def add_request_comments(request_id, params):
"""
Adds Comment for particular request
"""
request_primary_id = None
try:
request_object = get_request_object(request_id)
if request_object:
request_primary_id = request_object.id
if request_primary_id:
request_comment = RequestComment(params['comment'],
request_primary_id,
params['username'],
params['username'])
db_util.db_add_query(request_comment)
db_util.db_commit()
logger.info(
"Comment record for request id [{}] added successfully.".
format(request_id))
return "Successfully added comment for request {}".format(
request_id)
else:
raise Exception(
"Failed to add comment for request {}".format(request_id))
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
raise Exception(
'Failed to add Comments for Request as error in query: ', e)
def add_tx_method(params):
"""
Adds tx_method record or returns tx_method record if already exists
"""
method_name = params['tx_method']
try:
tx_method = TxMethod.query.filter_by(method_name=method_name) \
.one_or_none()
if tx_method:
logger.info(
"TxMethod with method name [{}] already exists.".format(
method_name))
return tx_method
tx_method = TxMethod(method_name)
db_util.db_add_query(tx_method)
db_util.db_commit()
logger.info(
"Transformation method record for method {} added successfully.".
format(method_name))
tx_method = TxMethod.query.filter_by(method_name=method_name) \
.one_or_none()
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
raise Exception('Failed to fetch Transformation method id for method '
'[{}] with error {} '.format(method_name, e))
return tx_method
def add_record(observed_map):
try:
db_util.db_add_query(observed_map)
db_util.db_commit()
logger.info("Observed Map added successfully.")
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
raise Exception('Failed to add Observed Map with error: ', e)
return observed_map
def add_endo_junction_set(endo_set_name):
# Add Endogenous Set record if not present
endo_set = EndogenousJunctionSet.query \
.filter_by(name=endo_set_name) \
.one_or_none
if not endo_set:
crop_id = None
endo_set = EndogenousJunctionSet(crop_id, endo_set_name)
db_util.db_add_query(endo_set)
db_util.db_commit()
return endo_set
def add_analysis(params):
"""
Adds ANALYSIS record
"""
try:
analysis = create_analysis(params)
db_util.db_add_query(analysis)
db_util.db_commit()
logger.info("Analysis record added successfully.")
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
raise Exception('Failed to add Analysis with error: ', e)
return analysis
def add_map(params):
"""
Adds Map
"""
version = 0
construct_id = params.get('construct_id', None)
if construct_id:
logger.info('Adding Map for construct_id [{}]'.format(construct_id))
map = get_map_by_construct_id(construct_id)
if map:
logger.info('Map {} already exists'.format(map.construct_id))
return map
else:
construct_id_no_ver = '.'.join(
[params['map_id'], params['sample_id'], '']).lower()
obs_map_ver = ObservedMap.query \
.with_entities(ObservedMap.version) \
.outerjoin(Map) \
.outerjoin(MapAnalysis) \
.filter(MapAnalysis.analysis_id == params['analysis_id']) \
.filter(Map.construct_id.ilike(construct_id_no_ver + '%')) \
.order_by(ObservedMap.version.desc()) \
.limit(1) \
.one_or_none()
if obs_map_ver:
version = int(obs_map_ver[0]) + 1
else:
version = 1
construct_id = construct_id_no_ver + str(version)
try:
map = Map(construct_id.upper())
db_util.db_add_query(map)
db_util.db_commit()
if version > 0:
map.obs_map_version = version
logger.info("Successfully added Map {}".format(construct_id))
except Exception as e:
logger.error('Failed to add Map with error: {}'.format(str(e)))
raise Exception('Failed to add Map with error: ', e)
return map
def batch_insert_integrities(integrities_dict_list):
"""
Adds variation
"""
try:
for variation in integrities_dict_list:
if variation:
position = variation.get('position', None)
type = variation.get('type', None)
gt = variation.get('gt', None)
ref_base = variation.get('ref_base', None)
total_read_depth = variation.get('total_read_depth', None)
sample_base = variation.get('sample_base', None)
read_depth = variation.get('read_depth', None)
purity = variation.get('purity', None)
feature_type = variation.get('feature_type', None)
annotation = variation.get('annotation', None)
effects = variation.get('effects', None)
translation = variation.get('translation', None)
organism = variation.get('organism', None)
tier_label = variation.get('tier_label', None)
coverage = variation.get('coverage', None)
tier = variation.get('tier', None)
is_tier_label_updated = variation.get('is_tier_label_updated',
False)
map_analysis_id = variation.get('map_analysis_id', None)
if not check_duplicate_variation(
position, type, gt, ref_base, total_read_depth,
sample_base, read_depth, purity, feature_type,
annotation, effects, translation, organism, tier_label,
map_analysis_id):
variation = Variation(position, type, ref_base,
sample_base, translation, coverage,
purity, tier, read_depth, annotation,
tier_label, is_tier_label_updated,
gt, total_read_depth, feature_type,
effects, organism, map_analysis_id)
db_util.db_add_query(variation)
db_util.db_commit()
logger.info("Variation record added successfully.")
