| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-04-21 | logging: Set LOG LEVEL on root logger to enable logs | Frederick Muriuki Muriithi | |
| 2023-04-21 | auth: Attach linked data to specific resources. | Frederick Muriuki Muriithi | |
| 2023-04-21 | Setup module for logging | Frederick Muriuki Muriithi | |
| During development, we need logging sometimes to help with troubleshooting problems. This commit provides a module to help set up the logging in a separate module from the app module. | |||
| 2023-04-21 | auth: Fetch user group phenotypes not attached to a resource. | Frederick Muriuki Muriithi | |
| 2023-04-19 | oauth2: Link the phenotype traits to user groups. | Frederick Muriuki Muriithi | |
| 2023-04-19 | Fix minor linting and typing issues | Frederick Muriuki Muriithi | |
| 2023-04-19 | auth: Setup selected traits correctly | Frederick Muriuki Muriithi | |
| Fix bugs with setting up of the selected traits for use while filtering the search results. | |||
| 2023-04-19 | auth: phenotypes - provide default empty list for selected traits. | Frederick Muriuki Muriithi | |
| 2023-04-18 | auth: Pass `--per-page` and `--selected` options. | Frederick Muriuki Muriithi | |
| 2023-04-18 | auth: Consistently JSON encode values. | Frederick Muriuki Muriithi | |
| Consistently encode all values for the top-level keys stored in redis to avoid issues with json encode/decode | |||
| 2023-04-17 | Fix typo, os.environment -> os.environ | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-04-17 | Update the default SPARQL endpoint | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-04-17 | Create new endpoint for fetching GeneRIF entries | Munyoki Kilyungi | |
| * gn3/api/metadata.py: Import Template, sparql_query and RDF_PREFIXES. (get_genewiki_entries): New endpoint. * gn3/db/rdf.py: Add new constant for storing rdf prefixes. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-04-17 | Hook up code to use external search script for phenotypes | Frederick Muriuki Muriithi | |
| 2023-04-17 | auth: Delete code that is no longer used | Frederick Muriuki Muriithi | |
| 2023-04-15 | Decouple `gn3.db_utils` from `flask.current_app`. | Frederick Muriuki Muriithi | |
| Decouple the `gn3.db_utils` module from the global `flask.current_app` object, ensuring that the database uri value is passed in as a required argument to the `gn3.db_utils.database_connection` function. | |||
| 2023-04-14 | auth: Add external script to search for phenotypes | Frederick Muriuki Muriithi | |
| We need a search through the available phenotype traits in the database when linking the traits to user groups. Unfortunately, the Xapian Search indexes do not (and should not) include the internal identifiers we use to disambiguate the traits. On the other hand, we do not want to present the user with traits that have already been linked to any user group within the search results. The script in this commit, together with the modified queries for fetching the phenotype data form a "hack" of sorts to wrap around the way the search works while ensuring we do not present the user with "non-actionable" (linked) traits in the search results. | |||
| 2023-04-14 | auth: Disconnect module from flask application | Frederick Muriuki Muriithi | |
| To avoid application context errors in external scripts, disconnect the `gn3.auth.db` module from the `flask.current_app` dependency. | |||
| 2023-04-12 | auth: Enable listing of unlinked genotype/mRNA group data. | Frederick Muriuki Muriithi | |
| 2023-04-10 | Add search and link for mRNA Assay datasets. | Frederick Muriuki Muriithi | |
| 2023-04-10 | Migrations for linking genotype files. | Frederick Muriuki Muriithi | |
| 2023-04-10 | Update expected request key. | Frederick Muriuki Muriithi | |
| 2023-04-10 | Enable search, filtering out selected, but not linked data | Frederick Muriuki Muriithi | |
| When a user selects some datasets and does a new search, we filter out the selected datasets too, even though they are yet to be linked. | |||
| 2023-04-08 | auth: Link genotype datasets to groups. | Frederick Muriuki Muriithi | |
| 2023-04-06 | Fix linting issues | Frederick Muriuki Muriithi | |
| 2023-04-06 | Remove deprecated `gn3.db_utils.database_connector` function | Frederick Muriuki Muriithi | |
| Remove the deprecated function and fix a myriad of bugs that arise from removing the function. Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils | |||
