def insert_abstract(pmid, reference_id, record, source_id, journal_abbrev,
journal_title, issn_print, created_by):
text = record.get('AB', '')
if text == '':
return
locus_names_ids = DBSession.query(Locusdbentity.display_name,
Locusdbentity.sgdid).all()
html = link_gene_names(text, locus_names_ids)
x = Referencedocument(document_type='Abstract',
source_id=source_id,
reference_id=reference_id,
text=text,
html=html,
created_by=created_by)
DBSession.add(x)
entries = create_bibentry(pmid, record, journal_abbrev, journal_title,
issn_print)
y = Referencedocument(document_type='Medline',
source_id=source_id,
reference_id=reference_id,
text='\n'.join([
key + ' - ' + str(value)
for key, value in entries if value is not None
]),
html='\n'.join([
key + ' - ' + str(value)
for key, value in entries if value is not None
]),
created_by=created_by)
DBSession.add(y)
DBSession.flush()
DBSession.refresh(x)
def insert_abstract(pmid, reference_id, record, source_id, journal_abbrev,
journal_title, issn_print, created_by):
""" Add abstract to Referencedocument table
This method does not return anything, just does the necessary CRUD operations
Parameters
----------
pmid: int
reference_id: int
source_id: int
journal_abbrev: str
journal_title: str
issn_print: str
created_by: str
Return
------
empty
does not return anything
"""
text = record.get('AB', '')
if text == '':
return
locus_names_ids = DBSession.query(Locusdbentity.display_name,
Locusdbentity.sgdid).all()
html = link_gene_names(text, locus_names_ids)
x = Referencedocument(document_type='Abstract',
source_id=source_id,
reference_id=reference_id,
text=text,
html=html,
created_by=created_by)
DBSession.add(x)
entries = create_bibentry(pmid, record, journal_abbrev, journal_title,
issn_print)
y = Referencedocument(document_type='Medline',
source_id=source_id,
reference_id=reference_id,
text='\n'.join([
key + ' - ' + str(value)
for key, value in entries if value is not None
]),
html='\n'.join([
key + ' - ' + str(value)
for key, value in entries if value is not None
]),
created_by=created_by)
DBSession.add(y)
DBSession.flush()
DBSession.refresh(x)
def validate_file_content_and_process(file_content, nex_session, username):
''' Check file content, process and save to db
Parameters
----------
file_content: csv-reader object
csv-reader reads a tvs file and returns an object
nex_session: database_session object
username: str
authorized user to make CRUD operations
Returns
-------
dictionary
number of entries
number of updates
database entries(dictionary)
Note:
Accepted summary types: Phenotype, Regulation, Disease, Interaction
Sequence, Protein
Checks correct number of columns in the header and valid IDs
'''
header_literal = [
'# Feature',
'Summary Type (phenotype, regulation, disease, interaction, sequence, protein )',
'Summary', 'PMIDs'
]
accepted_summary_types = [
'Phenotype', 'Regulation', 'Disease', 'Interaction', 'Sequence',
'Protein'
]
file_gene_ids = []
file_pmids = []
copied = []
already_used_genes = []
clear_target_urls = []
# use regex to get keys from dictionary
key_feature = re.compile(r".*feature$", re.IGNORECASE)
key_summary_type = re.compile(r"^summary type.*", re.IGNORECASE)
# use regex to get keys from dictionary
key_feature = re.compile(r".*feature$", re.IGNORECASE)
key_summary_type = re.compile(r"^summary type.*", re.IGNORECASE)
try:
for item in file_content:
if (len(item) != len(header_literal)):
raise ValueError(
'Row or header has incorrect number of columns.')
