| Age | Commit message (Expand) | Author |
|---|
| 2024-02-08 | Generalise error retrieval: extract common structure...Extract the common structure into a separate function and pass in
checkers that return the errors they find.
| Frederick Muriuki Muriithi |
| 2024-02-08 | Use error objects rather than plain tuple values. | Frederick Muriuki Muriithi |
| 2024-02-07 | ShortName is optional, remove check and set default...The ShortName is optional, and can be set to the same value as
Name. This commit removes the check that made it mandatory.
| Frederick Muriuki Muriithi |
| 2024-02-07 | Prevent infinite redirect. | Frederick Muriuki Muriithi |
| 2024-02-07 | Fix error display: setup correct error class | Frederick Muriuki Muriithi |
| 2024-02-07 | Set up limits for inputs in UI | Frederick Muriuki Muriithi |
| 2024-02-06 | Check that pheno values are numerical and at least 3 decimal places | Frederick Muriuki Muriithi |
| 2024-02-06 | Bug: Fix routing issues...Fix the routing issues that were redirecting the flow to the wrong
endpoints.
| Frederick Muriuki Muriithi |
| 2024-02-05 | Run QC on the 'geno' file in R/qtl2 bundle. | Frederick Muriuki Muriithi |
| 2024-02-05 | Check that data in geno file is valid...Add a function to ensure the values in the geno files are all listed
in the control data under the "genotypes" key.
| Frederick Muriuki Muriithi |
| 2024-02-05 | Add a QC step: Check all listed files exist...Add a QC step to the R/qtl2 bundle processing - check that all files
that are listed in the control file also exist in the bundle.
| Frederick Muriuki Muriithi |
| 2024-02-05 | Fix linting and type errors. | Frederick Muriuki Muriithi |
| 2024-02-05 | Do general bundle validation and show errors...* Display any and all errors on the UI
* Move `validate_bundle` to QC module and refactor to use
`missing_files`
| Frederick Muriuki Muriithi |
| 2024-02-05 | Retrieve list of all files, and list of missing files...Add QC a function to list all files listed in the control file, and
another to list only the files missing from the bundle.
| Frederick Muriuki Muriithi |
| 2024-02-05 | Update UI documentation...Improve the UI documentation by making it more explicit what each
section deals with to help aleviate confusion of what the different
features do.
| Frederick Muriuki Muriithi |
| 2024-02-02 | List file types in a single place for easier reuse | Frederick Muriuki Muriithi |
| 2024-02-02 | Ensure control file defaults are set up in code. | Frederick Muriuki Muriithi |
| 2024-02-02 | Bug: Specify DictCursor class to return dict-like result...Without specifying the `cursorclass`, the result is a tuple of the
form:
((query_col01_val, query_col02_val, ...), ...)
where the ellipsis specify the possibility of more than one of the
previous form.
We specify the DictCursor class instead so that the form changes to:
({query_col01_name: query_col01_val, ...}, ...)
which allows us to pick the value we want with a string index.
| Frederick Muriuki Muriithi |
| 2024-01-24 | Checks: Update code and tests to ensure all checks pass. | Frederick Muriuki Muriithi |
| 2024-01-24 | redis-prefix: update "upload samples" path | Frederick Muriuki Muriithi |
| 2024-01-24 | redis-prefix: Update "insert data" path. | Frederick Muriuki Muriithi |
| 2024-01-24 | redis-prefix: Update file validation code...Update the file validation script and routes to use the redis prefix
for jobs.
| Frederick Muriuki Muriithi |
| 2024-01-23 | Update scripts to use redis prefix. | Frederick Muriuki Muriithi |
| 2024-01-23 | Add prefix to redis keys...Since the GNQC application might find itself sharing the same redis
server and/or database with other applications, add a prefix to its
keys.
| Frederick Muriuki Muriithi |
| 2024-01-23 | Tests: Use prefixes in tests rather than starting redis server...It's easier, and more robust to put the data under a prefix within a
redis database rather than try to run a redis server, especially
within the test environment. This commit updates the tests to use a
redis prefix instead.
| Frederick Muriuki Muriithi |
| 2024-01-22 | UI: Fix some UI bugs. | Frederick Muriuki Muriithi |
| 2024-01-22 | scripts: Pass in logger to get detailed updates. | Frederick Muriuki Muriithi |
| 2024-01-22 | UI: Show progress of R/qtl2 bundle processing. | Frederick Muriuki Muriithi |
| 2024-01-20 | Fetch sample/case names from database...Fetch the sample/case names from the database rather than from a
static file in the repository.
