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Management review 2024 update #92

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merged 2 commits into from
Feb 18, 2025
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Management review 2024 update #92

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86f8f88
2024 update
rernst Jan 31, 2025
f830ddb
Remove duplicate line
rernst Feb 17, 2025
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190 changes: 125 additions & 65 deletions scripts/management_review.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,66 +5,91 @@
from genologics.entities import Artifact

# Setup lims connection
baseuri = 'https://usf-lims.umcutrecht.nl'
username = 'lims_user'
password = 'lims_user_password'
baseuri = "https://usf-lims.umcutrecht.nl"
username = "lims_user"
password = "lims_user_password"
lims = Lims(baseuri, username, password)

# month quarter
quarters = ['Q1', 'Q2', 'Q3', 'Q4']
quarters = ["Q1", "Q2", "Q3", "Q4"]
month_quarter = {
'01': 'Q1', '02': 'Q1', '03': 'Q1',
'04': 'Q2', '05': 'Q2', '06': 'Q2',
'07': 'Q3', '08': 'Q3', '09': 'Q3',
'10': 'Q4', '11': 'Q4', '12': 'Q4'
"01": "Q1",
"02": "Q1",
"03": "Q1",
"04": "Q2",
"05": "Q2",
"06": "Q2",
"07": "Q3",
"08": "Q3",
"09": "Q3",
"10": "Q4",
"11": "Q4",
"12": "Q4",
}

# Get DX projects and filter on year based on project name
dx_projects = [project for project in lims.get_projects(udf={'Application': 'DX'}) if project.name.startswith('Dx WL23')]
dx_projects = [
project
for project in lims.get_projects(udf={"Application": "DX"})
if project.name.startswith("Dx WL24")
]
sample_count = 0

# Expected actions
action_list = ['total', 'complete', 'nextstep', 'remove', 'rework', 'repeat', 'completerepeat', 'store', 'leave', 'None']
action_list = [
"total",
"complete",
"nextstep",
"remove",
"rework",
"repeat",
"completerepeat",
"store",
"leave",
"None",
]

# Expected processes
processes = [
'Dx Sample registratie zuivering', 'Dx Hamilton uitvullen', 'Dx Hamilton zuiveren',
'Dx Zuiveren gDNA manueel', 'Dx manueel gezuiverd placement', 'Dx gDNA Normalisatie Caliper', 'Dx Fragmenteren',
'Dx Library Prep & Target Enrichment Magnis', 'Dx Placement Enrichment Magnis',
'Dx 3nM verdunning Magnis', 'Dx Multiplexen Enrichment samples (3nM) Magnis', 'Dx Multiplexen Enrichment pools Magnis',
'Dx Multiplexen sequence pool', 'Dx Library pool denatureren en laden (NovaSeq)', 'AUTOMATED - NovaSeq Run (NovaSeq 6000)',
'Dx Library pool denatureren en laden (NovaSeq) Dx QC controle Lab sequencen',
'Dx Library pool denatureren en laden (NovaSeq) Dx NovaSeq QC controle Lab sequencen',
'Dx NGS labwerk afronden', 'Dx Bioinformatica analyses', 'Dx Fingerprint match maken', 'Dx NGS onderzoeken afronden',
'Dx sample registratie pool', 'Dx Capture', 'Dx Exonuclease behandeling', 'Dx PCR na exonuclease behandeling',
'Dx smMIP multiplexen & BBSS sequence pool', 'Dx NGS smMIP onderzoeken afronden', 'Dx smMIP sequence pool verdunning',
'Dx Library pool denatureren en laden (Nextseq)', 'Dx NextSeq Run',
'Dx Library pool denatureren en laden (Nextseq) Dx QC controle Lab sequencen',
'Dx Sample registratie', 'Dx gDNA handmatige normalisatie', 'Dx Uitvullen en zuiveren (Fluent 480)',
'Dx Uitvullen en zuiveren (Fluent 480)', 'Dx Normaliseren (Fluent 480)', 'Dx gDNA handmatige normalisatie WES',

