def new_entry(conn, mid, units, notes):
"""
Adds a new entry to the ArtifactInfo table
If molecule already exists, returns null
:param conn: Sqlite3 database connection
:param mid: Molecule id of the associated molecule
:param type: type of experiment
:param units: frequency units (i.e [MHz, cm-1]
:param composition: composition of the molecule (i.e C2H2)
:param notes: additional information
:return:
"""
if mid_exists(conn, mid) is False:
return "[ERROR: Molecule entry does not exist!"
elif info_exists(conn, mid) is True:
# If entry already exists, return that mid.
return "[ ERROR: ArtifactInfo entry associated already exists. Cancelling action. ]"
# If entry does not exist.
# Add new entry to table
conn.execute('INSERT INTO ArtifactInfo (mid, units, notes)'
' VALUES (?,?,?)', (mid, units, notes))
print "[ Added info entry: " + mid + " to molecules ]"
# Get the new entry's id (iid)
cursor = conn.execute('SELECT max(kid) FROM ArtifactInfo')
kid = cursor.fetchone()[0]
# Commit Changes
conn.commit()
return kid
def new_artifact_entry(conn, mid, notes):
"""
Adds a new entry to the KnownInfo table
If molecule already exists, returns null
:param conn: Sqlite3 database connection
:param mid: Molecule id of the associated molecule
:param type: type of experiment
:param units: frequency units (i.e [MHz, cm-1]
:param composition: composition of the molecule (i.e C2H2)
:param notes: additional information
:return:
"""
if mid_exists(conn, mid) is False:
return "[ERROR: Molecule entry does not exist!"
elif info_exists(conn, mid) is True:
# If entry already exists, return that mid.
return "[ ERROR: KnownInfo entry associated already exists. Cancelling action. ]"
# If entry does not exist.
# Add new entry to table
conn.execute('INSERT INTO KnownInfo (mid, notes)'
' VALUES (?,?)', (mid, notes))
print "[ Added info entry: " + str(mid) + " to molecules ]"
# Get the new entry's id (iid)
cursor = conn.execute('SELECT max(kid) FROM KnownInfo')
kid = cursor.fetchone()[0]
# Commit Changes
conn.commit()
return kid
def remove_all(conn, mid):
"""
Removes all entries for a specified molecule
:param conn: Connection to sqlite3 database
:param mid: Molecule entry ID (mid) to remove associated peaks
:return: True, if peaks are removed successfuly, otherwise False
"""
if(mid_exists(conn, mid) is False):
print "[ ERROR: Molecule entry does not exist. Cancelling action! ]"
return False
conn.execute("DELETE FROM peaks WHERE mid={m}".format(m=mid))
conn.commit()
return True
def import_file(conn, filepath, mid, peaks=False):
"""
Imports file to peak table in spectrum database to it's associative molecule
Molecule must exist for import
Supports '.cat' , '.sp', '.lines', '.list', .txt', files.
:param filepath: Path to import file
:param mid: Molecule ID
:return:
"""
# Check if molecule entry exists
if mid_exists(conn, mid) is False:
# Molecule does not exist, ERR return
print "[ ERROR: Molecule entry does not exist. Cancelling action! ]"
return False
# Check if file can be opened
if __checkfile(filepath) is False:
# File cannot be opened. ERR return
return False
# Get File extention
extention = str.split(filepath, ".")[-1]
print(extention)
# Match extention to its appropriate import function
if extention == 'cat':
__import_catfile(conn, filepath, mid)
elif extention == 'sp':
__import_spfile(conn, filepath, mid)
elif extention == 'lines':
__import_linesfile(conn, filepath, mid)
elif extention == 'dpt':
__import_dptfile(conn, filepath, mid)
elif extention == 'txt':
__import_txtfile(conn, filepath, mid, peaks)
elif extention == 'list':
__import_listfile(conn, filepath, mid)
elif extention == 'ftb':
__import_ftbfile(conn, filepath, mid, peaks)
else:
print "Invalid import file. EXTENTION must be: '.cat' , '.sp', '.lines'"
return False
return True
def import_file(conn, filepath, mid, peaks=False):
"""
Imports file to peak table in spectrum database to it's associative molecule
Molecule must exist for import
Supports '.cat' , '.sp', '.lines', '.list', .txt', files.
:param filepath: Path to import file
:param mid: Molecule ID
:return:
"""
# Check if molecule entry exists
if mid_exists(conn, mid) is False:
# Molecule does not exist, ERR return
print "[ ERROR: Molecule entry does not exist. Cancelling action! ]"
return False
# Check if file can be opened
if __checkfile(filepath) is False:
# File cannot be opened. ERR return
return False
# Get File extention
extention = str.split(filepath, ".")[1]
# Match extention to its appropriate import function
if extention == 'cat':
__import_catfile(conn, filepath, mid)
elif extention == 'sp':
__import_spfile(conn, filepath, mid)
elif extention == 'lines':
__import_linesfile(conn, filepath, mid)
elif extention == 'dpt':
__import_dptfile(conn, filepath, mid)
elif extention == 'txt':
__import_txtfile(conn, filepath, mid, peaks)
elif extention == 'list':
__import_listfile(conn, filepath, mid)
elif extention == 'ftb':
__import_ftbfile(conn, filepath, mid, peaks)
else:
print "Invalid import file. EXTENTION must be: '.cat' , '.sp', '.lines'"
return False
return True
def remove_all(conn, mid):
"""
Removes all entries for a specified molecule
:param conn: Connection to sqlite3 database
:param mid: Molecule entry ID (mid) to remove associated peaks
:return: True, if assignments are removed successfuly, otherwise False
"""
if (mid_exists(conn, mid) is False):
print "[ ERROR: Molecule entry does not exist. Cancelling action! ]"
return False
sql="DELETE FROM assignments WHERE aid IN (" \
" SELECT aid" \
" FROM peaks INNER JOIN assignments ON (assignments.pid=peaks.pid)"\
" WHERE peaks.mid={m}" \
");".format(m=mid)
conn.execute(sql)
conn.commit()
return True
def remove_all(conn, mid):
"""
Removes all entries for a specified molecule
:param conn: Connection to sqlite3 database
:param mid: Molecule entry ID (mid) to remove associated peaks
:return: True, if assignments are removed successfuly, otherwise False
"""
if(mid_exists(conn, mid) is False):
print "[ ERROR: Molecule entry does not exist. Cancelling action! ]"
return False
sql="DELETE FROM assignments WHERE aid IN (" \
" SELECT aid" \
" FROM peaks INNER JOIN assignments ON (assignments.pid=peaks.pid)"\
" WHERE peaks.mid={m}" \
");".format(m=mid)
conn.execute(sql)
conn.commit()
return True