diff options
Diffstat (limited to 'uploader')
| -rw-r--r-- | uploader/db/datasets.py | 4 | ||||
| -rw-r--r-- | uploader/phenotypes/models.py | 5 | ||||
| -rw-r--r-- | uploader/phenotypes/views.py | 23 | ||||
| -rw-r--r-- | uploader/publications/models.py | 4 | ||||
| -rw-r--r-- | uploader/publications/pubmed.py | 4 | ||||
| -rw-r--r-- | uploader/publications/views.py | 10 | ||||
| -rw-r--r-- | uploader/samples/views.py | 8 | ||||
| -rw-r--r-- | uploader/species/models.py | 2 |
8 files changed, 33 insertions, 27 deletions
diff --git a/uploader/db/datasets.py b/uploader/db/datasets.py index 767ec41..4b263f5 100644 --- a/uploader/db/datasets.py +++ b/uploader/db/datasets.py @@ -53,7 +53,7 @@ def probeset_study_by_id(conn: mdb.Connection, studyid) -> Optional[dict]: _study = cursor.fetchone() return dict(_study) if bool(_study) else None -def probeset_create_study(conn: mdb.Connection,#pylint: disable=[too-many-arguments] +def probeset_create_study(conn: mdb.Connection,#pylint: disable=[too-many-arguments, too-many-positional-arguments] populationid: int, platformid: int, tissueid: int, @@ -87,7 +87,7 @@ def probeset_create_study(conn: mdb.Connection,#pylint: disable=[too-many-argume (studyid, studyid)) return {**studydata, "studyid": studyid} -def probeset_create_dataset(conn: mdb.Connection,#pylint: disable=[too-many-arguments] +def probeset_create_dataset(conn: mdb.Connection,#pylint: disable=[too-many-arguments, too-many-positional-arguments] studyid: int, averageid: int, datasetname: str, diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py index 4a1b2d5..4b8b223 100644 --- a/uploader/phenotypes/models.py +++ b/uploader/phenotypes/models.py @@ -92,7 +92,8 @@ def dataset_phenotypes(conn: mdb.Connection, limit: Optional[int] = None) -> tuple[dict, ...]: """Fetch the actual phenotypes.""" _query = ( - "SELECT pheno.*, pxr.Id AS xref_id, pxr.InbredSetId, ist.InbredSetCode FROM Phenotype AS pheno " + "SELECT pheno.*, pxr.Id AS xref_id, pxr.InbredSetId, ist.InbredSetCode " + "FROM Phenotype AS pheno " "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId " "INNER JOIN PublishFreeze AS pf ON pxr.InbredSetId=pf.InbredSetId " "INNER JOIN InbredSet AS ist ON pf.InbredSetId=ist.Id " @@ -218,7 +219,7 @@ def phenotype_by_id( ).values()) } if bool(_pheno) and len(_pheno.keys()) > 1: - raise Exception( + raise Exception(# pylint: disable=[broad-exception-raised] "We found more than one phenotype with the same identifier!") return None diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 04cdc3b..0e626ad 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -385,7 +385,7 @@ def process_phenotypes_individual_files(error_uri): arcname=filedata["original-name"]) cdata[rqtlkey] = cdata.get(rqtlkey, []) + [filedata["original-name"]] else: - # TODO: Check this path: fix any bugs. + # T0DO: Check this path: fix any bugs. _sentfile = request.files[formkey] if not bool(_sentfile): flash(f"Expected file ('{formkey}') was not provided.", @@ -640,12 +640,16 @@ def load_data_to_database( **kwargs ):# pylint: disable=[unused-argument] """Load the data from the given QC job into the database.""" - jobs_db = app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"] + _jobs_db = app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"] with (Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn, - sqlite3.connection(jobs_db) as conn): + sqlite3.connection(_jobs_db) as conn): + # T0DO: Maybe break the connection between the jobs here, pass: + # - the bundle name (rebuild the full path here.) + # - publication details, where separate + # - details about the files: e.g. total lines, etc qc_job = jobs.job(rconn, jobs.jobsnamespace(), request.form["data-qc-job-id"]) _meta = json.loads(qc_job["job-metadata"]) - load_job_id = uuid.uuid4() + _load_job_id = uuid.uuid4() _loglevel = logging.getLevelName(app.logger.getEffectiveLevel()).lower() command = [ sys.executable, @@ -653,8 +657,8 @@ def load_data_to_database( "-m", "scripts.load_phenotypes_to_db", app.config["SQL_URI"], - jobs_db, - str(load_job_id), + _jobs_db, + str(_load_job_id), "--log-level", _loglevel ] @@ -674,7 +678,7 @@ def load_data_to_database( ).then( lambda token: gnlibs_jobs.initialise_job( conn, - load_job_id, + _load_job_id, command, "load-new-phenotypes-data", extra_meta={ @@ -692,7 +696,7 @@ def load_data_to_database( ).then( lambda job: gnlibs_jobs.launch_job( job, - jobs_db, + _jobs_db, Path(f"{app.config['UPLOAD_FOLDER']}/job_errors"), worker_manager="gn_libs.jobs.launcher", loglevel=_loglevel) @@ -972,6 +976,7 @@ def load_data_success( job_id: uuid.UUID, **kwargs ):# pylint: disable=[unused-argument] + """Display success page if loading data to database was successful.""" with (database_connection(app.config["SQL_URI"]) as conn, sqlite3.connection(app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"]) as jobsconn): @@ -1016,5 +1021,5 @@ def load_data_success( "FormID": "searchResult" }), fragment=""))) - except JobNotFound as jnf: + except JobNotFound as _jnf: return render_template("jobs/job-not-found.html", job_id=job_id) diff --git a/uploader/publications/models.py b/uploader/publications/models.py index f37b67d..f83be58 100644 --- a/uploader/publications/models.py +++ b/uploader/publications/models.py @@ -30,6 +30,7 @@ def create_new_publications( conn: Connection, publications: tuple[dict, ...] ) -> tuple[dict, ...]: + """Create new publications in the database.""" if len(publications) > 0: with conn.cursor(cursorclass=DictCursor) as cursor: cursor.executemany( @@ -47,7 +48,8 @@ def create_new_publications( return tuple({ **row, "publication_id": row["Id"] } for row in cursor.fetchall()) - return tuple() + + return tuple() def update_publications(conn: Connection , publications: tuple[dict, ...]) -> tuple[dict, ...]: diff --git a/uploader/publications/pubmed.py b/uploader/publications/pubmed.py index e8b0584..2531c4a 100644 --- a/uploader/publications/pubmed.py +++ b/uploader/publications/pubmed.py @@ -29,9 +29,7 @@ def __journal__(journal: etree.Element) -> dict: } def __author__(author: etree.Element) -> str: - return "%s %s" % ( - author.find("LastName").text, - author.find("Initials").text) + return f'{author.find("LastName").text} {author.find("Initials").text}' def __pages__(pagination: etree.Element) -> str: diff --git a/uploader/publications/views.py b/uploader/publications/views.py index e7aa412..a88f754 100644 --- a/uploader/publications/views.py +++ b/uploader/publications/views.py @@ -27,21 +27,21 @@ pubbp = Blueprint("publications", __name__) @require_login def index(): """Index page for publications.""" - with database_connection(app.config["SQL_URI"]) as conn: - return render_template("publications/index.html") + return render_template("publications/index.html") @pubbp.route("/list", methods=["GET"]) @require_login def list_publications(): + """Fetch publications that fulfill a specific search, or all of them, if + there is no search term.""" # request breakdown: # https://datatables.net/manual/server-side _page = int(request.args.get("draw")) _length = int(request.args.get("length") or '-1') _start = int(request.args.get("start") or '0') _search = request.args["search[value]"] - with (database_connection(app.config["SQL_URI"]) as conn, - conn.cursor(cursorclass=DictCursor) as cursor): + with database_connection(app.config["SQL_URI"]) as conn: _publications, _current_rows, _totalfiltered, _totalrows = fetch_publications( conn, _search, @@ -73,7 +73,7 @@ def view_publication(publication_id: int): @require_login def create_publication(): """Create a new publication.""" - if(request.method == "GET"): + if request.method == "GET": return render_template("publications/create-publication.html") form = request.form authors = form.get("publication-authors").encode("utf8") diff --git a/uploader/samples/views.py b/uploader/samples/views.py index c0adb88..4705a96 100644 --- a/uploader/samples/views.py +++ b/uploader/samples/views.py @@ -96,7 +96,7 @@ def list_samples(species: dict, population: dict, **kwargs):# pylint: disable=[u activelink="list-samples") -def build_sample_upload_job(# pylint: disable=[too-many-arguments] +def build_sample_upload_job(# pylint: disable=[too-many-arguments, too-many-positional-arguments] speciesid: int, populationid: int, samplesfile: Path, @@ -159,7 +159,7 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma "alert-error") return samples_uploads_page - firstlineheading = (request.form.get("first_line_heading") == "on") + firstlineheading = request.form.get("first_line_heading") == "on" separator = request.form.get("separator", ",") if separator == "other": @@ -172,7 +172,7 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma redisuri = app.config["REDIS_URL"] with Redis.from_url(redisuri, decode_responses=True) as rconn: - #TODO: Add a QC step here — what do we check? + #T0DO: Add a QC step here — what do we check? # 1. Does any sample in the uploaded file exist within the database? # If yes, what is/are its/their species and population? # 2. If yes 1. above, provide error with notes on which species and @@ -251,7 +251,7 @@ def upload_status(species: dict, population: dict, job_id: uuid.UUID, **kwargs): @require_login @with_population(species_redirect_uri="species.populations.samples.index", redirect_uri="species.populations.samples.select_population") -def upload_failure(species: dict, population: dict, job_id: uuid.UUID, **kwargs): +def upload_failure(species: dict, population: dict, job_id: uuid.UUID, **kwargs):# pylint: disable=[unused-argument] """Display the errors of the samples upload failure.""" job = with_redis_connection(lambda rconn: jobs.job( rconn, jobs.jobsnamespace(), job_id)) diff --git a/uploader/species/models.py b/uploader/species/models.py index db53d48..acfa51e 100644 --- a/uploader/species/models.py +++ b/uploader/species/models.py @@ -92,7 +92,7 @@ def save_species(conn: mdb.Connection, } -def update_species(# pylint: disable=[too-many-arguments] +def update_species(# pylint: disable=[too-many-arguments, too-many-positional-arguments] conn: mdb.Connection, species_id: int, common_name: str, |