except Exception as e:
logger.error(
'Failed to batch insert Variation records with error: {}'.format(
str(e)))
raise Exception('Error occurred: {}'.format(e))
def add_analysis_tools(analysis_tools):
"""
Adds Analysis Tools record
"""
analysis_tool_list = []
for name in analysis_tools:
analysis_tool = AnalysisTools.query.filter(
AnalysisTools.name == name).one_or_none()
if not analysis_tool:
analysis_tool = AnalysisTools(name)
db_util.db_add_query(analysis_tool)
db_util.db_commit()
# Get all the five tools records
all_tool_records = AnalysisTools.query.all()
for tool_obj in all_tool_records:
analysis_tool_list.append(tool_obj)
return analysis_tool_list
def add_analysis_comments(analysis_id, params):
"""
Adds Comment for particular analysis
"""
try:
analysis_comment = AnalysisComment(params['comment'], analysis_id,
params['username'],
params['username'])
db_util.db_add_query(analysis_comment)
db_util.db_commit()
logger.info("Comment record for analysis id [{}] added "
"successfully.".format(analysis_id))
return "Successfully added comment for analysis {}".format(analysis_id)
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
raise Exception('Failed to add Comments for Analysis as error in '
'query: ', e)
def add_map_analysis(analysis_id, map_id, read_count):
"""
Adds Map record
"""
logger.info('Adding MapAnalysis for map_id [{}] and analysis_id [{}]')
map_analysis = get_map_analysis(map_id, analysis_id)
if map_analysis:
logger.info('MapAnalysis already exists')
return map_analysis
try:
map_analysis = MapAnalysis(read_count, analysis_id, map_id)
db_util.db_add_query(map_analysis)
db_util.db_commit()
logger.info("Successfully added MapAnalysis.".format(
analysis_id, map_id))
except Exception as e:
logger.error('Failed to add MapAnalysis with error: {}'.format(str(e)))
raise Exception('Failed to add MapAnalysis with error: ', e)
return map_analysis
def add_observed_map_comments(observed_map_id, params):
"""
Adds Comment for particular ObservedMap
"""
try:
observed_map_comment = ObservedMapComment(params['comment'],
observed_map_id,
params['username'],
params['username'])
db_util.db_add_query(observed_map_comment)
db_util.db.session.commit()
observed_map_comment = observed_map_comment.as_dict()
db_util.db.session.close()
except Exception as e:
logger.error('Failed to add ObservedMap comments with error: {}'
.format(str(e)))
raise Exception('Failed to add Comments for ObservedMap as error in '
'query: ', e)
logger.info("Comment record for ObservedMap id [{}] added successfully."
.format(observed_map_id))
return observed_map_comment
def add_request(params):
"""
Adds request record or raise exception if already exists
"""
request = None
try:
request_id = params['request_id'].rstrip('/')
request = Request.query.filter_by(request_id=request_id).one_or_none()
if request:
logger.info("Request with request id [{}] already exists." \
.format(params['request_id']))
return request
sample_prep_methods = params.get('sample_prep_methods', None)
sbs_internalpipeline_version = params.get(
'sbs_internalpipeline_version', None)
request_name = params.get('request_name', None)
released_on = params.get('released_on', None)
sbs_status = params.get('sbs_status', None)
researcher = params.get('researcher', None)
tx_method_id = params.get('tx_method_id', None)
organism_id = params.get('organism_id', None)
request = Request(request_id, sample_prep_methods,
sbs_internalpipeline_version, request_name,
released_on, sbs_status, tx_method_id, researcher,
organism_id)
db_util.db_add_query(request)
db_util.db_commit()
logger.info(
"Request record for request id [{}] added successfully.".format(
params['request_id']))
request = Request.query.filter_by(request_id=request_id).one_or_none()
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
raise Exception('Failed to add Request with error: ', e)
return request
def add_crop(params):
"""
Adds crop record or returns crop record if already exists
"""
organism = params['organism']
try:
crop = Crop.query.filter_by(organism=organism).one_or_none()
if crop:
logger.info("Crop with organism [{}] already exists." \
.format(organism))
return crop
crop = Crop(organism)
db_util.db_add_query(crop)
db_util.db_commit()
logger.info("Crop record for organism [{}] added successfully."
