def causatives(institute_id):
institute_obj = institute_and_case(store, institute_id)
query = request.args.get('query', '')
hgnc_id = None
if '|' in query:
# filter accepts an array of IDs. Provide an array with one ID element
try:
hgnc_id = [int(query.split(' | ', 1)[0])]
except ValueError:
flash('Provided gene info could not be parsed!', 'warning')
variants = store.check_causatives(institute_obj=institute_obj,
limit_genes=hgnc_id)
if variants:
variants.sort("hgnc_symbols", pymongo.ASCENDING)
all_variants = {}
all_cases = {}
for variant_obj in variants:
if variant_obj['case_id'] not in all_cases:
case_obj = store.case(variant_obj['case_id'])
all_cases[variant_obj['case_id']] = case_obj
else:
case_obj = all_cases[variant_obj['case_id']]
if variant_obj['variant_id'] not in all_variants:
# capture ACMG classification for this variant
if isinstance(variant_obj.get('acmg_classification'), int):
acmg_code = ACMG_MAP[variant_obj['acmg_classification']]
variant_obj['acmg_classification'] = ACMG_COMPLETE_MAP[
acmg_code]
all_variants[variant_obj['variant_id']] = []
all_variants[variant_obj['variant_id']].append((case_obj, variant_obj))
return dict(institute=institute_obj, variant_groups=all_variants)
def panel(panel_id):
"""Display (and add pending updates to) a specific gene panel."""
panel_obj = store.gene_panel(panel_id) or store.panel(panel_id)
if request.method == 'POST':
raw_hgnc_id = request.form['hgnc_id']
if '|' in raw_hgnc_id:
raw_hgnc_id = raw_hgnc_id.split(' | ', 1)[0]
hgnc_id = int(raw_hgnc_id)
action = request.form['action']
if action == 'add':
panel_gene = controllers.existing_gene(store, panel_obj, hgnc_id)
if panel_gene:
flash("gene already in panel: {}".format(panel_gene['symbol']),
'warning')
else:
# ask user to fill-in more information about the gene
return redirect(
url_for('.gene_edit', panel_id=panel_id, hgnc_id=hgnc_id))
elif action == 'delete':
log.debug("marking gene to be deleted: %s", hgnc_id)
store.add_pending(panel_obj, hgnc_id, action='delete')
data = controllers.panel(store, panel_obj)
if request.args.get('case_id'):
data['case'] = store.case(request.args['case_id'])
if request.args.get('institute_id'):
data['institute'] = store.institute(request.args['institute_id'])
return data
def get_timeline_data(limit):
"""Retrieve chronologially ordered events from the database to display them in the timeline page
Args:
limit(str): for instance "50" to display last 50 events. "-1" to display all events
Returns:
timeline_results(dict): dictionary containing timeline data
"""
timeline_results = []
results = store.user_timeline(current_user.email, int(limit))
for eventg in results: # Add links to cases pages
case_obj = store.case(case_id=eventg["_id"]["case_id"])
if case_obj is None:
continue
# Some events are captured both for case and variant. Display them only once (for the variant)
if (eventg["_id"].get("category") == "case"
and eventg["_id"].get("verb") in VAR_SPECIFIC_EVENTS):
continue
# Build link to case page
eventg["_id"]["case_name"] = case_obj.get("display_name")
eventg["_id"]["link"] = url_for(
"cases.case",
institute_id=eventg["_id"]["institute"],
case_name=case_obj["display_name"],
)
timeline_results.append(eventg)
return timeline_results
def get_sanger_unevaluated(store, institute_id, user_id):
"""Get all variants for an institute having Sanger validations ordered but still not evaluated
Args:
store(scout.adapter.MongoAdapter)
institute_id(str)
Returns:
unevaluated: a list that looks like this: [ {'case1': [varID_1, varID_2, .., varID_n]}, {'case2' : [varID_1, varID_2, .., varID_n]} ],
