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udpate annotation service & bugfixes
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@MarvinDo
MarvinDo committed Feb 16, 2024
1 parent 6fa8b25 commit 27f05ea
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Showing 10 changed files with 209 additions and 126 deletions.
53 changes: 31 additions & 22 deletions src/annotation_service/annotation_jobs/automatic_classification_job.py
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Original file line number Diff line number Diff line change
Expand Up @@ -262,37 +262,46 @@ def get_autoclass_json(self, variant_id, conn: Connection) -> str:

# mRNA analyses: currently missing
"""
"mRNA_analysis" :
"mRNA_analysis" : [
{"performed": true,
"pathogenic": true,
"benign": true},
"minigene": true,
"patient_rna": false,
"allelic" : "Construct",
"quantification": null}
],
"""
assays_dict = variant.order_assays_by_type()
splicing_assays = assays_dict.get("splicing")
splicing_assay_performed = False
pathogenic_splicing_assay = False
benign_splicing_assay = False
if splicing_assays is not None and len(splicing_assays) > 0:
splicing_assay_performed = True
for splicing_assay in splicing_assays:
if splicing_assay.metadata.get("functional_category", "") == "pathogenic":
pathogenic_splicing_assay = True
if splicing_assay.metadata.get("functional_category", "") == "benign":
benign_splicing_assay = True
result["mRNA_analysis"] = {"performed": splicing_assay_performed,
"pathogenic": pathogenic_splicing_assay,
"benign": benign_splicing_assay}



# functional data: currently missing
"""
"functional_data":
"functional_data": [
{"performed": true,
"pathogenic": true,
"pathogenic": false,
"benign": true},
{"performed": true,
"pathogenic": false,
"benign": true}
]
"""
result["functional_data"] = {"performed": False,
"pathogenic": False,
"benign": False}
functional_assays = assays_dict.get("functional")

all_functional_assays = []
if functional_assays is not None and len(functional_assays) > 0:
for assay in functional_assays:
is_performed = True
is_pathogenic = False
is_benign = False
if assay.metadata.get("functional_category", "") == "pathogenic":
is_pathogenic = True
if assay.metadata.get("functional_category", "") == "benign":
is_benign = True
all_functional_assays.append({"performed": is_performed,
"pathogenic": is_pathogenic,
"benign": is_benign})
result["functional_data"] = all_functional_assays


# heredicare computed scores: currently missing
"""
Expand Down
11 changes: 10 additions & 1 deletion src/annotation_service/annotation_jobs/heredicare_job.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,8 +79,17 @@ def save_to_db(self, info, variant_id, conn):
err_msg += "The date could not be saved in the database. Format should be dd.mm.yyyy, but was: " + str(classification_date)
status_code = 1

heredicare_annotation_id = None
if status_code == 0:
conn.insert_heredicare_annotation(variant_id, vid, n_fam, n_pat, consensus_class, classification_date, comment, lr_cooc, lr_coseg, lr_family)
heredicare_annotation_id = conn.insert_heredicare_annotation(variant_id, vid, n_fam, n_pat, consensus_class, classification_date, comment, lr_cooc, lr_coseg, lr_family)

for key in heredicare_variant:
if key.startswith("PATH_Z") and heredicare_variant[key] is not None:
zid = int(key[6:])
print(zid)
classification = heredicare_variant[key] if heredicare_variant[key] != "-1" else None
conn.insert_heredicare_center_classification(heredicare_annotation_id, zid, classification, comment = None) # TODO! COMMENT!


return status_code, err_msg

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60 changes: 33 additions & 27 deletions src/common/db_IO.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1376,9 +1376,9 @@ def invalidate_previous_consensus_classifications(self, variant_id):
self.cursor.execute(command, (variant_id,))
self.conn.commit()

def insert_heredicare_center_classification(self, variant_id, classification, center_name, comment, date):
command = "INSERT INTO heredicare_center_classification (variant_id, classification, center_name, comment, date) VALUES (%s, %s, %s, %s, %s)"
self.cursor.execute(command, (variant_id, classification, center_name, comment, date))
def insert_heredicare_center_classification(self, heredicare_annotation_id, zid, classification, comment):
command = "INSERT INTO heredicare_center_classification (variant_heredicare_annotation_id, heredicare_ZID, classification, comment) VALUES (%s, %s, %s, %s)"
self.cursor.execute(command, (heredicare_annotation_id, zid, classification, comment))
self.conn.commit()

