def save(self, data=True):
assert self.id
if data:
self.write_data()
self.modified = now()
self.db.execute('UPDATE task SET title=?,status=?,pid=?,'
' size=?,cpu_time=?,modified=? WHERE id=?',
self.title,
self.status,
self.pid,
self.size,
self.cpu_time,
self.modified,
self.id)
self.db.commit()
def create(self, account):
assert self.id is None
assert account
self.iui = uuid.uuid4().hex
self._status = configuration.CREATED
self.account = account
self.write_data()
self.modified = now()
cursor = self.db.execute('INSERT INTO task(iui,tool,title,status,'
' pid,size,cpu_time,account,modified)'
' VALUES(?,?,?,?,?,?,?,?,?)',
self.iui,
self.tool,
self.title,
self.status,
self.pid,
self.size,
self.cpu_time,
self.account,
self.modified)
self.id = cursor.lastrowid
self.db.commit()
def __init__(self, db, doc=None, values=dict(), force=False):
self.db = db
self.doc = doc or dict()
if self.doc.has_key('_id'):
if values:
try:
rev = values.get('_rev', values['rev'])
if rev != self.doc['_rev']:
raise ValueError('document revision mismatch;'
' document has been edited'
' by someone else')
except KeyError:
raise ValueError('document revision missing')
elif force:
try:
doc['_rev'] = db.revisions(doc['_id']).next().rev
except StopIteration:
pass
else:
self.doc['_id'] = uuid.uuid4().hex
if self.entitytype and not self.doc.has_key('entitytype'):
self.doc['entitytype'] = self.entitytype
self.doc['created'] = now()
def __exit__(self, type, value, tb):
if type is not None: return False # No exceptions handled here
if self.entitytype:
self.doc['modified'] = now()
self.db.save(self.doc)
pmids = set()
for year in years:
search = pubmed.Search()
for affiliation in affiliations:
pmids.update(search(author=pi,
affiliation=affiliation,
published=year))
record['count'] = len(pmids)
record['added'] = []
for pmid in pmids:
if add_publication(db, pmid):
record['added'].append(pmid)
doc['pis'].append(record)
except Exception, message:
doc['error'] = traceback.format_exc(limit=20)
doc['created'] = now()
db.save(doc)
def get_pis_affiliations(db, explicit=[]):
"""Get the list of (PI name, affiliations).
If any explicit names given (e.g. from command-line arguments),
then pick only those from the db, else get all.
"""
pis = db['pilist']['pis']
names = set([n.lower().replace('_', ' ') for n in explicit])
if names:
for i, pi in enumerate(pis):
name = pi.get('normalized_name', pi['name'])
if name.lower() not in names:
pis[i] = None
pis = [pi for pi in pis if pi is not None]