where the keys are case_ids and the values are lists of variants with Sanger ordered but not yet validated
"""
# Retrieve a list of ids for variants with Sanger ordered grouped by case from the 'event' collection
# This way is much faster than querying over all variants in all cases of an institute
sanger_ordered_by_case = store.sanger_ordered(institute_id, user_id)
unevaluated = []
# for each object where key==case and value==[variant_id with Sanger ordered]
for item in sanger_ordered_by_case:
case_id = item["_id"]
# Get the case to collect display name
case_obj = store.case(case_id=case_id)
if not case_obj: # the case might have been removed
continue
case_display_name = case_obj.get("display_name")
# List of variant document ids
varid_list = item["vars"]
unevaluated_by_case = {}
unevaluated_by_case[case_display_name] = []
for var_id in varid_list:
# For each variant with sanger validation ordered
variant_obj = store.variant(document_id=var_id, case_id=case_id)
# Double check that Sanger was ordered (and not canceled) for the variant
if (
variant_obj is None
or variant_obj.get("sanger_ordered") is None
or variant_obj.get("sanger_ordered") is False
):
continue
validation = variant_obj.get("validation", "not_evaluated")
# Check that the variant is not evaluated
if validation in ["True positive", "False positive"]:
continue
unevaluated_by_case[case_display_name].append(variant_obj["_id"])
# If for a case there is at least one Sanger validation to evaluate add the object to the unevaluated objects list
if len(unevaluated_by_case[case_display_name]) > 0:
unevaluated.append(unevaluated_by_case)
return unevaluated
def gene_variants(store,
pymongo_cursor,
variant_count,
institute_id,
page=1,
per_page=50):
"""Pre-process list of variants."""
skip_count = per_page * max(page - 1, 0)
more_variants = True if variant_count > (skip_count + per_page) else False
variant_res = pymongo_cursor.skip(skip_count).limit(per_page)
my_institutes = set(inst["_id"]
for inst in user_institutes(store, current_user))
variants = []
for variant_obj in variant_res:
# Populate variant case_display_name
variant_case_obj = store.case(case_id=variant_obj["case_id"])
if not variant_case_obj:
# A variant with missing case was encountered
continue
case_display_name = variant_case_obj.get("display_name")
variant_obj["case_display_name"] = case_display_name
# hide other institutes for now
other_institutes = set([variant_case_obj.get("owner")])
other_institutes.update(set(variant_case_obj.get("collaborators", [])))
if my_institutes.isdisjoint(other_institutes):
# If the user does not have access to the information we skip it
continue
genome_build = get_genome_build(variant_case_obj)
variant_genes = variant_obj.get("genes")
gene_object = update_HGNC_symbols(store, variant_genes, genome_build)
# Populate variant HGVS and predictions
variant_genes = variant_obj.get("genes")
hgvs_c = []
hgvs_p = []
if variant_genes is not None:
for gene_obj in variant_genes:
hgnc_id = gene_obj["hgnc_id"]
gene_symbol = gene(store, hgnc_id)["symbol"]
gene_symbols = [gene_symbol]
# gather HGVS info from gene transcripts
(hgvs_nucleotide, hgvs_protein) = get_hgvs(gene_obj)
hgvs_c.append(hgvs_nucleotide)
hgvs_p.append(hgvs_protein)
if len(gene_symbols) == 1:
variant_obj["hgvs"] = hgvs_str(gene_symbols, hgvs_p, hgvs_c)
# populate variant predictions for display
variant_obj.update(predictions(variant_genes))
variants.append(variant_obj)
return {"variants": variants, "more_variants": more_variants}
def panel(panel_id):
"""Display (and add pending updates to) a specific gene panel."""