#TODO: abstract the loop below in the next release
gene_id = ''
summary_type = ''
for k, v in item.items():
if key_feature.match(k):
gene_id = item.get(k)
if key_summary_type.match(k):
summary_type = item.get(k)
pmid_temp = item.get('PMIDs', None)
if pmid_temp:
pmids = str(pmid_temp).replace(' ', '').replace('0.0', '')
else:
pmids = ''
summary_text = item.get('Summary', '')
if gene_id:
file_gene_ids.append(gene_id.strip())
if summary_type:
gene_id_with_summary = gene_id + summary_type
if gene_id_with_summary in already_used_genes:
raise ValueError(
'The same gene summary cannot be updated twice in the same\
file: ' + str(gene_id))
already_used_genes.append(gene_id_with_summary)
if summary_type.lower() not in ''.join(
accepted_summary_types).lower():
raise ValueError(
'Unaccepted summary type. Must be one of ' +
', '.join(accepted_summary_types))
if len(pmids) > 0:
pmids = re.split('\||,', pmids)
for pmid in pmids:
file_pmids.append(str(pmid))
copied.append(item)
except IndexError:
raise ValueError(
'The file is not a valid TSV with the correct number of columns. Check the file and try again.'
)
nex_session.execute('SET LOCAL ROLE ' + username)
# check that gene names are valid
valid_genes = nex_session.query(Locusdbentity.format_name).filter(
Locusdbentity.format_name.in_(file_gene_ids)).all()
valid_genes = [str(d[0]) for d in valid_genes]
invalid_genes = [d for d in file_gene_ids if d not in valid_genes]
if len(invalid_genes):
raise ValueError('Invalid gene identifier: ' +
', '.join(invalid_genes))
# must be valid PMIDs in last column or nothing
matching_refs = nex_session.query(Referencedbentity).filter(
Referencedbentity.pmid.in_(file_pmids)).all()
temp_matching_refs = [str(d.pmid) for d in matching_refs]
invalid_refs = [d for d in file_pmids if d not in temp_matching_refs]
if len(invalid_refs):
# raise ValueError('Invalid PMID: ' + ', '.join(invalid_refs) + '. Must be a pipe-separated list of PMIDs from SGD.')
print(len(invalid_refs))
# update
receipt_entries = []
locus_names_ids = nex_session.query(Locusdbentity.display_name,
Locusdbentity.sgdid).all()
inserts = 0
updates = 0
for item in copied:
if item:
for k, v in item.items():
if key_feature.match(k):
file_id = item.get(k)
if key_summary_type.match(k):
file_summary_type = item.get(k)
#file_id = item.get('# Feature', '')
#file_summary_type = item.get(
# 'Summary Type (phenotype, regulation)', '')
file_summary_val = item.get('Summary', '')
file_summary_html = link_gene_names(file_summary_val,
locus_names_ids)
if file_id:
gene = nex_session.query(Locusdbentity).filter_by(
format_name=file_id).one_or_none()
if file_summary_type:
summaries = nex_session.query(
Locussummary.summary_type, Locussummary.summary_id,
Locussummary.html, Locussummary.date_created).filter_by(
locus_id=gene.dbentity_id,
summary_type=file_summary_type).all()
# update
summary = None
if len(summaries):
summary = summaries[0]
nex_session.query(Locussummary).filter_by(
summary_id=summary.summary_id).update({
'text':
file_summary_val,
'html':
file_summary_html
})
updates += 1
else:
mod_summary_type = file_summary_type.lower().capitalize()
new_summary = Locussummary(locus_id=gene.dbentity_id,
summary_type=mod_summary_type,
text=file_summary_val,
html=file_summary_html,
created_by=username,
source_id=SGD_SOURCE_ID)
nex_session.add(new_summary)
inserts += 1
summary = nex_session.query(
Locussummary.summary_type, Locussummary.summary_id,
Locussummary.html, Locussummary.date_created).filter_by(
locus_id=gene.dbentity_id,
summary_type=mod_summary_type).all()[0]
# add LocussummaryReference(s)
if item:
if item.get('PMIDs'):