def check_heredicare_center_classification(self, variant_id, classification, center_name, comment, date): # this returns true if this classification is already in there and fals if it is not
Expand Down Expand Up @@ -1618,6 +1618,7 @@ def insert_user_classification(self, variant_id, classification, user_id, commen

def update_user_classification(self, user_classification_id, classification, comment, date, scheme_class):
command = "UPDATE user_classification SET classification = %s, comment = %s, date = %s, scheme_class = %s WHERE id = %s"
print(command % (str(classification), comment, date, str(scheme_class), user_classification_id))
self.cursor.execute(command, (str(classification), comment, date, str(scheme_class), user_classification_id))
self.conn.commit()

Expand Down Expand Up @@ -1885,9 +1886,9 @@ def get_import_request(self, import_queue_id = '', date = ''):
return None
"""

def get_heredicare_center_classifications(self, variant_id):
command = 'SELECT * FROM heredicare_center_classification WHERE variant_id = %s'
self.cursor.execute(command, (variant_id, ))
def get_heredicare_center_classifications(self, heredicare_annotation_id):
command = 'SELECT id, heredicare_ZID, (SELECT name FROM heredicare_ZID WHERE heredicare_ZID.ZID = heredicare_center_classification.heredicare_ZID) as center_name, classification, comment FROM heredicare_center_classification WHERE variant_heredicare_annotation_id = %s'
self.cursor.execute(command, (heredicare_annotation_id, ))
result = self.cursor.fetchall()
if len(result) == 0:
return None
Expand Down Expand Up @@ -2382,21 +2383,8 @@ def get_variant(self, variant_id,
automatic_classification = models.AutomaticClassification(id = automatic_classification_id, scheme_id = scheme_id, scheme_display_title = scheme_display_title, classification_splicing = classification_splicing, classification_protein = classification_protein, date = date, criteria = all_criteria)


heredicare_classifications = None
all_heredicare_annotations = None
if include_heredicare_classifications:
heredicare_classifications_raw = self.get_heredicare_center_classifications(variant_id)
if heredicare_classifications_raw is not None:
heredicare_classifications = []
for cl_raw in heredicare_classifications_raw:
id = int(cl_raw[0])
selected_class = cl_raw[1]
comment = cl_raw[4]
center = cl_raw[3]
date = cl_raw[5].strftime('%Y-%m-%d')
new_heredicare_classification = models.HeredicareClassification(id = id, selected_class = selected_class, comment = comment, center = center, classification_date = date, vid="")
heredicare_classifications.append(new_heredicare_classification)


heredicare_annotations_raw = self.get_heredicare_annotations(variant_id)
all_heredicare_annotations = []
Expand All @@ -2407,14 +2395,31 @@ def get_variant(self, variant_id,
n_fam = annot[2]
n_pat = annot[3]
consensus_class = annot[4]
comment = annot[5]
consensus_comment = annot[5]
classification_date = annot[6]
lr_cooc = annot[7]
lr_coseg = annot[8]
lr_family = annot[9]

classification = models.HeredicareClassification(id = heredicare_annotation_id, selected_class = consensus_class, comment = comment, classification_date = classification_date, center = "VUSTF", vid = vid)
new_heredicare_annotation = models.HeredicareAnnotation(id = heredicare_annotation_id, vid = vid, n_fam = n_fam, n_pat = n_pat, vustf_classification = classification, lr_cooc = lr_cooc, lr_coseg = lr_coseg, lr_family = lr_family)
consensus_classification = models.HeredicareConsensusClassification(id = heredicare_annotation_id, selected_class = consensus_class, comment = consensus_comment, classification_date = classification_date)