panel_obj = store.gene_panel(panel_id) or store.panel(panel_id)
if not panel_obj:
flash("Panel with id {} not found.".format(panel_id), "warning")
return redirect(url_for("panels.panels"))
if request.method == "POST":
if request.form.get("update_description"):
panel_obj["description"] = request.form["panel_description"]
if controllers.panel_write_granted(panel_obj, current_user):
store.update_panel(panel_obj=panel_obj)
else:
flash(
"Permission denied: please ask a panel maintainer or admin for help.",
"danger",
)
return redirect(url_for("panels.panel", panel_id=panel_obj["_id"]))
raw_hgnc_id = request.form["hgnc_id"]
if "|" in raw_hgnc_id:
raw_hgnc_id = raw_hgnc_id.split(" | ", 1)[0]
hgnc_id = 0
try:
hgnc_id = int(raw_hgnc_id)
except ValueError:
flash("Provided HGNC is not valid : '{}'".format(raw_hgnc_id),
"danger")
return redirect(request.referrer)
action = request.form["action"]
gene_obj = store.hgnc_gene_caption(
hgnc_identifier=hgnc_id, build="37") or store.hgnc_gene_caption(
hgnc_identifier=hgnc_id, build="38")
if gene_obj is None:
flash("HGNC id not found: {}".format(hgnc_id), "warning")
return redirect(request.referrer)
if action == "add":
panel_gene = controllers.existing_gene(store, panel_obj, hgnc_id)
if panel_gene:
flash("gene already in panel: {}".format(panel_gene["symbol"]),
"warning")
else:
# ask user to fill-in more information about the gene
return redirect(
url_for(".gene_edit", panel_id=panel_id, hgnc_id=hgnc_id))
elif action == "delete":
LOG.debug("marking gene to be deleted: %s", hgnc_id)
panel_obj = store.add_pending(panel_obj, gene_obj, action="delete")
data = controllers.panel(store, panel_obj)
if request.args.get("case_id"):
data["case"] = store.case(request.args["case_id"])
if request.args.get("institute_id"):
data["institute"] = store.institute(request.args["institute_id"])
return data
def causatives(institute_obj, request):
"""Create content to be displayed on institute causatives page
Args:
institute_obj(dict) An institute object
request(flask.request) request sent by user's browser
Returns:
data(dict)
"""
# Retrieve variants grouped by case
query = request.args.get("query", "")
hgnc_id = None
if "|" in query:
# filter accepts an array of IDs. Provide an array with one ID element
try:
hgnc_id = [int(query.split(" | ", 1)[0])]
except ValueError:
flash("Provided gene info could not be parsed!", "warning")
variants = list(
store.check_causatives(institute_obj=institute_obj,
limit_genes=hgnc_id))
if variants:
variants = sorted(
variants,
key=lambda k: k.get("hgnc_symbols", [None])[0] or k.get("str_repid"
) or "",
)
all_variants = {}
all_cases = {}
for variant_obj in variants:
if variant_obj["category"] in ["snv", "cancer"]:
update_representative_gene(variant_obj, variant_obj.get(
"genes", [])) # required to display cDNA and protein change
if variant_obj["case_id"] not in all_cases:
case_obj = store.case(variant_obj["case_id"])
all_cases[variant_obj["case_id"]] = case_obj
else:
case_obj = all_cases[variant_obj["case_id"]]
if variant_obj["variant_id"] not in all_variants:
all_variants[variant_obj["variant_id"]] = []
all_variants[variant_obj["variant_id"]].append((case_obj, variant_obj))
data = dict(
institute=institute_obj,
variant_groups=all_variants,
acmg_map={
key: ACMG_COMPLETE_MAP[value]
for key, value in ACMG_MAP.items()
},
)
return data
def causatives(institute_id):
institute_obj = institute_and_case(store, institute_id)
variants = store.check_causatives(institute_obj=institute_obj)
all_variants = {}
all_cases = {}
for variant_obj in variants:
if variant_obj['case_id'] not in all_cases:
case_obj = store.case(variant_obj['case_id'])
all_cases[variant_obj['case_id']] = case_obj
else:
case_obj = all_cases[variant_obj['case_id']]
if variant_obj['variant_id'] not in all_variants:
all_variants[variant_obj['variant_id']] = []
all_variants[variant_obj['variant_id']].append((case_obj, variant_obj))
return dict(institute=institute_obj, variant_groups=all_variants)
def causatives(institute_id):
institute_obj = institute_and_case(store, institute_id)
variants = store.check_causatives(institute_obj=institute_obj)
all_variants = {}
all_cases = {}
for variant_obj in variants:
if variant_obj['case_id'] not in all_cases:
case_obj = store.case(variant_obj['case_id'])
all_cases[variant_obj['case_id']] = case_obj
else:
case_obj = all_cases[variant_obj['case_id']]
if variant_obj['variant_id'] not in all_variants:
all_variants[variant_obj['variant_id']] = []
all_variants[variant_obj['variant_id']].append((case_obj, variant_obj))
return dict(institute=institute_obj, variant_groups=all_variants)
def panel(panel_id):
"""Display (and add pending updates to) a specific gene panel."""
