frederick Muriuki Muriithi
2024-03-04Display flash messages correctly.Frederick Muriuki Muriithi
2024-02-28tests: test with just the message - don't include markupFrederick Muriuki Muriithi
Markup can, and will change as improvements are made, but the error messages will not change that often, plus that is what we want to actually test for, not the markup.
2024-02-28tests: Update unit tests: remove use of obsoleted functions.Frederick Muriuki Muriithi
2024-02-28Remove last vestiges of flask's "instance path" configurations.Frederick Muriuki Muriithi
2024-02-28Fix bug: fetch from cursor, not return from cursor.execute(…)load-raw-data-no-parsingFrederick Muriuki Muriithi
2024-02-27Remove use of instance path in configurations.Frederick Muriuki Muriithi
2024-02-21Check that samples/cases are consistentFrederick Muriuki Muriithi
Ensure that **ALL** samples/cases/individuals mentioned in any of the pheno files actually exist in at least one of the geno files.
2024-02-21Pass 'filename' value to error checker function.Frederick Muriuki Muriithi
2024-02-20Track filename in the errorsFrederick Muriuki Muriithi
R/qtl2 bundles can contain more than one file, of the same type. When errors are encountered in any of the files, we need to be able to inform the user which file it is, in addition to the line and column number.
2024-02-20Generalise fetching of samples/cases/individuals.Frederick Muriuki Muriithi
2024-02-20Read samples from geno file.Frederick Muriuki Muriithi
2024-02-20Read each file separatelyFrederick Muriuki Muriithi
Provide the function 'read_file_data' in the 'r_qtl.r_qtl2' module to read each file in the bundle separately. The function 'file_data' in the 'r_qtl.r_qtl2' module reads *ALL* the files of a particular type (e.g. geno files) and returns a single generator object with the data from *ALL* the files. This does not render itself very useful for error checking. We needed a way to check for errors, and report them for each and every file in the bundle, for easier tracking and fixing.
2024-02-20Stand-alone function to read control fileFrederick Muriuki Muriithi
Add a function that, given the path to the zip file, will read the control data. It creates its own context manager.
2024-02-16Replace genotype codes with values in control file.Frederick Muriuki Muriithi