def species_page(species):
return render_template(
'untabbed_datatables.html',
species,
tables=[
util.datatable_cfg(
'Summary',
'species',
util.construct_url('species', where={'name': species}),
minimal=True
),
util.datatable_cfg(
'Supported genomes',
'genomes',
util.construct_url('genomes', where={'species': species}, max_results=1000),
minimal=True
),
util.datatable_cfg(
'Yield requirements',
'yields',
ajax_call={
'func_name': 'required_yields',
'api_url': util.construct_url('species', where={'name': species})
},
default_sort_col='yield_x_coverage',
minimal=True
)
]
)
def bioinformatics_activity():
return render_template(
'bioinformatics_activity.html',
'Bioinformatics pipeline activity',
proc_base=util.construct_url('analysis_driver_procs'),
stage_base=util.construct_url('analysis_driver_stages')
)
def report_run(run_id):
lanes = sorted(set(e['lane_number'] for e in rest_api().get_documents('lanes', where={'run_id': run_id})))
return render_template(
'run_report.html',
run_id + ' Run Report',
include_review_modal=True,
lane_aggregation=util.datatable_cfg(
'Aggregation per lane',
'lane_aggregation',
api_url=util.construct_url('lanes', where={'run_id': run_id}),
default_sort_col='lane_number',
minimal=True,
create_row='color_filter',
review={'entity_field': 'aggregated.sample_ids', 'button_name': 'runreview'}
),
tab_sets=[
util.tab_set_cfg(
'Demultiplexing reports per lane',
[
util.datatable_cfg(
'Demultiplexing lane ' + str(lane),
'demultiplexing',
api_url=util.construct_url('run_elements', where={'run_id': run_id, 'lane': lane}),
minimal=True,
create_row='color_filter',
review={'entity_field': 'sample_id', 'button_name': 'runreview'}
)
for lane in lanes
]
),
util.tab_set_cfg(
'Unexpected barcodes',
[
util.datatable_cfg(
'Unexpected barcodes lane ' + str(lane),
'unexpected_barcodes',
api_url=util.construct_url('unexpected_barcodes', where={'run_id': run_id, 'lane': lane}),
default_sort_col='passing_filter_reads',
minimal=True,
create_row='color_filter'
)
for lane in lanes
]
)
],
procs=rest_api().get_documents(
'analysis_driver_procs',
where={'dataset_type': 'run', 'dataset_name': run_id},
embedded={'stages': 1},
sort='-_created'
)
)
def all_species():
return render_template(
'untabbed_datatables.html',
'Species',
tables=[
util.datatable_cfg(
'Available species',
'species',
util.construct_url('species', max_results=1000)
),
util.datatable_cfg(
'Installed genomes',
'genomes',
util.construct_url('genomes', max_results=10000)
)
]
)
def project_reports():
return render_template(
'untabbed_datatables.html',
'Projects',
table=util.datatable_cfg(
'All projects list',
'projects',
ajax_call={
'func_name': 'dt_merge_multi_sources',
'api_urls': [
util.construct_url('projects', max_results=10000),
util.construct_url('lims/project_info', match={'project_status': 'all'}),
],
'merge_on': 'project_id'
}
)
)
def runs_report(view_type):
ajax_call = {'func_name': 'dt_merge_multi_sources', 'merge_on': 'run_id'}
if view_type == 'all':
ajax_call['api_urls'] = [
util.construct_url('runs', max_results=10000),
util.construct_url('lims/run_status'),
]
elif view_type in ['recent', 'current_year', 'last_12_months']:
if view_type == 'recent':
time_ago = util.now() - datetime.timedelta(days=30)
elif view_type == 'last_12_months':
time_ago = util.now() - datetime.timedelta(days=365)
elif view_type == 'current_year':
y = util.now().year
time_ago = datetime.datetime(year=y, month=1, day=1)
view_type = str(y)
ajax_call['api_urls'] = [
util.construct_url('runs', where={'_created': {'$gte': time_ago.strftime(settings.DATE_FORMAT)}}, max_results=10000),
util.construct_url('lims/run_status', createddate=time_ago.strftime(settings.DATE_FORMAT)),
]
else:
fl.abort(404)
return None
title = util.capitalise(view_type).replace('_', ' ') + ' Runs'
return render_template(
'untabbed_datatables.html',
title,