heredicare_classifications_raw = self.get_heredicare_center_classifications(heredicare_annotation_id)
heredicare_center_classifications = None
if heredicare_classifications_raw is not None:
heredicare_center_classifications = []
for cl_raw in heredicare_classifications_raw:
#id, heredicare_ZID, center_name, classification, comment
id = int(cl_raw[0])
zid = cl_raw[1]
center_name = cl_raw[2]
selected_class = cl_raw[3]
comment = cl_raw[4]
#date = cl_raw[5].strftime('%Y-%m-%d')
new_heredicare_classification = models.HeredicareCenterClassification(id = id, selected_class = selected_class, comment = comment, center_name = center_name, zid = zid)
heredicare_center_classifications.append(new_heredicare_classification)


new_heredicare_annotation = models.HeredicareAnnotation(id = heredicare_annotation_id, vid = vid, n_fam = n_fam, n_pat = n_pat, consensus_classification = consensus_classification, lr_cooc = lr_cooc, lr_coseg = lr_coseg, lr_family = lr_family, center_classifications = heredicare_center_classifications)
all_heredicare_annotations.append(new_heredicare_annotation)

# add clinvar annotation
Expand Down Expand Up @@ -2527,7 +2532,6 @@ def get_variant(self, variant_id,
annotations = annotations,
consensus_classifications = consensus_classifications,
user_classifications = user_classifications,
heredicare_classifications = heredicare_classifications,
automatic_classification = automatic_classification,
heredicare_annotations = all_heredicare_annotations,
cancerhotspots_annotations = cancerhotspots_annotations,
Expand Down Expand Up @@ -2557,7 +2561,6 @@ def get_variant(self, variant_id,
annotations = annotations,
consensus_classifications = consensus_classifications,
user_classifications = user_classifications,
heredicare_classifications = heredicare_classifications,
automatic_classification = automatic_classification,
heredicare_annotations = all_heredicare_annotations,
cancerhotspots_annotations = cancerhotspots_annotations,
Expand Down Expand Up @@ -2838,9 +2841,11 @@ def get_selected_literature(self, is_user, classification_id):
def insert_update_heredivar_clinvar_submission(self, variant_id, submission_id, accession_id, status, message, last_updated, previous_clinvar_accession):
if previous_clinvar_accession is None:
command = "INSERT INTO heredivar_clinvar_submissions (variant_id, submission_id, accession_id, status, message, last_updated) VALUES (%s, %s, %s, %s, %s, %s) ON DUPLICATE KEY UPDATE submission_id=VALUES(submission_id), accession_id=VALUES(accession_id), status=VALUES(status),message=VALUES(message), last_updated=VALUES(last_updated)"
actual_information = (variant_id, submission_id, accession_id, status, message, last_updated)
else: # do not reset the accession id - this one is stable once it was created by clinvar
command = "INSERT INTO heredivar_clinvar_submissions (variant_id, submission_id, status, message, last_updated) VALUES (%s, %s, %s, %s, %s, %s) ON DUPLICATE KEY UPDATE submission_id=VALUES(submission_id), status=VALUES(status),message=VALUES(message), last_updated=VALUES(last_updated)"
self.cursor.execute(command, (variant_id, submission_id, accession_id, status, message, last_updated))
command = "INSERT INTO heredivar_clinvar_submissions (variant_id, submission_id, status, message, last_updated) VALUES (%s, %s, %s, %s, %s) ON DUPLICATE KEY UPDATE submission_id=VALUES(submission_id), status=VALUES(status),message=VALUES(message), last_updated=VALUES(last_updated)"
actual_information = (variant_id, submission_id, status, message, last_updated)
self.cursor.execute(command, actual_information)
self.conn.commit()

def get_heredivar_clinvar_submission(self, variant_id):
Expand Down Expand Up @@ -2981,6 +2986,7 @@ def insert_heredicare_annotation(self, variant_id, vid, n_fam, n_pat, consensus_
command = "INSERT INTO variant_heredicare_annotation (variant_id, vid, n_fam, n_pat, consensus_class, date, comment, lr_cooc, lr_coseg, lr_family) VALUES (%s, %s, %s, %s, %s, %s, %s, %s, %s, %s)"
self.cursor.execute(command, (variant_id, vid, n_fam, n_pat, consensus_class, classification_date, comment, lr_cooc, lr_coseg, lr_family))
self.conn.commit()
return self.get_last_insert_id()

def clear_heredicare_annotation(self, variant_id):
command = "DELETE FROM variant_heredicare_annotation WHERE variant_id = %s"
Expand Down
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