aboutsummaryrefslogtreecommitdiff
AgeCommit message (Collapse)Author
2024-01-16Build a sha512 hash from the uploaded file's name and timestampFrederick Muriuki Muriithi
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.
2024-01-16Filter out items with values of `None`.Frederick Muriuki Muriithi
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.
2024-01-16Provide defaults for various control variablesFrederick Muriuki Muriithi
`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 ...
2024-01-15Update imports: `take` was moved to different package.Frederick Muriuki Muriithi
2024-01-15Process `na.strings` even for default casesFrederick Muriuki Muriithi
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.
2024-01-15Extract common functional tools to separate package.Frederick Muriuki Muriithi
2024-01-15Process the `pheno` files.Frederick Muriuki Muriithi
Process the data in the pheno files and insert it into the database.
2024-01-15Initialise `install_phenos` script.Frederick Muriuki Muriithi
2024-01-15Extract common structure into separate modules.Frederick Muriuki Muriithi
2024-01-11Update pmap data in the database.Frederick Muriuki Muriithi
2024-01-11Update gmap data in the databaseFrederick Muriuki Muriithi
Update the genetic positions (in centiMorgans) in the database.
2024-01-11Cleanup linting and typing errors.Frederick Muriuki Muriithi
2024-01-11CLI: Require datasetid as an argument.Frederick Muriuki Muriithi
2024-01-10Provide convenience functions to avoid subtle call errorsFrederick Muriuki Muriithi
2024-01-10Cross-reference genotype data to the dataset.Frederick Muriuki Muriithi
2024-01-10Insert genotype data.Frederick Muriuki Muriithi
2024-01-10Cross-reference individuals to populations.Frederick Muriuki Muriithi
2024-01-10Insert any new individuals/samples into the database.Frederick Muriuki Muriithi
2024-01-10Insert any new markersFrederick Muriuki Muriithi
Insert any new markers found into the database.
2024-01-10Make identifier column name explicitFrederick Muriuki Muriithi
Since the R/qtl2 bundle generator could name the identifier column anything, this commit converts the incoming identifier column name into something explicit that we know and can use.
2024-01-09WIP: Install genotypes from R/qtl2 bundleFrederick Muriuki Muriithi
Load the genotype information from the R/qtl2 bundle and insert it into the database.
2024-01-09Raise exception on reading non-existing fileFrederick Muriuki Muriithi
The validation checks ensure that whatever files are listed in the control file exist in the zip file bundle. It is still possible, however, that the code tries to read a file that does not exist in the file and is not listed in the control file. In those cases, raise the appropriate exception.
2024-01-09Fix linting errorsFrederick Muriuki Muriithi
2024-01-09scripts: Log to redisFrederick Muriuki Muriithi
Add a logger that will log output to a redis list. This will be useful to retrieve the output(s) of the running script to help display some form of progress to the user.
2024-01-08Add channel authorization.Frederick Muriuki Muriithi
2024-01-08Fix errors with types.Frederick Muriuki Muriithi
2024-01-08Upload R/qtl2 zip bundle and check for errors.Frederick Muriuki Muriithi
2024-01-08Implement "create-population" route.Frederick Muriuki Muriithi
2024-01-08Implement "POST" path for "select-population" route.Frederick Muriuki Muriithi
2024-01-08Use extracted functions and fix bugsFrederick Muriuki Muriithi
2024-01-08Extract common database functions into a separate package.Frederick Muriuki Muriithi
2024-01-05Improve styling.Frederick Muriuki Muriithi
2024-01-05UI to select the population under which the data falls.Frederick Muriuki Muriithi
2024-01-05Initialise R/qtl2 bundle upload pathFrederick Muriuki Muriithi
Initialise the upload path for R/qtl2 bundles. This commit adds UI that allows the user to select from existing species, before proceeding to the next stage.
2024-01-05Add missing import.Frederick Muriuki Muriithi
2024-01-05Revert "QC: Check for only one decimal place."Frederick Muriuki Muriithi
This reverts commit c213b0010c3ddc8d3215adab65bd489a9b884e30. After a larger discussion with Arthur, Rob and Pjotr present, it was verified that the strict checks are important. This reverts the commit that allowed for looser checks.
2024-01-04Parse sex information from R/qtl bundle.Frederick Muriuki Muriithi
2024-01-04Parse cross information from R/qtl2 bundle.Frederick Muriuki Muriithi
2024-01-04Process sex and cross information data in "covar" files.Frederick Muriuki Muriithi
2024-01-04Rename test moduleFrederick Muriuki Muriithi
While 'covar' files can contain cross information, they do not have to, and therefore, we need to test for cross information separately.
2024-01-04Parse multiple files with same file key.Frederick Muriuki Muriithi
2024-01-04Test parsing of multiple files for single keyFrederick Muriuki Muriithi
2024-01-04Add tests for parsing cross information (covar) files.Frederick Muriuki Muriithi
2024-01-04Add tests for parsing 'phenocovar' files.Frederick Muriuki Muriithi
2024-01-04Rename test module.Frederick Muriuki Muriithi
2024-01-03Use generic parser. Remove obsoleted functions.Frederick Muriuki Muriithi
2024-01-03Parse founder_geno files. Generalise parsing files.Frederick Muriuki Muriithi
* Add tests for parsing "founder_geno" files * Extract common file parsing structure out to more general function * Use generic function to parse "founder_geno" file in test
2024-01-03Add tests for `founder_geno` parsing.Frederick Muriuki Muriithi
2024-01-03Parse the phenotype data from the R/qtl2 bundle.Frederick Muriuki Muriithi
2024-01-03Rename argument and add documentation to functions.Frederick Muriuki Muriithi