include_review_modal=True,
table=util.datatable_cfg(
title,
'runs',
ajax_call=ajax_call,
create_row='color_filter',
fixed_header=True,
review={'entity_field': 'sample_ids', 'button_name': 'runreview'}
)
)
def plot_library(library):
return render_template(
'plate_view.html',
'Library ' + library,
table=util.datatable_cfg(
'Library ' + library,
['simple_plot_child', 'library_plot_metrics'],
ajax_call={
'func_name': 'dt_merge_lims_container_and_qc_data',
'lims_url': util.construct_url('lims/library_info', match={'container_id': library}, flatten=True),
'qc_url': util.construct_url('samples'),
},
initComplete='load_data_to_chart',
page_length=10
),
container_id=library,
qc_url=util.construct_url('samples'),
lims_url=util.construct_url('lims/genotyping_info'),
plate_view_metrics=resolve_cols('library_plot_metrics')
)
def plot_genotyping(genotype):
return render_template(
'plate_view.html',
'Genotyping: ' + genotype,
table=util.datatable_cfg(
'Genotyping ' + genotype,
['simple_plot_child', 'genotype_plot_metrics'],
ajax_call={
'func_name': 'dt_merge_lims_container_and_qc_data',
'lims_url': util.construct_url('lims/genotyping_info', match={'container_id': genotype}, flatten=True),
'qc_url': util.construct_url('samples'),
},
initComplete='load_data_to_chart',
page_length=10
),
container_id=genotype,
qc_url=util.construct_url('samples'),
lims_url=util.construct_url('lims/genotyping_info'),
plate_view_metrics=resolve_cols('genotype_plot_metrics'),
plate_type='384'
)
def sequencing_charts(view_type):
if view_type == 'last_month':
time_ago = util.now() - datetime.timedelta(days=30)
elif view_type == 'last_3_months':
time_ago = util.now() - datetime.timedelta(days=92)
elif view_type == 'last_12_months':
time_ago = util.now() - datetime.timedelta(days=365)
else:
fl.abort(404)
return None
time_str = time_ago.strftime(settings.DATE_FORMAT)
return render_template(
'charts.html',
'Sequencing metrics charts',
api_urls=[
util.construct_url('lanes', max_results=10000, where={'_created': {'$gte': time_str}}),
util.construct_url('lims/run_status', createddate=time_str),
],
merge_on='run_id',
merge_properties=['run'],
metric_options=resolve_cols('seq_plot_metrics'),
color_options=resolve_cols('seq_plot_colors')
)
def step_view(step_type, view_type):
if step_type == 'libraries':
endpoint = 'library_info'
columns = 'libraries'
child_columns = 'libraries_child'
elif step_type == 'genotypes':
endpoint = 'genotyping_info'
columns = 'genotyping'
child_columns = 'genotyping_child'
else:
fl.abort(404)
time_ago = None
if view_type == 'recent':
time_ago = util.now() - datetime.timedelta(days=30)
elif view_type == 'last_12_months':
time_ago = util.now() - datetime.timedelta(days=365)
elif view_type == 'current_year':
y = util.now().year
time_ago = datetime.datetime(year=y, month=1, day=1)
view_type = str(y)
elif view_type == 'all':
pass
else:
fl.abort(404)
return None
query_params = {}
if time_ago:
query_params['time_from'] = time_ago.strftime(settings.DATE_FORMAT)
title = util.capitalise(view_type).replace('_', ' ') + ' ' + util.capitalise(step_type)
return render_template(
'untabbed_datatables.html',
title,
table=util.datatable_cfg(
title,
columns,
util.construct_url('lims/' + endpoint, **query_params),
default_sort_col='-date_completed',
child_datatable=util.datatable_cfg(
'', # No title provided
child_columns,
data_source='samples', # Where to find the data of the child datatable
name_source='id', # Where to find the name of the child datatable
minimal=True
)
)
)
def project_status_reports(prj_status):
status_order = []
for s in project_status_cfg.status_order:
status_order.append(
{
'name': s,
'completed': [step for step, st in project_status_cfg.step_completed_to_status.items() if st == s],
'queued': [step for step, st in project_status_cfg.step_queued_to_status.items() if st == s]
}
)
