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| author | Frederick Muriuki Muriithi | 2022-07-07 13:07:55 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2022-07-07 13:07:55 +0300 |
| commit | b367d04c57b21c0a9e2da22e8b20404de076768d (patch) | |
| tree | 85e58879965fc2da1d90dd0a39a30732bcb8ffc2 | |
| parent | 23a5e2c8dc2cbbf1ce55c22f80519824e413b883 (diff) | |
| download | gn-uploader-b367d04c57b21c0a9e2da22e8b20404de076768d.tar.gz | |
Add filetype details to database update code
The filetype determines the queries to be run to update the database,
therefore, this commit adds filetype information.
| -rw-r--r-- | qc_app/dbinsert.py | 14 | ||||
| -rw-r--r-- | qc_app/jobs.py | 3 |
2 files changed, 11 insertions, 6 deletions
diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py index 5381fb5..fac546b 100644 --- a/qc_app/dbinsert.py +++ b/qc_app/dbinsert.py @@ -81,7 +81,8 @@ def select_dataset(): types=group_types, datasets=datasets, menu_contents=json.dumps(menu_contents), genechips_data=json.dumps(gchips), - genechips=gchips.get(default_species, [])) + genechips=gchips.get(default_species, []), + filetype=job["filetype"]) return render_error(f"File '{filename}' no longer exists.") return render_error(f"Job '{job_id}' no longer exists.") return render_error("Unknown error") @@ -95,10 +96,13 @@ def insert_data(): filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}" if os.path.exists(filepath): try: - dataset_id = int(form["dataset"]) - return (f"Would insert data in file '{filepath}' " - "into the database with the dataset " - f"{dataset_id}") + species = form["species"] + filetype = form["filetype"] + datasetid = int(form["dataset"]) + genechipid = int(form["genechipid"]) + return (f"Would insert '{species}' data in '{filetype}' file " + f"'{filepath}' into the database with the dataset " + f"'{datasetid}' and genechip '{genechipid}'.") except ValueError as ve: msg = "::".join(ve.args) return render_error(f"Invalid value: {msg}") diff --git a/qc_app/jobs.py b/qc_app/jobs.py index 4e6a11e..275f9c8 100644 --- a/qc_app/jobs.py +++ b/qc_app/jobs.py @@ -20,7 +20,8 @@ def launch_job(# pylint: disable=[too-many-arguments] "python3", "-m", "scripts.worker", filetype, filepath, redisurl, job_id] the_job = { "job_id": job_id, "command": shlex.join(command), "status": "pending", - "filename": os.path.basename(filepath), "percent": 0 + "filename": os.path.basename(filepath), "percent": 0, + "filetype": filetype } redis_conn.hset(name=the_job["job_id"], mapping=the_job) redis_conn.expire(name=the_job["job_id"], time=timedelta(seconds=ttl_seconds)) |