panel_obj = store.gene_panel(panel_id) or store.panel(panel_id)
if request.method == 'POST':
if request.form.get('update_description'):
panel_obj['description'] = request.form['panel_description']
store.update_panel(panel_obj=panel_obj)
return redirect( url_for('panels.panel', panel_id=panel_obj['_id']) )
raw_hgnc_id = request.form['hgnc_id']
if '|' in raw_hgnc_id:
raw_hgnc_id = raw_hgnc_id.split(' | ', 1)[0]
hgnc_id = 0
try:
hgnc_id = int(raw_hgnc_id)
except:
flash("Provided HGNC is not valid : '{}'". format(raw_hgnc_id), 'danger')
return redirect(request.referrer)
action = request.form['action']
gene_obj = store.hgnc_gene(hgnc_id)
if gene_obj is None:
flash("HGNC id not found: {}".format(hgnc_id), 'warning')
return redirect(request.referrer)
if action == 'add':
panel_gene = controllers.existing_gene(store, panel_obj, hgnc_id)
if panel_gene:
flash("gene already in panel: {}".format(panel_gene['symbol']),
'warning')
else:
# ask user to fill-in more information about the gene
return redirect(url_for('.gene_edit', panel_id=panel_id,
hgnc_id=hgnc_id))
elif action == 'delete':
log.debug("marking gene to be deleted: %s", hgnc_id)
panel_obj = store.add_pending(panel_obj, gene_obj, action='delete')
data = controllers.panel(store, panel_obj)
if request.args.get('case_id'):
data['case'] = store.case(request.args['case_id'])
if request.args.get('institute_id'):
data['institute'] = store.institute(request.args['institute_id'])
return data
def individual(case_id, ind, key, value):
"""Update information on individual level in Scout"""
case_obj = store.case(case_id)
if not case_obj:
click.echo(f"Could not find case {case_id}")
return
individuals = {
ind_info["display_name"]: ind_info
for ind_info in case_obj["individuals"]
}
# If ind name is empty, print available individual names for this case to help the user to build the command
if ind is None:
click.echo(
f"Please specify individual name with '-n' option. Available individuals for this case:{list(individuals.keys())}"
)
return
if ind not in individuals:
click.echo(
f"Could not find individual '{ind}' in case individuals. Available individuals for this case: {list(individuals.keys())}"
)
return
# If key is null or non-valid, print a list of all the keys that can be updated using this function
if key is None or not key in UPDATE_KEYS:
click.echo(
f"Please specify a valid key to update. Valid keys:{ UPDATE_KEYS }"
)
return
if value is None:
click.echo(f"Please specify a file path for key {key}")
return
file_path = Path(value)
# If file is not found on the server, ask if user wants to update the key anyway
if file_path.exists() is False:
click.confirm(
"The provided path was not found on the server, update key anyway?",
abort=True,
)
# perform the update
for ind_obj in case_obj["individuals"]:
if ind_obj["display_name"] == ind:
ind_obj[key] = value
store.update_case(case_obj)
def gene_variants(store, pymongo_cursor, variant_count, page=1, per_page=50):
"""Pre-process list of variants."""