# CREv2
'Dx Fragmenteren & BBSS', 'Dx LibraryPrep Caliper KAPA', 'Dx Library Prep amplificatie & clean up KAPA',
'Dx Multiplexen library prep', 'Dx Enrichment DNA fragments', 'Dx Post Enrichment clean up',
'Dx Aliquot Post Enrichment (clean)', 'Dx Post Enrichment PCR & clean up', 'Dx Aliquot Post Enrichment PCR (clean)',
'Dx Library pool verdunnen', 'Dx Multiplexen library pool', 'Dx Automated NovaSeq Run (standaard)',
"Dx Sample registratie zuivering",
"Dx Uitvullen en zuiveren (Fluent 480)",
"Dx Normaliseren (Fluent 480)",
"Dx gDNA handmatige normalisatie WES",
"Dx Fragmenteren",
"Dx Library Prep & Target Enrichment Magnis",
"Dx 3nM verdunning Magnis",
"Dx Multiplexen Enrichment samples (3nM) Magnis",
"Dx Multiplexen Enrichment pools Magnis",
"Dx Multiplexen sequence pool",
"Dx Library pool denatureren en laden (NovaSeq)",
"AUTOMATED - NovaSeq Run (NovaSeq 6000 v3.1)",
"Dx Library pool denatureren en laden (NovaSeqXPlus)",
"Dx NovaSeqXPlus Run",
"Dx NovaSeq QC controle Lab sequencen",
"Dx Bioinformatica analyses",
"Dx NGS onderzoeken afronden",
"Dx maken mengfractie",
"Dx Placement Enrichment Magnis",
"Dx NovaSeqXPlus Run Dx NovaSeq QC controle Lab sequencen",
"AUTOMATED - NovaSeq Run (NovaSeq 6000)",
"Dx Library pool denatureren en laden (NovaSeq) Dx NovaSeq QC controle Lab sequencen",
]

# Append combined process name for qc processes
qc_processes = [
'Dx Qubit QC', 'Dx Tecan Spark 10M QC', 'Dx Bioanalyzer QC',
'Dx Tapestation 2200 QC', 'Dx Tapestation 4200 QC', 'Dx Aggregate QC'
"Dx Qubit QC",
"Dx Tecan Spark 10M QC",
"Dx Bioanalyzer QC",
"Dx Tapestation 2200 QC",
"Dx Tapestation 4200 QC",
"Dx Aggregate QC",
]
processes_before_qc = [
'Dx Hamilton uitvullen', 'Dx Hamilton zuiveren', 'Dx Zuiveren gDNA manueel', 'Dx Placement Enrichment Magnis',
'Dx Multiplexen Enrichment pools Magnis', 'Dx sample registratie pool', 'Dx smMIP multiplexen & BBSS sequence pool',
'Dx PCR na exonuclease behandeling', 'Dx Sample registratie', 'Dx Exonuclease behandeling',
'Dx Sample registratie zuivering',

# CREv2
'Dx Fragmenteren & BBSS', 'Dx LibraryPrep Caliper KAPA', 'Dx Library Prep amplificatie & clean up KAPA',
'Dx Post Enrichment PCR & clean up', 'Dx Multiplexen library pool'
"Dx Sample registratie zuivering",
"Dx Multiplexen Enrichment pools Magnis",
"Dx Placement Enrichment Magnis",
]

for process in processes_before_qc:
for qc_process in qc_processes:
processes.append("{0} {1}".format(process, qc_process))
Expand All @@ -81,30 +106,52 @@

for project in dx_projects:
for sample in lims.get_samples(projectlimsid=project.id):
if 'Dx Onderzoeksreden' not in sample.udf or sample.udf['Dx Onderzoeksreden'] == 'Research': # skip research
if (
"Dx Onderzoeksreden" not in sample.udf
or sample.udf["Dx Onderzoeksreden"] == "Research"
): # skip research
continue
sample_count += 1
sample_quarter = month_quarter[sample.date_received.split('-')[1]]
for artifact in lims.get_artifacts(samplelimsid=sample.id, resolve=True, type='Analyte'):
sample_quarter = month_quarter[sample.date_received.split("-")[1]]
for artifact in lims.get_artifacts(
samplelimsid=sample.id, resolve=True, type="Analyte"
):
for process in lims.get_processes(inputartifactlimsid=artifact.id):