.format(organism))
crop = Crop.query.filter_by(organism=organism).one_or_none()
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
raise Exception('Failed to add Crop with error: ', e)
return crop
def save_map_analysis_junctions(map_analysis_id, junction_id, masked):
try:
map_analysis_junction = MapAnalysisJunctions.query \
.with_entities(MapAnalysisJunctions) \
.filter(MapAnalysisJunctions.map_analysis_id == map_analysis_id) \
.filter(MapAnalysisJunctions.junction_id == junction_id) \
.one_or_none()
if not map_analysis_junction:
map_analysis_junction = MapAnalysisJunctions(map_analysis_id,
junction_id, masked,
None,
None)
else:
map_analysis_junction.masked = masked
db_util.db_add_query(map_analysis_junction)
db_util.db_commit()
logger.info("Record for map_analysis_junction id [{}] added "
"successfully.".format(junction_id))
except Exception as e:
logger.error(
'An error occurred while saving map analysis junctions : {}'
.format(str(e)))
raise Exception('Failed to save map analysis junction : ', e)
def insert_junctions(junctions_dict_list):
"""
Adds JUNCTION records
"""
try:
for junction in junctions_dict_list:
if junction:
if 'map_analysis_id' not in junction or not junction[
'map_analysis_id']:
logger.error('map_analysis_id is required')
raise Exception('map_analysis_id is required in junction')
map_analysis_id = junction['map_analysis_id']
masked = junction['masked']
masked = set_boolean_junction_values(masked)
endogenous = junction['endogenous']
endogenous = set_boolean_junction_values(endogenous)
junction['endogenous'] = endogenous
junction, is_duplicate = get_duplicate_junctions(junction)
if is_duplicate:
try:
junction_id = junction.id
save_map_analysis_junctions(map_analysis_id,
junction_id, masked)
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
raise Exception(
'Failed to insert map_analysis_junction records with error: {}'.format(
e))
elif not is_duplicate:
try:
end = junction.get('end', None)
position = junction.get('position', None)
proximal_mapping = junction.get('proximal_mapping',
None)
if proximal_mapping == "NA" or not proximal_mapping:
proximal_percent_identity = None
else:
proximal_percent_identity = proximal_mapping \
.split(",")[-1]
proximal_sequence = junction.get('proximal_sequence',
None)
junction_sequence = junction.get('junction_sequence',
None)
proximal_sequence_length = junction.get(
'proximal_sequence_length', None)
distal_sequence = junction.get('distal_sequence', None)
distal_mapping = junction.get('distal_mapping', None)
if distal_mapping == "NA" or not distal_mapping:
distal_percent_identity = None
else:
distal_percent_identity = distal_mapping \
.split(",")[-1]
distal_sequence_length = junction.get(
'distal_sequence_length', None)
element = junction.get('element', None)
unique_reads = junction.get('unique_reads', None)
supporting_reads = junction.get('supporting_reads',
None)
endogenous = junction.get('endogenous', endogenous)
source = junction.get('source', None)
duplicates = junction.get('duplicates', None)
junction_record = Junction(end, position,
proximal_mapping,
proximal_percent_identity,
proximal_sequence,
junction_sequence,
proximal_sequence_length,
distal_sequence,
distal_mapping,
distal_percent_identity,
distal_sequence_length,
element, unique_reads,
supporting_reads,
endogenous, source,
duplicates)
db_util.db_add_query(junction_record)
db_util.db_commit()
logger.info(
"Junction record for added successfully {}".format(
junction_record))
junction_id = junction_record.id
save_map_analysis_junctions(map_analysis_id,
junction_id, masked)
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
raise Exception(
'Failed to insert map_analysis_junction records with error: {}'.format(
e))
else:
logger.info("something went wrong")
logger.info("Junction record added successfully.")
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
raise Exception(
'Failed to batch insert Junction records with error: {}'.format(e))
return SUCCESS
def add_sample(params):
"""
Adds sample record or raise exception if already exists
"""
try:
request_id = params['request_id']
request = Request.query.filter_by(id=request_id).one_or_none()
if not request:
logger.error("Request with id [{}] does not exist."
.format(params['request_id']))
sample_id = params['sample_id']
sample = Sample.query.filter_by(sample_id=sample_id).one_or_none()
if sample:
logger.info("Sample with sample_id [{}] already exists."
.format(params['sample_id']))
return sample
primary_map = params.get('primary_map', None)
ev_man_event = params.get('ev_man_event', None)
other_maps = params.get('other_maps', None)
construct_name = params.get('construct_name', None)
event_id = params.get('event_id', None)
geno_type = params.get('geno_type', None)
organism = params.get('organism', None)
sample_name = params.get('sample_name', None)
develop_stage = params.get('develop_stage', None)
growth_location = params.get('growth_location', None)
treated = params.get('treated', False)
eu_id = params.get('eu_id', None)
curr_alpha_analysis = params.get('curr_alpha_analysis', None)
if curr_alpha_analysis:
update_analysis_type(curr_alpha_analysis)
sample = Sample(sample_id,
primary_map,
ev_man_event,
other_maps,
request_id,
construct_name,
event_id,
geno_type,
organism,
sample_name,
develop_stage,
growth_location,
treated,
eu_id,
curr_alpha_analysis)
db_util.db_add_query(sample)
db_util.db_commit()
logger.info("Sample record for request id [{}] added successfully."
.format(params['request_id']))
sample = Sample.query.filter_by(sample_id=sample_id).one_or_none()
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
raise Exception('Failed to add Sample with error: ', e)
return sample
def add_tool_record(analysis_tool_details):
db_util.db_add_query(analysis_tool_details)
db_util.db_commit()
return analysis_tool_details