pmids = item.get('PMIDs').replace(' ', '')
else:
pmids = ''
if len(pmids) > 0:
pmids = re.split('\||,', pmids)
for idx, pmid in enumerate(pmids):
matching_ref = [
x for x in matching_refs if x.pmid == int(pmid)
][0]
summary_id = summary.summary_id
reference_id = matching_ref.dbentity_id
order = _idx + 1
# look for matching LocussummaryReference
matching_locussummary_refs = nex_session.query(
LocussummaryReference).filter_by(
summary_id=summary_id,
reference_id=reference_id).all()
if len(matching_locussummary_refs):
nex_session.query(LocussummaryReference).filter_by(
summary_id=summary_id,
reference_id=reference_id).update(
{'reference_order': order})
else:
new_locussummaryref = LocussummaryReference(
summary_id=summary_id,
reference_id=reference_id,
reference_order=order,
source_id=SGD_SOURCE_ID,
created_by=username)
nex_session.add(new_locussummaryref)
# add receipt
summary_type_url_segment = file_summary_type.lower()
if summary_type_url_segment not in [
'phenotype', 'regulation', 'interaction', 'sequence',
'disease', 'protein'
]:
summary_type_url_segment = ''
preview_url = '/locus/' + gene.sgdid + '/' + summary_type_url_segment
clear_target_urls.append(preview_url)
if summary:
summary_obj = {
'display_name':
gene.format_name,
'obj_url':
preview_url,
'activity_category':
summary.summary_type,
'json':
json.dumps({
'summary_data': item,
'modified_date': str(datetime.now())
}),
'created_by':
username,
'dbentity_id':
gene.dbentity_id
}
message = 'added'
new_curate_activity = CuratorActivity(
display_name=summary_obj['display_name'],
obj_url=summary_obj['obj_url'],
activity_category=summary_obj['activity_category'],
dbentity_id=summary_obj['dbentity_id'],
message=message,
json=summary_obj['json'],
created_by=summary_obj['created_by'])
nex_session.add(new_curate_activity)
receipt_entries.append({
'category': 'locus',
'href': preview_url,
'name': gene.display_name,
'type': file_summary_type,
'value': file_summary_val
})
transaction.commit()
nex_session.close()
if len(clear_target_urls) > 0:
ban_from_cache(clear_target_urls)
return {'inserts': inserts, 'updates': updates, 'entries': receipt_entries}
def validate_file_content_and_process(file_content, nex_session, username):
header_literal = [
'# Feature', 'Summary Type (phenotype, regulation)', 'Summary', 'PMIDs'
]
accepted_summary_types = ['Phenotype', 'Regulation']
file_gene_ids = []
file_pmids = []
copied = []
already_used_genes = []
try:
for i, val in enumerate(file_content):
# match header
if i is 0:
is_header_match = header_literal == val
if not is_header_match:
raise ValueError(
'File header does not match expected format. Please make your file match the template file linked below.'
)
else:
gene_id = val[0]
file_gene_ids.append(gene_id.strip())
gene_id_with_summary = gene_id + val[1]
if gene_id_with_summary in already_used_genes:
raise ValueError(
'The same gene summary cannot be updated twice in the same file: '
+ str(gene_id))
already_used_genes.append(gene_id_with_summary)
# match summary types
if val[1] not in accepted_summary_types:
raise ValueError(
'Unaccepted summary type. Must be one of ' +
', '.join(accepted_summary_types))
# collect PMIDs
if len(val) == 4:
pmids = val[3].replace(' ', '')
if len(pmids):
pmids = re.split('\||,', pmids)
for d in pmids:
file_pmids.append(str(d))
# match length of each row
if (len(val) != len(header_literal)
and len(val) != len(header_literal) - 1):
raise ValueError('Row has incorrect number of columns.')
copied.append(val)
except IndexError:
raise ValueError(
'The file is not a valid TSV with the correct number of columns. Check the file and try again.'
