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 update_category(conn, mid, category):
"""
Changes the category row of a molecule
:param conn: Connection to sqlite database
:param mid: Molecule ID (mid) to make changes
:param category: New category to replace
:return: True, if updated successfully
:return: False, if
"""
if (mid_exists(conn, mid) is False):
print "[ ERROR: Molecule entry does not exist. Cancelling action! ]"
return False
conn.execute("UPDATE molecules SET category={c} WHERE mid={m}".format(
c=category, m=mid))
conn.commit()
return True
def update_name(conn, mid, name):
"""
Changes the name row of a molecule
:param conn: Connection to sqlite database
:param mid: Molecule ID (mid) to make changes
:param name: New name to replace
:return: True, if updated successfully
:return: False, if
"""
if (mid_exists(conn, mid) is False):
print "[ ERROR: Molecule entry does not exist. Cancelling action! ]"
return False
conn.execute("UPDATE molecules SET name={n} WHERE mid={m}".format(n=name,
m=mid))
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
def new_info_entry(conn, mid, vibration, notes):
"""
Adds a new info entry to info table
Associative molecule entry must exist, and it's info entry must not.
:param conn: Connection to sqlite3 database
:param mid: Molecule ID (mid) for the associate info entry
:param vibration: Vibration of molecule
:param notes: Notes regarding the molecule
:return: Info entry id (iid) of new entry
:return None if info entry already exists or molecule entry does not exist
"""
# 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.]"
return #none
iid = get_iid(conn, mid) # Get iid
# If entry already exists, return that mid.
if iid is not None:
# Entry exists
print "[ ERROR: Info entry already exists.]"
return #none
# If entry does not exist.
# Add new entry to info table
conn.execute('INSERT INTO info (mid, vibration, notes) VALUES (?,?,?)', (mid, vibration, notes))
# Get the new entry's info id (iid)
cursor = conn.execute('SELECT max(mid) FROM info')
iid = cursor.fetchone()[0]
print "[ Added entry: iid:" + str(iid) + " to info ]"
# Commit Changes
conn.commit()
return iid
def remove_molecule(conn, mid):
"""
Removes all info, peak and molecule entries of given mid
:param conn: Sqlite database connection
:param mid: Molecule ID (mid) of molecule to be removed
:return: True if successfully removed
:return: False, if not removed
"""
if (mid_exists(conn, mid) is False):
print "[ ERROR: Molecule entry does not exist. Cancelling action! ]"
return False
# Delete Info Entry
conn.execute("DELETE FROM info WHERE mid={m}".format(m=mid))
# Delete peak entry
conn.execute("DELETE FROM peaks WHERE mid={m}".format(m=mid))
# Delete Molecule entry
conn.execute("DELETE FROM molecules WHERE mid={m}".format(m=mid))
conn.commit()
print "[ Successfully removed " + str(mid) + "from database ]"
return True
def import_file(conn, filepath, mid):
"""
Imports file to peak table in spectrum database to it's associative molecule
Molecule must exist for import
Supports '.cat' , '.sp', '.lines' 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)
else:
print "Invalid import file. EXTENTION must be: '.cat' , '.sp', '.lines'"
return False
return True