| 2023-04-05 | Enable use of `database_connection` in scripts without current_app | Frederick Muriuki Muriithi | |
| There is need to run external scripts using the same configurations as the application but without the need to couple the script to the application. In this case, we provide the needed configuration directly in the CLI, and modify the existing `gn3.db_utils.database_connection` function to allow it to work coupled to the app or otherwise. | |||
| 2023-04-04 | auth: Search for linking genotype datasets. | Frederick Muriuki Muriithi | |
| 2023-04-04 | Add tables to link genotype data | Frederick Muriuki Muriithi | |
| 2023-03-23 | tests: Set up fixture and mock out config variable | Frederick Muriuki Muriithi | |
| 2023-03-23 | auth: list the species in the database. | Frederick Muriuki Muriithi | |
| 2023-03-23 | Docs: Add a note on how the configuration system works. | Frederick Muriuki Muriithi | |
| 2023-03-23 | auth: Don't try loading the user if no client is found | Frederick Muriuki Muriithi | |
| Fix the bug where the system was trying to load a user from a non-existing OAuth2 client, leading to an exception. | |||
| 2023-03-23 | conf: use flask.current_app.config not in gn3.settings | Frederick Muriuki Muriithi | |
| The configuration in gn3.settings can (and does) get overwritten by values in the environment variable `GN3_CONF` and any configurations passed in the call to the `gn3.app.create_app` function; as such, this commit changes the configuration used in the code to user the final configuration values that are in the running application's `flask.current_app.config` object. | |||
| 2023-03-22 | auth: data linking: build functions to fetch unlinked phenotypes | Frederick Muriuki Muriithi | |
| This is an initial attempt: it does not allow a search to be carried out across the data available in the database. I will need to rework this, probably start from the UI and work backward. | |||
| 2023-03-22 | auth: migrations for linking phenotype data | Frederick Muriuki Muriithi | |
| 2023-03-22 | auth: Enable linking multiple datasets to the group at once. | Frederick Muriuki Muriithi | |
| 2023-03-22 | auth: Remove the tables used for linking data to resources | Frederick Muriuki Muriithi | |
| The way data is linked to the resources needs to be reworked. This commit removes all the existing migration scripts that created the tables formerly used for linking data in preparation for reworking the system. | |||
| 2023-03-20 | Disable fetching case-attributes when getting sample data | Munyoki Kilyungi | |
| * gn3/db/sample_data.py: Remove 're' import. (get_trait_csv_sample_data): Remove fetching sample data. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-03-20 | auth: data: Enable offset in queries | Frederick Muriuki Muriithi | |
| Enable the 'OFFSET' clause in the queries to allow for progressive fetching of data from the database using the 'Previous' and 'Next' buttons. | |||
| 2023-03-20 | auth: data: List Phenotypes at the trait level | Frederick Muriuki Muriithi | |
| For Phenotypes, list the Phenotype traits rather than the dataset(s). | |||
| 2023-03-20 | Fix get_all_species test | zsloan | |
| 2023-03-18 | oauth2: resources: toggle whether a resource is public or not | Frederick Muriuki Muriithi | |
| 2023-03-18 | auth: resources: Disallow duplicate resource names. | Frederick Muriuki Muriithi | |
| 2023-03-17 | Add conn.commit() to queries in sample_data.py | zsloan | |
| 2023-03-17 | Change get_all_species query to order by Family | zsloan | |
| 2023-03-15 | auth: Data Migrations: Rework migration trigger | Frederick Muriuki Muriithi | |
| Rework the migration trigger endpoint such that it does a bulk import of all the resources in the redis store. It also expects that the user that triggers the migration have the appropriate privileges. | |||
| 2023-03-14 | auth: Fix some linting and typing issues. | Frederick Muriuki Muriithi | |
| 2023-03-13 | Move doc to issue tracker | Pjotr Prins | |
| 2023-03-13 | oauth2: data: Temporarily escalate privileges to enable migration | Frederick Muriuki Muriithi | |
| The functions that fetch the unlinked data have checks to ensure they are called by users with the appropriate privileges. This commit enables a temporary escalation of privileges to enable fetching the data, so as to allow successful data migration. | |||
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| GeneNetwork3 REST API for data science and machine learning |
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