# Last week project status page is a special case and needs to be rendered slightly differently.
if prj_status == 'lastweek':
seven_days_ago = datetime.datetime.now() - datetime.timedelta(days=7)
page_title = 'Project status last week'
page_header = 'Status of Projects Last Week'
api_url = util.construct_url('lims/project_status',
match={'process_limit_date': seven_days_ago.strftime(settings.DATE_FORMAT)})
else:
page_title = prj_status.capitalize() + ' Project Status'
page_header = 'Status of ' + prj_status.capitalize() + ' Projects'
api_url = util.construct_url('lims/project_status', match={'project_status': prj_status})
return render_template(
'project_status.html',
page_title,
status_order=status_order,
table=util.datatable_cfg(
page_header,
'project_status',
api_url=api_url,
state_save=True,
fixed_header=True,
table_foot='sum_row_per_column'
)
)
def tat_charts():
return render_template(
'tat_charts.html',
'Turn around time charts',
api_url=util.construct_url('lims/sample_status', match={'project_status': 'all'})
)
def report_sample(sample_id):
return render_template(
'sample_report.html',
sample_id + ' Sample Report',
include_review_modal=True,
tables=[
util.datatable_cfg(
'Sample QC for ' + sample_id,
'sample_qc_child_flatten',
minimal=True,
default_sort_col='sample_id',
api_url=util.construct_url('lims/sample_qc_info', match={'sample_id': sample_id}, flatten=True),
collapse=True
),
util.datatable_cfg(
'Libraries preparations for ' + sample_id,
'libraries_child_flatten',
minimal=True,
default_sort_col='sample_id',
api_url=util.construct_url('lims/library_info', match={'sample_id': sample_id}, flatten=True),
collapse=True
),
util.datatable_cfg(
'Genotyping for ' + sample_id,
'genotyping_child_flatten',
minimal=True,
default_sort_col='sample_id',
api_url=util.construct_url('lims/genotyping_info', match={'sample_id': sample_id}, flatten=True),
collapse=True
),
util.datatable_cfg(
'Bioinformatics report for ' + sample_id,
'samples',
ajax_call={
'func_name': 'dt_merge_multi_sources',
'merge_on': 'sample_id',
'api_urls': [
util.construct_url('samples', where={'sample_id': sample_id}),
util.construct_url('lims/sample_status', match={'sample_id': sample_id, 'project_status': 'all'}),
util.construct_url('lims/sample_info', match={'sample_id': sample_id, 'project_status': 'all'})
]
},
minimal=True,
review={'entity_field': 'sample_id', 'button_name': 'samplereview'},
create_row='color_data_source'
),
util.datatable_cfg(
'Run elements generated for ' + sample_id,
'sample_run_elements',
api_url=util.construct_url('run_elements', where={'sample_id': sample_id}, max_results=1000),
minimal=True,
create_row='color_filter'
)
],
sample_id=sample_id,
sample_statuses=rest_api().get_document(
'lims/status/sample_status',
detailed=True,
match={'sample_id': sample_id, 'project_status': 'all'}
),
lims_url=cfg['lims_url'],
procs=rest_api().get_documents(
'analysis_driver_procs',
where={'dataset_type': 'sample', 'dataset_name': sample_id},
embedded={'stages': 1},
sort='-_created'
)
)
def report_project(project_ids):
if project_ids == 'SGP':
id_list = []
for p in rest_api().get_documents('lims/project_info', match={'project_status': 'open'}):
if p['project_id'].startswith('S'):
id_list.append(p['project_id'])
else:
id_list = project_ids.split(',')
if len(id_list) > 1:
project_status_call = {
'ajax_call': {
