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Merged
sawibo merged 2 commits into from
May 20, 2026
Merged

Develop #210

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ba1b83d
Added run comments field to finance overview
May 20, 2026
2316804
Merge branch 'develop' of github.com:UMCUGenetics/USEQ_tools into dev…
May 20, 2026
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12 changes: 10 additions & 2 deletions epp/useq_finance_overview.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,6 +81,7 @@ def initialize_project_run_data(pool_id: str) -> Dict[str, Any]:
'first_submission_date': None,
'received_date': set(),
'project_comments': None,
'run_comments' : None,
'times_sequenced': 0,
'pool': pool_id,
'lims_runtype': None,
Expand Down Expand Up @@ -274,6 +275,7 @@ def process_run_artifact(lims: Lims, sample_artifact: Artifact, sample_meta: Dic
pid_sequenced (Dict[str, Set]): Dictionary tracking when projects were sequenced
"""
protocol_name = get_step_protocol(lims, step_id=sample_artifact.parent_process.id)
# print('test', protocol_name)
run_data['lims_runtype'] = protocol_name.split("-", 1)[1].lower().strip()

if not run_data['run_date']:
Expand Down Expand Up @@ -518,6 +520,7 @@ def get_seq_finance(lims: Lims, step_uri: str) -> str:
runs[pool.id] = {}

run_date = None
run_comments = ''
pool_parent_process = pool.parent_process # BCL to FastQ

# Try to determine the date this run was sequenced
Expand All @@ -532,6 +535,7 @@ def get_seq_finance(lims: Lims, step_uri: str) -> str:
for process in processes:

if process.type.name in Config.RUN_PROCESSES:
run_comments = process.udf.get('Run Comments', '')
run_date = process.date_run
break

Expand Down Expand Up @@ -628,6 +632,8 @@ def get_seq_finance(lims: Lims, step_uri: str) -> str:
run_meta['date'] = sample.date_received
runs[pool.id][project_id]['run_date'] = run_meta['date']
else:


# Process sample artifacts
sample_artifacts = lims.get_artifacts(samplelimsid=sample.id)
for sample_artifact in sample_artifacts:
Expand All @@ -636,7 +642,7 @@ def get_seq_finance(lims: Lims, step_uri: str) -> str:
continue

process_name = sample_artifact.parent_process.type.name

# print('test', process_name)
# Handle different process types
if process_name in Config.ISOLATION_PROCESSES:
process_isolation_artifact(
Expand All @@ -660,7 +666,7 @@ def get_seq_finance(lims: Lims, step_uri: str) -> str:
runs[pool.id][project_id], run_meta,
run_date, pid_sequenced
)

# print('Run artifact found', project_id, process_name)
elif process_name in Config.ANALYSIS_PROCESSES and application != 'SNP Fingerprinting':
process_analysis_artifact(
sample_artifact, sample, sample_meta,
Expand Down Expand Up @@ -698,10 +704,12 @@ def get_seq_finance(lims: Lims, step_uri: str) -> str:
# sample_meta['Sequenced'] = True
###Check if sample_meta['Sequenced'] = True needs to be set####


# Fetch and update costs
costs = fetch_project_costs(project_id, run_meta)
update_run_costs(runs[pool.id][project_id], costs, application)

