Skip to content

harden: add parameterized queries in queues.py #1021

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
anupamme wants to merge 1 commit into
base: master
Choose a base branch
from
Open

harden: add parameterized queries in queues.py #1021

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 6 additions & 6 deletions status/queues.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -99,14 +99,14 @@ def get(self):
query = (
"select art.artifactid, art.name, CAST(st.lastmodifieddate as DATE), st.generatedbyid, ct.name, ctp.wellxposition, ctp.wellyposition, s.projectid "
"from artifact art, stagetransition st, container ct, containerplacement ctp, sample s, artifact_sample_map asm "
"where art.artifactid=st.artifactid and st.stageid in (select stageid from stage where stepid={}) and st.completedbyid is null and st.workflowrunid>0 "
"where art.artifactid=st.artifactid and st.stageid in (select stageid from stage where stepid=%s) and st.completedbyid is null and st.workflowrunid>0 "
"and ctp.processartifactid=st.artifactid and ctp.containerid=ct.containerid and s.processid=asm.processid and asm.artifactid=art.artifactid "
"group by art.artifactid, CAST(st.lastmodifieddate as DATE), st.generatedbyid, ct.name, ctp.wellxposition, ctp.wellyposition, s.projectid;"
)
lib_validation_query = (
"select st.artifactid, art.name, st.lastmodifieddate, st.generatedbyid, ct.name, ctp.wellxposition, ctp.wellyposition, s.projectid, e.udfvalue "
"from artifact art, stagetransition st, container ct, containerplacement ctp, sample s, artifact_sample_map asm, entity_udf_view e where "
"art.artifactid=st.artifactid and st.stageid in (select stageid from stage where membershipid in (select sectionid from workflowsection where protocolid={})) "
"art.artifactid=st.artifactid and st.stageid in (select stageid from stage where membershipid in (select sectionid from workflowsection where protocolid=%s)) "
"and st.workflowrunid>0 and st.completedbyid is null and ctp.processartifactid=st.artifactid and ctp.containerid=ct.containerid and s.processid=asm.processid "
f"and asm.artifactid=art.artifactid and art.name not in {tuple(control_names)} and s.projectid=e.attachtoid and e.udfname='Library construction method'"
"group by st.artifactid, art.name, st.lastmodifieddate, st.generatedbyid, ct.name, ctp.wellxposition, ctp.wellyposition, s.projectid, e.udfvalue;"
Expand All @@ -116,19 +116,19 @@ def get(self):
queue_defs = self.fetch_queue_definitions("qPCR")
for key, value in queue_defs.items():
if key != "LibraryValidation":
queues[key] = query.format(value["stepid"])
queues[key] = (query, (value["stepid"],))
else:
# Library validation has a different query
# Queue 41, but query is slightly different to use protocolid for Library Validation QC which is 8 and, also to exclude the controls
queues[key] = lib_validation_query.format(value["protocolid"])
queues[key] = (lib_validation_query, (value["protocolid"],))

methods = queues.keys()
cursor = self._get_lims_cursor()
pools = {}
for method in methods:
pools[method] = {}
query = queues[method]
cursor.execute(query)
query, params = queues[method]
cursor.execute(query, params)
records = cursor.fetchall()
for record in list(records):
queue_time = record[2].isoformat()
Expand Down