'func_name': 'dt_merge_multi_sources',
'merge_on': 'project_id',
'api_urls': [
util.construct_url('lims/project_status', match={'project_id': i, 'project_status': 'all'})
for i in id_list
]
}
}
plate_status_call = {
'ajax_call': {
'func_name': 'dt_merge_multi_sources',
'merge_on': 'plate_id',
'api_urls': [
util.construct_url('lims/plate_status', match={'project_id': i, 'project_status': 'all'})
for i in id_list
]
}
}
library_info_call = {
'ajax_call': {
'func_name': 'dt_merge_multi_sources',
'merge_on': 'library_id',
'api_urls': [
util.construct_url('lims/library_info', match={'project_id': id_list[i]})
for i in id_list
]
}
}
sample_qc_info_call = {
'ajax_call': {
'func_name': 'dt_merge_multi_sources',
'merge_on': 'library_id',
'api_urls': [
util.construct_url('lims/sample_qc_info', match={'project_id': id_list[i]})
for i in id_list
]
}
}
genotyping_info_call = {
'ajax_call': {
'func_name': 'dt_merge_multi_sources',
'merge_on': 'library_id',
'api_urls': [
util.construct_url('lims/genotyping_info', match={'project_id': id_list[i]})
for i in id_list
]
}
}
else:
project_status_call = {
'api_url': util.construct_url('lims/project_status', match={'project_id': id_list[0], 'project_status': 'all'})
}
plate_status_call = {
'api_url': util.construct_url('lims/plate_status', match={'project_id': id_list[0], 'project_status': 'all'})
}
library_info_call = {
'api_url': util.construct_url('lims/library_info', match={'project_id': id_list[0]})
}
sample_qc_info_call = {
'api_url': util.construct_url('lims/sample_qc_info', match={'project_id': id_list[0]})
}
genotyping_info_call = {
'api_url': util.construct_url('lims/genotyping_info', match={'project_id': id_list[0]})
}
procs = []
bioinformatics_urls = []
for i in id_list:
docs = rest_api().get_documents(
'analysis_driver_procs',
where={'dataset_type': 'project', 'dataset_name': i},
embedded={'stages': 1},
sort='-_created'
)
procs.extend(docs)
bioinformatics_urls += [
util.construct_url('samples', where={'project_id': i}, max_results=10000),
util.construct_url('lims/sample_status', match={'project_id': i, 'project_status': 'all'}),
util.construct_url('lims/sample_info', match={'project_id': i, 'project_status': 'all'})
]
return render_template(
'project_report.html',
'Project report for ' + project_ids,
include_review_modal=True,
tables=[
util.datatable_cfg(
'Project Status for ' + project_ids,
'project_status',
minimal=True,
**project_status_call
),
util.datatable_cfg(
'Plate Status for ' + project_ids,
'plate_status',
minimal=True,
default_sort_col='plate_id',
collapse=True,
**plate_status_call
),
util.datatable_cfg(
'Sample QC for ' + project_ids,
'sample_qc',
minimal=True,
default_sort_col='date_completed',
child_datatable=util.datatable_cfg(
'', # No title provided
'sample_qc_child',
data_source='samples', # Where to find the data of the child datatable
name_source='id', # Where to find the name of the child datatable
minimal=True
),
collapse=True,
**sample_qc_info_call
),
util.datatable_cfg(
'Libraries preparations for ' + project_ids,
'libraries',
minimal=True,
default_sort_col='date_completed',
child_datatable=util.datatable_cfg(
'', # No title provided
'libraries_child',
data_source='samples', # Where to find the data of the child datatable
name_source='id', # Where to find the name of the child datatable
minimal=True
),
collapse=True,