runs[pool.id][project_id]['run_comments'] = run_comments
# Deduplicate and convert sets to strings
runs_dedup = deduplicate_runs(runs)
return render_template('seq_finance_overview_template.csv', {'pools': runs_dedup})
Expand Down
4 changes: 2 additions & 2 deletions resources/seq_finance_overview_template.csv
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
errors;pool_name;project_name;project_id;open_date;contact_name;contact_email;account;project_budget_number;sample_type;nr_samples;isolation_step_costs;isolation_personell_costs;libraryprep_step_costs;libraryprep_personell_costs;plate_step_costs;plate_personell_costs;sequencing_step_costs;sequencing_personell_costs;analysis_step_costs;analysis_personell_costs;total_step_costs;total_personell_costs;billing_institute;billing_department;billing_street;billing_postalcode;billing_city;billing_country;requested_runtype;lims_runtype;requested_libraryprep;lims_libraryprep;lims_isolation;requested_analysis;sequencing_succesful;description;order_number;comments_and_agreements;deb_nr;vat_nr;nr_samples_isolated;nr_samples_prepped;nr_samples_sequenced;nr_samples_analyzed;nr_lanes;
errors;pool_name;project_name;project_id;open_date;contact_name;contact_email;account;project_budget_number;sample_type;nr_samples;isolation_step_costs;isolation_personell_costs;libraryprep_step_costs;libraryprep_personell_costs;plate_step_costs;plate_personell_costs;sequencing_step_costs;sequencing_personell_costs;analysis_step_costs;analysis_personell_costs;total_step_costs;total_personell_costs;billing_institute;billing_department;billing_street;billing_postalcode;billing_city;billing_country;requested_runtype;lims_runtype;requested_libraryprep;lims_libraryprep;lims_isolation;requested_analysis;sequencing_succesful;description;order_number;comments_and_agreements;deb_nr;vat_nr;nr_samples_isolated;nr_samples_prepped;nr_samples_sequenced;nr_samples_analyzed;nr_lanes;run_comments
{%- for pool in pools %}
{%- for run in pools[pool] %}
{{ pools[pool][run]['errors'] }};{{ pools[pool][run]['pool'] }};{{ pools[pool][run]['name'] }};{{ pools[pool][run]['id'] }};{{ pools[pool][run]['open_date'] }};{{ pools[pool][run]['contact_name'] }};{{ pools[pool][run]['contact_email'] }};{{ pools[pool][run]['lab_name'] }};{{ pools[pool][run]['budget_nr'] }};{{ pools[pool][run]['type'] }};{{ pools[pool][run]['nr_samples_submitted'] }};{{ pools[pool][run]['isolation_step_costs'] }};{{ pools[pool][run]['isolation_personell_costs'] }};{{ pools[pool][run]['libprep_step_costs'] }};{{ pools[pool][run]['libprep_personell_costs'] }};NA;NA;{{ pools[pool][run]['run_step_costs'] }};{{ pools[pool][run]['run_personell_costs'] }};{{ pools[pool][run]['analysis_step_costs'] }};{{ pools[pool][run]['analysis_personell_costs'] }};{{ pools[pool][run]['total_step_costs'] }};{{ pools[pool][run]['total_personell_costs'] }};{{ pools[pool][run]['institute'] }};{{ pools[pool][run]['department'] }};{{ pools[pool][run]['street'] }};{{ pools[pool][run]['postalcode'] }};{{ pools[pool][run]['city'] }};{{ pools[pool][run]['country'] }};{{ pools[pool][run]['requested_runtype'] }};{{ pools[pool][run]['lims_runtype'] }};{{ pools[pool][run]['requested_library_prep'] }};{{ pools[pool][run]['lims_library_prep'] }};{{ pools[pool][run]['lims_isolation'] }};{{ pools[pool][run]['requested_analysis'] }};{{ pools[pool][run]['succesful'] }};{{ pools[pool][run]['description'] }};{{ pools[pool][run]['order_nr'] }};{{ pools[pool][run]['project_comments'] }};{{ pools[pool][run]['deb_nr'] }};{{ pools[pool][run]['vat_nr'] }};{{ pools[pool][run]['nr_samples_isolated'] }};{{ pools[pool][run]['nr_samples_prepped'] }};{{ pools[pool][run]['nr_samples_sequenced'] }};{{ pools[pool][run]['nr_samples_analyzed'] }};{{ pools[pool][run]['run_lanes'] }}
{{ pools[pool][run]['errors'] }};{{ pools[pool][run]['pool'] }};{{ pools[pool][run]['name'] }};{{ pools[pool][run]['id'] }};{{ pools[pool][run]['open_date'] }};{{ pools[pool][run]['contact_name'] }};{{ pools[pool][run]['contact_email'] }};{{ pools[pool][run]['lab_name'] }};{{ pools[pool][run]['budget_nr'] }};{{ pools[pool][run]['type'] }};{{ pools[pool][run]['nr_samples_submitted'] }};{{ pools[pool][run]['isolation_step_costs'] }};{{ pools[pool][run]['isolation_personell_costs'] }};{{ pools[pool][run]['libprep_step_costs'] }};{{ pools[pool][run]['libprep_personell_costs'] }};NA;NA;{{ pools[pool][run]['run_step_costs'] }};{{ pools[pool][run]['run_personell_costs'] }};{{ pools[pool][run]['analysis_step_costs'] }};{{ pools[pool][run]['analysis_personell_costs'] }};{{ pools[pool][run]['total_step_costs'] }};{{ pools[pool][run]['total_personell_costs'] }};{{ pools[pool][run]['institute'] }};{{ pools[pool][run]['department'] }};{{ pools[pool][run]['street'] }};{{ pools[pool][run]['postalcode'] }};{{ pools[pool][run]['city'] }};{{ pools[pool][run]['country'] }};{{ pools[pool][run]['requested_runtype'] }};{{ pools[pool][run]['lims_runtype'] }};{{ pools[pool][run]['requested_library_prep'] }};{{ pools[pool][run]['lims_library_prep'] }};{{ pools[pool][run]['lims_isolation'] }};{{ pools[pool][run]['requested_analysis'] }};{{ pools[pool][run]['succesful'] }};{{ pools[pool][run]['description'] }};{{ pools[pool][run]['order_nr'] }};{{ pools[pool][run]['project_comments'] }};{{ pools[pool][run]['deb_nr'] }};{{ pools[pool][run]['vat_nr'] }};{{ pools[pool][run]['nr_samples_isolated'] }};{{ pools[pool][run]['nr_samples_prepped'] }};{{ pools[pool][run]['nr_samples_sequenced'] }};{{ pools[pool][run]['nr_samples_analyzed'] }};{{ pools[pool][run]['run_lanes'] }};{{ pools[pool][run]['run_comments'] }}
{%- endfor %}
{%- endfor %}
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