def discard_ref(pmid):
try:
RefTemp.delete(pmid)
RefBad.insert(pmid, current_user.name.upper())
db.session.commit()
except:
db.session.rollback()
return "An error occurred when deleting the reference for pmid=" + pmid + " from the database."
return "Reference for pmid=" + pmid + " has been removed from the database!"
def reference():
try:
# app.stop()
# app.run()
refs = RefTemp.search()
except:
Database(DBUSER, DBPASS)
refs = RefTemp.search()
num_of_refs = len(refs.all())
return render_template('literature_review.html',
ref_list=refs,
ref_count=num_of_refs)
def insert_and_associate(self):
ref_no = Reference.insert(self.pmid, self.user)
RefTemp.delete(self.pmid)
lg_feat_hash = {}
message = ''
topic_added = {}
task_added = {}
if len(self.tasks) == 0:
return None
for task_entry in self.tasks:
task = task_entry[0]
genes = task_entry[1]
comment = task_entry[2]
if len(genes) > 0:
feat_no_list = []
topic = ''
if 'Add to' in task:
topic = 'Additional Literature'
elif 'Review' in task:
topic = task
else:
topic = 'Primary Literature'
if 'Review' in task or 'Add to' in task:
task = 'Gene Link'
message += "Curation_task = '" + task
message += "', literature_topic = '" + topic + "'"
message += ", gene = "
for name in genes:
feat_no = self.feature_no_for_name[name]
feat_no_list.append(feat_no)
## insert into ref_curation
if not task_added.has_key((feat_no, task)):
RefCuration.insert(ref_no, task, self.user, feat_no,
comment)
task_added[(feat_no, task)] = 1
message += name + '|'
if comment:
message += ", comment = '" + comment + "'"
message += "<br>"
## insert into lit_guide + litguide_feat
if topic_added.has_key(topic):
litguide_no = topic_added[topic]
else:
litguide_no = LitGuide.insert(ref_no, topic, self.user)
topic_added[topic] = litguide_no
for feat_no in feat_no_list:
key = (feat_no, litguide_no)
if lg_feat_hash.has_key(key):
continue
lg_feat_hash[key] = 1
LitGuideFeat.insert(feat_no, litguide_no)
else: ## no gene name provided
## if no gene name provided and "Add to database" was checked,
## no need to add any association
if 'Add' in task:
continue
## if it is a review, no need to add to ref_curation
if 'Review' in task:
## topic = task = 'Reviews'
LitGuide.insert(ref_no, task, self.user)
message += "Literature_topic = '" + task + "'<br>"
continue
if not task_added.has_key((0, task)):
RefCuration.insert(ref_no, task, self.user, None, comment)
task_added[(0, task)] = 1
message += "Curation_task = '" + task + "'"
## insert into lit_guide
if 'HTP' in task or 'Review' in task:
topic = ''
if 'HTP' in task:
topic = 'Omics'
else:
# 'Review' in task:
topic = task
if topic_added.has_key(topic):
if comment:
message += ", comment = '" + comment + "'"
message += "<br>"
continue
else:
lit_guide_no = LitGuide.insert(ref_no, topic,
self.user)
topic_added[topic] = lit_guide_no
message += ", literature_topic = '" + topic
if comment:
message += ", comment = '" + comment + "'"
message += "<br>"
db.session.commit()
return message
def insert_and_associate(self):
ref_no = Reference.insert(self.pmid, self.user)
RefTemp.delete(self.pmid)
lg_feat_hash = {}
message = ''
topic_added = {}
task_added = {}
if len(self.tasks) == 0:
return None
for task_entry in self.tasks:
task = task_entry[0]
genes = task_entry[1]
comment = task_entry[2]
if len(genes) > 0:
feat_no_list = []
topic = ''
if 'Add to' in task:
topic = 'Additional Literature'
elif 'Review' in task:
topic = task
else:
topic = 'Primary Literature'
if 'Review' in task or 'Add to' in task:
task = 'Gene Link'
message += "Curation_task = '" + task
message += "', literature_topic = '" + topic + "'"
message += ", gene = "
for name in genes:
feat_no = self.feature_no_for_name[name]
feat_no_list.append(feat_no)
## insert into ref_curation
if not task_added.has_key((feat_no, task)):
RefCuration.insert(ref_no, task, self.user, feat_no, comment)
task_added[(feat_no, task)] = 1
message += name + '|'
if comment:
message += ", comment = '" + comment + "'"
message += "<br>"
## insert into lit_guide + litguide_feat
if topic_added.has_key(topic):
litguide_no = topic_added[topic]
else:
litguide_no = LitGuide.insert(ref_no, topic, self.user)
topic_added[topic] = litguide_no
for feat_no in feat_no_list:
key = (feat_no, litguide_no)
if lg_feat_hash.has_key(key):
continue
lg_feat_hash[key] = 1
LitGuideFeat.insert(feat_no, litguide_no)
else: ## no gene name provided
## if no gene name provided and "Add to database" was checked,
## no need to add any association
if 'Add' in task:
continue
## if it is a review, no need to add to ref_curation
if 'Review' in task:
## topic = task = 'Reviews'
LitGuide.insert(ref_no, task, self.user)
message += "Literature_topic = '" + task + "'<br>"
continue
if not task_added.has_key((0, task)):
RefCuration.insert(ref_no, task, self.user, None, comment)
task_added[(0, task)] = 1
message += "Curation_task = '" + task + "'"
## insert into lit_guide
if 'HTP' in task or 'Review' in task:
topic = ''
if 'HTP' in task:
topic = 'Omics'
else:
# 'Review' in task:
topic = task
if topic_added.has_key(topic):
if comment:
message += ", comment = '" + comment + "'"
message += "<br>"
continue
else:
lit_guide_no = LitGuide.insert(ref_no, topic, self.user)
topic_added[topic] = lit_guide_no
message += ", literature_topic = '" + topic
if comment:
message += ", comment = '" + comment + "'"
message += "<br>"
db.session.commit()
return message