)
nex_session.execute('SET LOCAL ROLE ' + username)
# check that gene names are valid
valid_genes = nex_session.query(Locusdbentity.format_name).filter(
Locusdbentity.format_name.in_(file_gene_ids)).all()
valid_genes = [str(d[0]) for d in valid_genes]
invalid_genes = [d for d in file_gene_ids if d not in valid_genes]
if len(invalid_genes):
raise ValueError('Invalid gene identifier: ' +
', '.join(invalid_genes))
# must be valid PMIDs in last column or nothing
matching_refs = nex_session.query(Referencedbentity).filter(
Referencedbentity.pmid.in_(file_pmids)).all()
temp_matching_refs = [str(d.pmid) for d in matching_refs]
invalid_refs = [d for d in file_pmids if d not in temp_matching_refs]
if len(invalid_refs):
raise ValueError('Invalid PMID: ' + ', '.join(invalid_refs) +
'. Must be a pipe-separated list of PMIDs from SGD.')
# update
receipt_entries = []
locus_names_ids = nex_session.query(Locusdbentity.display_name,
Locusdbentity.sgdid).all()
inserts = 0
updates = 0
for i, val in enumerate(copied):
if i != 0:
file_id = val[0]
file_summary_type = val[1]
file_summary_val = val[2]
file_summy_html = link_gene_names(file_summary_val,
locus_names_ids)
gene = nex_session.query(Locusdbentity).filter_by(
format_name=file_id).one_or_none()
summaries = nex_session.query(
Locussummary.summary_type, Locussummary.summary_id,
Locussummary.html, Locussummary.date_created).filter_by(
locus_id=gene.dbentity_id,
summary_type=file_summary_type).all()
# update
summary = None
if len(summaries):
summary = summaries[0]
nex_session.query(Locussummary).filter_by(
summary_id=summary.summary_id).update({
'text':
file_summary_val,
'html':
file_summy_html
})
updates += 1
else:
new_summary = Locussummary(locus_id=gene.dbentity_id,
summary_type=file_summary_type,
text=file_summary_val,
html=file_summy_html,
created_by=username,
source_id=SGD_SOURCE_ID)
nex_session.add(new_summary)
inserts += 1
summary = nex_session.query(
Locussummary.summary_type, Locussummary.summary_id,
Locussummary.html, Locussummary.date_created).filter_by(
locus_id=gene.dbentity_id,
summary_type=file_summary_type).all()[0]
# add LocussummaryReference(s)
if len(val) == 4:
pmids = val[3].replace(' ', '')
if len(pmids):
pmids = re.split('\||,', pmids)
for _i, p in enumerate(pmids):
matching_ref = [
x for x in matching_refs if x.pmid == int(p)
][0]
summary_id = summary.summary_id
reference_id = matching_ref.dbentity_id
order = _i + 1
# look for matching LocussummaryReference
matching_locussummary_refs = nex_session.query(
LocussummaryReference).filter_by(
summary_id=summary_id,
reference_id=reference_id).all()
if len(matching_locussummary_refs):
nex_session.query(LocussummaryReference).filter_by(
summary_id=summary_id,
reference_id=reference_id).update(
{'reference_order': order})
else:
new_locussummaryref = LocussummaryReference(
summary_id=summary_id,
reference_id=reference_id,
reference_order=order,
source_id=SGD_SOURCE_ID,
created_by=username)
nex_session.add(new_locussummaryref)
# add receipt
summary_type_url_segment = file_summary_type.lower()
if summary_type_url_segment not in ['phenotype', 'regulation']:
summary_type_url_segment = ''
preview_url = '/locus/' + gene.sgdid + '/' + summary_type_url_segment
receipt_entries.append({
'category': 'locus',
'href': preview_url,
'name': gene.display_name,
'type': file_summary_type,
'value': file_summary_val
})
transaction.commit()
nex_session.close()
return {'inserts': inserts, 'updates': updates, 'entries': receipt_entries}