# Parse process name, remov version. Add to count dictonary if not yet defined.
process_name = re.sub(r' v\d\.\d', '', process.type.name)
if 'QC' in process_name and artifact.parent_process:
process_name = "{0} {1}".format(re.sub(r' v\d\.\d', '', artifact.parent_process.type.name), process_name)
process_name = re.sub(r" v\d\.\d", "", process.type.name)
if "QC" in process_name and artifact.parent_process:
process_name = "{0} {1}".format(
re.sub(r" v\d\.\d", "", artifact.parent_process.type.name),
process_name,
)

# Find output artifacts
output_artifacts = []
if process.all_outputs(): # outputs_per_input returns TypeError if there is no output
output_artifacts = [output_artifact.id for output_artifact in process.outputs_per_input(artifact.id, Analyte=True)]
if (
process.all_outputs()
): # outputs_per_input returns TypeError if there is no output
output_artifacts = [
output_artifact.id
for output_artifact in process.outputs_per_input(
artifact.id, Analyte=True
)
]

# For 'Bioinformatica analyses' and 'NGS onderzoeken afronden' we need to demux to get correct artifact
if process_name in ['Dx Bioinformatica analyses', 'Dx NGS onderzoeken afronden']:
artifact_demux = lims.get('/demux?'.join(artifact.uri.split('?')))
for node in artifact_demux.getiterator('artifact'):
if node.find('samples') and len(node.find('samples').findall('sample')) == 1:
demux_artifact = Artifact(lims, uri=node.attrib['uri'])
if sample == demux_artifact.samples[0]: # 1 sample per artifact.
if process_name in [
"Dx Bioinformatica analyses",
"Dx NGS onderzoeken afronden",
]:
artifact_demux = lims.get("/demux?".join(artifact.uri.split("?")))
for node in artifact_demux.getiterator("artifact"):
if (
node.find("samples")
and len(node.find("samples").findall("sample")) == 1
):
demux_artifact = Artifact(lims, uri=node.attrib["uri"])
if (
sample == demux_artifact.samples[0]
): # 1 sample per artifact.
output_artifacts = [demux_artifact.id]
break

Expand All @@ -114,18 +161,31 @@

# Get action for artifact
for action in process.step.actions.get_next_actions():
if action['artifact'].id in output_artifacts:
process_action_counts[sample_quarter][process_name]['total'] += 1
process_action_counts[sample_quarter][process_name][str(action['action'])] += 1
if action["artifact"].id in output_artifacts:
process_action_counts[sample_quarter][process_name][
"total"
] += 1
process_action_counts[sample_quarter][process_name][
str(action["action"])
] += 1

print('Total Sample count: {0}'.format(str(sample_count)))
print("Total Sample count: {0}".format(str(sample_count)))

for quarter in quarters:
print(quarter)
print('Process\t{action_list}'.format(action_list='\t'.join(action_list)))
print("Process\t{action_list}".format(action_list="\t".join(action_list)))
for process in process_action_counts[quarter]:
if process_action_counts[quarter][process]['total']:
print('{process}\t{action_list}'.format(
process=process,
action_list='\t'.join([str(process_action_counts[quarter][process][action]) if action in process_action_counts[quarter][process] else '0' for action in action_list])
))
if process_action_counts[quarter][process]["total"]:
print(
"{process}\t{action_list}".format(
process=process,
action_list="\t".join(
[
str(process_action_counts[quarter][process][action])
if action in process_action_counts[quarter][process]
else "0"
for action in action_list
]
),
)
)
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