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Enable copy_field_art2samp to copy values from Aggregate QC steps #303

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merged 6 commits into from
Jan 22, 2024
Merged

Enable copy_field_art2samp to copy values from Aggregate QC steps #303

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fd53882
Merge pull request #23 from SciLifeLab/master
chuan-wang Jan 9, 2024
73f313d
Merge pull request #24 from SciLifeLab/master
chuan-wang Jan 22, 2024
5a160b2
Enable copy_field_art2samp to copy values from Aggregate QC steps
chuan-wang Jan 22, 2024
2c8259c
Fix bug
chuan-wang Jan 22, 2024
7603b64
Refactors based on AAs comments
chuan-wang Jan 22, 2024
6536d3f
Ruff check fixed
chuan-wang Jan 22, 2024
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4 changes: 4 additions & 0 deletions VERSIONLOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,9 @@
# Scilifelab_epps Version Log

## 20240122.1

Enable copy_field_art2samp to copy values from Aggregate QC steps

## 20230111.1

Add CI-check to see versionlog is updated for a given pull request
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28 changes: 24 additions & 4 deletions scripts/copy_field_art2samp.py
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Expand Up @@ -19,6 +19,7 @@
"""

import logging
import re
import sys
from argparse import ArgumentParser

Expand All @@ -28,6 +29,8 @@

from scilifelab_epps.epp import CopyField, EppLogger

NGISAMPLE_PAT = re.compile("P[0-9]+_[0-9]+")


def main(lims, args, epp_logger):
source_udfs = args.source_udf
Expand All @@ -53,10 +56,21 @@ def main(lims, args, epp_logger):
for artifact in artifacts:
if source_udf in artifact.udf:
correct_artifacts = correct_artifacts + 1
copy_sesion = CopyField(
artifact, artifact.samples[0], source_udf, dest_udf
)
test = copy_sesion.copy_udf(changelog_f)
# Special case for copying values from Aggregate QC step;
# Only copy for NGI samples and skip controls
if NGISAMPLE_PAT.findall(artifact.samples[0].name):
if args.aggregate:
art_sample_dest = artifact.samples[0].artifact
else:
art_sample_dest = artifact.samples[0]

copy_sesion = CopyField(
artifact, art_sample_dest, source_udf, dest_udf
)
test = copy_sesion.copy_udf(changelog_f)
else:
test = ""

if test:
no_updated = no_updated + 1
else:
Expand Down Expand Up @@ -134,6 +148,12 @@ def main(lims, args, epp_logger):
"Prepends the old changelog file by default."
),
)
parser.add_argument(
"--aggregate",
dest="aggregate",
action="store_true",
help=("Used for Aggregate QC step specially."),
)
args = parser.parse_args()

lims = Lims(BASEURI, USERNAME, PASSWORD)
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16 changes: 9 additions & 7 deletions scripts/write_notes_to_couchdb.py
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Expand Up @@ -75,15 +75,17 @@ def write_note_to_couch(pid, timestamp, note, lims):
trans_table = proj_coord_name.maketrans("áéíóú", "aeiou")
proj_coord_name_trans = proj_coord_name.translate(trans_table)
proj_coord = ".".join(proj_coord_name_trans.split()) + "@scilifelab.se"
text = "A note has been created from LIMS in the project {}, {}! The note is as follows\n\
text = (
"A note has been created from LIMS in the project {}, {}! The note is as follows\n\
>{} - {}{}\
>{}".format(
pid,
doc["project_name"],
note["user"],
time_in_format,
note.get("category"),
note,
pid,
doc["project_name"],
note["user"],
time_in_format,
note.get("category"),
note,
)
)

html = '<html>\
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