Issue:
https://issues.genenetwork.org/issues/quality-control/read-samples-from-database-by-species
| Frederick Muriuki Muriithi |
| 2024-01-19 | scripts: Process R/qtl2 bundle...Build script to start the processing of the R/qtl2 bundle.
| Frederick Muriuki Muriithi |
| 2024-01-19 | UI: Present entry point for R/qtl2 bundles upload. | Frederick Muriuki Muriithi |
| 2024-01-18 | UI: Display summary information. | Frederick Muriuki Muriithi |
| 2024-01-18 | UI: Create new ProbeSet dataset. | Frederick Muriuki Muriithi |
| 2024-01-18 | UI: Select from existing ProbeSet datasets. | Frederick Muriuki Muriithi |
| 2024-01-18 | Create new ProbeSet study. | Frederick Muriuki Muriithi |
| 2024-01-17 | UI: Select ProbeSet study. | Frederick Muriuki Muriithi |
| 2024-01-17 | UI: Implement creating new genotype datasets. | Frederick Muriuki Muriithi |
| 2024-01-17 | UI: Initialise summary page. | Frederick Muriuki Muriithi |
| 2024-01-17 | Enable selecting from existing genotype datasets. | Frederick Muriuki Muriithi |
| 2024-01-17 | Update flash-messages' categories. | Frederick Muriuki Muriithi |
| 2024-01-16 | UI: Create UI for creating a new Genotype dataset. | Frederick Muriuki Muriithi |
| 2024-01-16 | UI: Create UI to select from existing genotype datasets. | Frederick Muriuki Muriithi |
| 2024-01-16 | Create intermediate step...We do not have the option to modify the request and then redirect with
the modification in place. To go around that, this commit creates an
intermediate step that informs the user of their progress, while
allowing us to store the filename for future steps.
| Frederick Muriuki Muriithi |
| 2024-01-16 | Build a sha512 hash from the uploaded file's name and timestamp...Build a sha512 message digest from the file's name and the timestamp
of when the file was uploaded.
This ensures that the filename is URL-safe, and reduces chances of
name conflicts in the upload directory which could lead to data
corruption when processing the files and saving the files into the
database.
| Frederick Muriuki Muriithi |
| 2024-01-16 | Filter out items with values of `None`....The ProbeSetData table does not allow `NULL` for the `value` column
for good reason - if there is no value, just don't have a record for
that particular sample.
| Frederick Muriuki Muriithi |
| 2024-01-16 | Provide defaults for various control variables...`na.strings` has a default value of "NA" as stated in
https://kbroman.org/qtl2/assets/vignettes/input_files.html#CSV_files
quote:
> Missing value codes will be specified in the control file (as
> na.strings, with default value "NA") and will apply across all
> files, so a missing value code for one file cannot be an allowed
> value in another file.
for `comment.char`
> The CSV files can include a header with a set of comment lines
> initiated by a value specified in the control file as comment.char
> (with default value "#").
for `sep`:
The default separator is expected to be the comma, as stated in
https://kbroman.org/qtl2/assets/vignettes/input_files.html#field-separator
quote:
> If the data files use a separator other than a comma ...
| Frederick Muriuki Muriithi |
| 2024-01-15 | Update imports: `take` was moved to different package. | Frederick Muriuki Muriithi |
| 2024-01-15 | Process `na.strings` even for default cases...There was a bug where the `na.strings` were not processed correctly if
the user called the `r_qtl.r_qtl2.file_data(...)` function without
explicitly providing the `process_*` arguments.
This commit fixes that.
| Frederick Muriuki Muriithi |
| 2024-01-15 | Extract common functional tools to separate package. | Frederick Muriuki Muriithi |
| 2024-01-15 | Process the `pheno` files....Process the data in the pheno files and insert it into the database.
| Frederick Muriuki Muriithi |
