aboutsummaryrefslogtreecommitdiff
path: root/qc_app/dbinsert.py
diff options
context:
space:
mode:
Diffstat (limited to 'qc_app/dbinsert.py')
-rw-r--r--qc_app/dbinsert.py36
1 files changed, 20 insertions, 16 deletions
diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
index 32043a7..e9dc3ff 100644
--- a/qc_app/dbinsert.py
+++ b/qc_app/dbinsert.py
@@ -134,8 +134,9 @@ def select_platform():
gchips = genechips()
return render_template(
"select_platform.html", filename=filename,
- filetype=job["filetype"], default_species=default_species,
- species=species(), genechips=gchips[default_species],
+ filetype=job["filetype"], totallines=int(job["currentline"]),
+ default_species=default_species, species=species(),
+ genechips=gchips[default_species],
genechips_data=json.dumps(gchips))
return render_error(f"File '{filename}' no longer exists.")
return render_error(f"Job '{job_id}' no longer exists.")
@@ -159,8 +160,9 @@ def select_study():
organise_groups_by_family, groups_by_species(speciesid), {})
return render_template(
"select_study.html", filename=form["filename"],
- filetype=form["filetype"], species=speciesid, genechipid=genechipid,
- studies=the_studies, groups=the_groups, tissues = tissues(),
+ filetype=form["filetype"], totallines=form["totallines"],
+ species=speciesid, genechipid=genechipid, studies=the_studies,
+ groups=the_groups, tissues = tissues(),
selected_group=int(form.get("inbredsetid", -13)),
selected_tissue=int(form.get("tissueid", -13)))
except AssertionError as aserr:
@@ -198,8 +200,8 @@ def create_study():
return render_template(
"continue_from_create_study.html",
filename=form["filename"], filetype=form["filetype"],
- species=form["species"], genechipid=form["genechipid"],
- studyid=new_studyid)
+ totallines=form["totallines"], species=form["species"],
+ genechipid=form["genechipid"], studyid=new_studyid)
except AssertionError as aserr:
flash(f"Missing data: {aserr.args[0]}", "alert-error")
return redirect(url_for("dbinsert.select_study"), code=307)
@@ -252,9 +254,10 @@ def select_dataset():
datasets = datasets_by_study(studyid)
return render_template(
"select_dataset.html", filename=form["filename"],
- filetype=form["filetype"], species=form["species"],
- genechipid=form["genechipid"], studyid=studyid, datasets=datasets,
- avgmethods=averaging_methods(), datascales=dataset_datascales())
+ filetype=form["filetype"], totallines=form["totallines"],
+ species=form["species"], genechipid=form["genechipid"],
+ studyid=studyid, datasets=datasets, avgmethods=averaging_methods(),
+ datascales=dataset_datascales())
except AssertionError as aserr:
return render_error(f"Missing data: {aserr.args[0]}")
@@ -295,7 +298,8 @@ def create_dataset():
"continue_from_create_dataset.html",
filename=form["filename"], filetype=form["filetype"],
species=form["species"], genechipid=form["genechipid"],
- studyid=form["studyid"], datasetid=new_datasetid)
+ studyid=form["studyid"], datasetid=new_datasetid,
+ totallines=form["totallines"])
except AssertionError as aserr:
flash(f"Missing data {aserr.args[0]}", "alert-error")
return redirect(url_for("dbinsert.select_dataset"), code=307)
@@ -343,9 +347,9 @@ def final_confirmation():
datasetid=form["datasetid"]
return render_template(
"final_confirmation.html", filename=form["filename"],
- filetype=form["filetype"], species=speciesid, genechipid=genechipid,
- studyid=studyid, datasetid=datasetid,
- the_species=selected_keys(
+ filetype=form["filetype"], totallines=form["totallines"],
+ species=speciesid, genechipid=genechipid, studyid=studyid,
+ datasetid=datasetid, the_species=selected_keys(
species_by_id(speciesid), ("SpeciesName", "Name", "MenuName")),
platform=selected_keys(
platform_by_id(genechipid),
@@ -378,9 +382,9 @@ def insert_data():
with Redis.from_url(redisurl, decode_responses=True) as rconn:
job = jobs.launch_job(
jobs.data_insertion_job(
- rconn, filepath, form.get("filetype"),
- form.get("species"), form.get("genechipid"),
- form.get("datasetid"), app.config["SQL_URI"], redisurl,
+ rconn, filepath, form["filetype"], form["totallines"],
+ form["species"], form["genechipid"], form["datasetid"],
+ app.config["SQL_URI"], redisurl,
app.config["JOBS_TTL_SECONDS"]),
redisurl, f"{app.config['UPLOAD_FOLDER']}/job_errors")