**library_info_call
),
util.datatable_cfg(
'Genotyping for ' + project_ids,
'genotyping',
minimal=True,
default_sort_col='date_completed',
child_datatable=util.datatable_cfg(
'', # No title provided
'genotyping_child',
data_source='samples', # Where to find the data of the child datatable
name_source='id', # Where to find the name of the child datatable
minimal=True
),
collapse=True,
**genotyping_info_call
),
util.datatable_cfg(
'Bioinformatics report for ' + project_ids,
'samples',
ajax_call={
'func_name': 'dt_merge_multi_sources',
'api_urls': bioinformatics_urls,
'merge_on': 'sample_id'
},
fixed_header=True,
review={'entity_field': 'sample_id', 'button_name': 'samplereview'},
create_row='color_data_source'
)
],
procs=procs
)
def report_samples(view_type):
six_months_ago = util.now() - datetime.timedelta(days=182)
ajax_call = {'func_name': 'dt_merge_multi_sources_keep_first', 'merge_on': 'sample_id'}
if view_type == 'all':
title = 'All samples'
ajax_call['api_urls'] = [
util.construct_url('samples', max_results=15000),
util.construct_url('lims/sample_status', match={'project_status': 'all'}),
util.construct_url('lims/sample_info', match={'project_status': 'all'})
]
elif view_type == 'processing':
title = 'Samples processing'
ajax_call['api_urls'] = [
util.construct_url('samples', where={'aggregated.most_recent_proc.status': 'processing'}, max_results=10000),
util.construct_url('lims/sample_status', match={'createddate': six_months_ago.strftime(settings.DATE_FORMAT), 'project_status': 'open'}),
util.construct_url('lims/sample_info', match={'createddate': six_months_ago.strftime(settings.DATE_FORMAT), 'project_status': 'open'})
]
elif view_type == 'toreview':
title = 'Samples to review'
ajax_call['api_urls'] = [
util.construct_url('samples', where={'useable': 'not%20marked', 'aggregated.most_recent_proc.status': 'finished'}, max_results=10000),
util.construct_url('lims/sample_status', match={'createddate': six_months_ago.strftime(settings.DATE_FORMAT), 'project_status': 'open'}),
util.construct_url('lims/sample_info', match={'createddate': six_months_ago.strftime(settings.DATE_FORMAT), 'project_status': 'open'})
]
elif view_type == 'notprocessing':
# Samples which have clean yield value populated, and have not started processing yet, or have a status of
# reprocess, force_ready, resume or null.
title = 'Samples not processing'
ajax_call['api_urls'] = [
util.construct_url('samples', where={"$and": [{"aggregated.clean_yield_in_gb": {"$exists": True, "$ne": None}},
{"$or": [
{"aggregated.most_recent_proc": None},
{"aggregated.most_recent_proc.status": None},
{"aggregated.most_recent_proc.status": "reprocess"},
{"aggregated.most_recent_proc.status": "force_ready"},
{"aggregated.most_recent_proc.status": "resume"}
]}]}, max_results=10000),
util.construct_url('lims/sample_status', match={'createddate': six_months_ago.strftime(settings.DATE_FORMAT), 'project_status': 'open'}),
util.construct_url('lims/sample_info', match={'createddate': six_months_ago.strftime(settings.DATE_FORMAT), 'project_status': 'open'})
]
else:
fl.abort(404)
return None
return render_template(
'untabbed_datatables.html',
title,
include_review_modal=True,
table=util.datatable_cfg(
title,
'samples',
ajax_call=ajax_call,
review={'entity_field': 'sample_id', 'button_name': 'samplereview'},
create_row='color_data_source'
)
)