diff options
Diffstat (limited to 'uploader/upload')
| -rw-r--r-- | uploader/upload/rqtl2.py | 19 |
1 files changed, 19 insertions, 0 deletions
diff --git a/uploader/upload/rqtl2.py b/uploader/upload/rqtl2.py index 6aed1f7..ff7556d 100644 --- a/uploader/upload/rqtl2.py +++ b/uploader/upload/rqtl2.py @@ -32,6 +32,7 @@ from uploader.files import save_file, fullpath from uploader.dbinsert import species as all_species from uploader.db_utils import with_db_connection, database_connection +from uploader.authorisation import require_login from uploader.db.platforms import platform_by_id, platforms_by_species from uploader.db.averaging import averaging_methods, averaging_method_by_id from uploader.db.tissues import all_tissues, tissue_by_id, create_new_tissue @@ -53,8 +54,10 @@ from uploader.db.datasets import ( rqtl2 = Blueprint("rqtl2", __name__) + @rqtl2.route("/", methods=["GET", "POST"]) @rqtl2.route("/select-species", methods=["GET", "POST"]) +@require_login def select_species(): """Select the species.""" if request.method == "GET": @@ -72,6 +75,7 @@ def select_species(): @rqtl2.route("/upload/species/<int:species_id>/select-population", methods=["GET", "POST"]) +@require_login def select_population(species_id: int): """Select/Create the population to organise data under.""" with database_connection(app.config["SQL_URI"]) as conn: @@ -101,6 +105,7 @@ def select_population(species_id: int): @rqtl2.route("/upload/species/<int:species_id>/create-population", methods=["POST"]) +@require_login def create_population(species_id: int): """Create a new population for the given species.""" population_page = redirect(url_for("upload.rqtl2.select_population", @@ -143,6 +148,7 @@ class __RequestError__(Exception): #pylint: disable=[invalid-name] @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle"), methods=["GET", "POST"]) +@require_login def upload_rqtl2_bundle(species_id: int, population_id: int): """Allow upload of R/qtl2 bundle.""" with database_connection(app.config["SQL_URI"]) as conn: @@ -241,6 +247,7 @@ def chunks_directory(uniqueidentifier: str) -> Path: @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle-chunked"), methods=["GET"]) +@require_login def upload_rqtl2_bundle_chunked_get(# pylint: disable=["unused-argument"] species_id: int, population_id: int @@ -285,6 +292,7 @@ def __merge_chunks__(targetfile: Path, chunkpaths: tuple[Path, ...]) -> Path: @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle-chunked"), methods=["POST"]) +@require_login def upload_rqtl2_bundle_chunked_post(species_id: int, population_id: int): """ Extension to the `upload_rqtl2_bundle` endpoint above that allows large @@ -343,6 +351,7 @@ def upload_rqtl2_bundle_chunked_post(species_id: int, population_id: int): @rqtl2.route("/upload/species/rqtl2-bundle/qc-status/<uuid:jobid>", methods=["GET", "POST"]) +@require_login def rqtl2_bundle_qc_status(jobid: UUID): """Check the status of the QC jobs.""" with (Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn, @@ -564,6 +573,7 @@ def with_errors(endpointthunk: Callable, *checkfns): @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/select-geno-dataset"), methods=["POST"]) +@require_login def select_geno_dataset(species_id: int, population_id: int): """Select from existing geno datasets.""" with database_connection(app.config["SQL_URI"]) as conn: @@ -602,6 +612,7 @@ def select_geno_dataset(species_id: int, population_id: int): @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/create-geno-dataset"), methods=["POST"]) +@require_login def create_geno_dataset(species_id: int, population_id: int): """Create a new geno dataset.""" with database_connection(app.config["SQL_URI"]) as conn: @@ -671,6 +682,7 @@ def create_geno_dataset(species_id: int, population_id: int): @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/select-tissue"), methods=["POST"]) +@require_login def select_tissue(species_id: int, population_id: int): """Select from existing tissues.""" with database_connection(app.config["SQL_URI"]) as conn: @@ -701,6 +713,7 @@ def select_tissue(species_id: int, population_id: int): @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/create-tissue"), methods=["POST"]) +@require_login def create_tissue(species_id: int, population_id: int): """Add new tissue, organ or biological material to the system.""" form = request.form @@ -745,6 +758,7 @@ def create_tissue(species_id: int, population_id: int): @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/select-probeset-study"), methods=["POST"]) +@require_login def select_probeset_study(species_id: int, population_id: int): """Select or create a probeset study.""" with database_connection(app.config["SQL_URI"]) as conn: @@ -780,6 +794,7 @@ def select_probeset_study(species_id: int, population_id: int): @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/select-probeset-dataset"), methods=["POST"]) +@require_login def select_probeset_dataset(species_id: int, population_id: int): """Select or create a probeset dataset.""" with database_connection(app.config["SQL_URI"]) as conn: @@ -820,6 +835,7 @@ def select_probeset_dataset(species_id: int, population_id: int): @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/create-probeset-study"), methods=["POST"]) +@require_login def create_probeset_study(species_id: int, population_id: int): """Create a new probeset study.""" errorclasses = "alert-error error-rqtl2 error-rqtl2-create-probeset-study" @@ -882,6 +898,7 @@ def create_probeset_study(species_id: int, population_id: int): @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/create-probeset-dataset"), methods=["POST"]) +@require_login def create_probeset_dataset(species_id: int, population_id: int):#pylint: disable=[too-many-return-statements] """Create a new probeset dataset.""" errorclasses = "alert-error error-rqtl2 error-rqtl2-create-probeset-dataset" @@ -973,6 +990,7 @@ def create_probeset_dataset(species_id: int, population_id: int):#pylint: disabl @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/dataset-info"), methods=["POST"]) +@require_login def select_dataset_info(species_id: int, population_id: int): """ If `geno` files exist in the R/qtl2 bundle, prompt user to provide the @@ -1065,6 +1083,7 @@ def select_dataset_info(species_id: int, population_id: int): @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/confirm-bundle-details"), methods=["POST"]) +@require_login def confirm_bundle_details(species_id: int, population_id: int): """Confirm the details and trigger R/qtl2 bundle processing...""" redisuri = app.config["REDIS_URL"] |