skip_count = per_page * max(page - 1, 0)
more_variants = True if variant_count > (skip_count + per_page) else False
variant_res = pymongo_cursor.skip(skip_count).limit(per_page)
variants = []
for variant_obj in variant_res:
# Populate variant case_display_name
variant_case_obj = store.case(case_id=variant_obj["case_id"])
case_display_name = variant_case_obj.get("display_name")
variant_obj["case_display_name"] = case_display_name
genome_build = get_genome_build(variant_case_obj)
variant_genes = variant_obj.get("genes")
update_HGNC_symbols(store, variant_genes, genome_build)
# Populate variant HGVS and predictions
variant_genes = variant_obj.get("genes")
hgvs_c = []
hgvs_p = []
if variant_genes is not None:
for gene_obj in variant_genes:
hgnc_id = gene_obj["hgnc_id"]
gene_caption = store.hgnc_gene_caption(hgnc_id)
gene_symbols = [gene_caption["hgnc_symbol"]]
# gather HGVS info from gene transcripts
(hgvs_nucleotide, hgvs_protein) = get_hgvs(gene_obj)
hgvs_c.append(hgvs_nucleotide)
hgvs_p.append(hgvs_protein)
if len(gene_symbols) == 1:
variant_obj["hgvs"] = hgvs_str(gene_symbols, hgvs_p, hgvs_c)
# populate variant predictions for display
variant_obj.update(predictions(variant_genes))
variants.append(variant_obj)
return {"variants": variants, "more_variants": more_variants}
def panel(panel_id):
"""Display (and add pending updates to) a specific gene panel."""
panel_obj = store.gene_panel(panel_id) or store.panel(panel_id)
if request.method == 'POST':
raw_hgnc_id = request.form['hgnc_id']
if '|' in raw_hgnc_id:
raw_hgnc_id = raw_hgnc_id.split(' | ', 1)[0]
hgnc_id = 0
try:
hgnc_id = int(raw_hgnc_id)
except:
flash("Provided HGNC is not valid : '{}'". format(raw_hgnc_id), 'danger')
return redirect(request.referrer)
action = request.form['action']
gene_obj = store.hgnc_gene(hgnc_id)
if gene_obj is None:
flash("HGNC id not found: {}".format(hgnc_id), 'warning')
return redirect(request.referrer)
if action == 'add':
panel_gene = controllers.existing_gene(store, panel_obj, hgnc_id)
if panel_gene:
flash("gene already in panel: {}".format(panel_gene['symbol']),
'warning')
else:
# ask user to fill-in more information about the gene
return redirect(url_for('.gene_edit', panel_id=panel_id,
hgnc_id=hgnc_id))
elif action == 'delete':
log.debug("marking gene to be deleted: %s", hgnc_id)
panel_obj = store.add_pending(panel_obj, gene_obj, action='delete')
data = controllers.panel(store, panel_obj)
if request.args.get('case_id'):
data['case'] = store.case(request.args['case_id'])
if request.args.get('institute_id'):
data['institute'] = store.institute(request.args['institute_id'])
return data
def causatives(institute_id):
institute_obj = institute_and_case(store, institute_id)
query = request.args.get("query", "")
hgnc_id = None
if "|" in query:
# filter accepts an array of IDs. Provide an array with one ID element
try:
hgnc_id = [int(query.split(" | ", 1)[0])]
except ValueError:
flash("Provided gene info could not be parsed!", "warning")
variants = store.check_causatives(institute_obj=institute_obj,
limit_genes=hgnc_id)
if variants:
variants.sort("hgnc_symbols", pymongo.ASCENDING)
all_variants = {}
all_cases = {}
for variant_obj in variants:
if variant_obj["case_id"] not in all_cases:
case_obj = store.case(variant_obj["case_id"])
all_cases[variant_obj["case_id"]] = case_obj
else:
case_obj = all_cases[variant_obj["case_id"]]
if variant_obj["variant_id"] not in all_variants:
all_variants[variant_obj["variant_id"]] = []
all_variants[variant_obj["variant_id"]].append((case_obj, variant_obj))
acmg_map = {
key: ACMG_COMPLETE_MAP[value]
for key, value in ACMG_MAP.items()
}
return dict(institute=institute_obj,
variant_groups=all_variants,
acmg_map=acmg_map)
