def deleteGenomeList(self, genome_list_ids):
"""Delete genome list and associated genomes.
Parameters
----------
genome_list_ids : iterable
Unique identifier of genome lists in database.
Returns
-------
bool
True if successful.
"""
for genome_list_id in genome_list_ids:
try:
edit_permission = self.permissionToModify(genome_list_id)
if edit_permission is False:
raise GenomeDatabaseError(
"Insufficient permissions to delete genome list. Offending list id: {0}"
.format(genome_list_id))
if not confirm(
"Are you sure you want to delete {0} lists (this action cannot be undone)"
.format(len(genome_list_ids))):
raise GenomeDatabaseError("User aborted database action.")
list_genomes_ids = self.getGenomeIdsFromGenomeListIds(
[genome_list_id])
self.editGenomeList(genome_list_id, list_genomes_ids, 'remove')
except GenomeDatabaseError as e:
raise e
return True
def deleteMarkerSets(self, marker_set_ids):
"""Delete marker set and associated markers.
Parameters
----------
marker_set_ids : iterable
Unique identifier of marker sets in database.
Returns
-------
bool
True if successful.
"""
for marker_set_id in marker_set_ids:
try:
edit_permission = self.permissionToModify(marker_set_id)
if edit_permission is False:
raise GenomeDatabaseError(
"Insufficient permissions to delete marker set. Offending marker set id: {0}"
.format(marker_set_id))
if not confirm(
"Are you sure you want to delete {0} set(s) (this action cannot be undone)"
.format(len(marker_set_ids))):
raise GenomeDatabaseError("User aborted database action.")
list_marker_ids = self.getMarkerIdsFromMarkerSetIds(
[marker_set_id])
self.editMarkerSet(marker_set_id, list_marker_ids, 'remove')
except GenomeDatabaseError as e:
raise e
return True
def deleteGenomeList(self, genome_list_ids):
"""Delete genome list and associated genomes.
Parameters
----------
genome_list_ids : iterable
Unique identifier of genome lists in database.
Returns
-------
bool
True if successful.
"""
for genome_list_id in genome_list_ids:
try:
edit_permission = self.permissionToModify(genome_list_id)
if edit_permission is False:
raise GenomeDatabaseError(
"Insufficient permissions to delete genome list. Offending list id: {0}".format(genome_list_id))
if not confirm("Are you sure you want to delete {0} lists (this action cannot be undone)".format(len(genome_list_ids))):
raise GenomeDatabaseError("User aborted database action.")
list_genomes_ids = self.getGenomeIdsFromGenomeListIds(
[genome_list_id])
self.editGenomeList(genome_list_id, list_genomes_ids, 'remove')
except GenomeDatabaseError as e:
raise e
return True
def deleteMarkerSets(self, marker_set_ids):
"""Delete marker set and associated markers.
Parameters
----------
marker_set_ids : iterable
Unique identifier of marker sets in database.
Returns
-------
bool
True if successful.
"""
for marker_set_id in marker_set_ids:
try:
edit_permission = self.permissionToModify(marker_set_id)
if edit_permission is False:
raise GenomeDatabaseError(
"Insufficient permissions to delete marker set. Offending marker set id: {0}".format(marker_set_id))
if not confirm("Are you sure you want to delete {0} set(s) (this action cannot be undone)".format(len(marker_set_ids))):
raise GenomeDatabaseError("User aborted database action.")
list_marker_ids = self.getMarkerIdsFromMarkerSetIds(
[marker_set_id])
self.editMarkerSet(marker_set_id, list_marker_ids, 'remove')
except GenomeDatabaseError as e:
raise e
return True
def deleteGenomes(self, batchfile=None, db_genome_ids=None, reason=None):
"""
Delete Genomes
Returns True for success or False for fail
Parameters:
:param batchfile: text file listing a range of ids to delete
:param db_genome_ids: a list of ids can be written directly in the command line
"""
self._loggerSetup()
try:
if db_genome_ids is False:
raise GenomeDatabaseError("Unable to delete genomes. Unable to retrieve genome ids.")
# restrict deletion to genomes owned by user
has_permission, username, genomes_owners = self._hasPermissionToEditGenomes(db_genome_ids)
if has_permission is None:
raise GenomeDatabaseError("Unable to delete genomes. Unable to retrieve permissions for genomes.")
if has_permission is False:
raise GenomeDatabaseError("Unable to delete genomes. Insufficient permissions.")
if db_genome_ids:
if not confirm(
"Are you sure you want to delete %i genomes (this action cannot be undone)" % len(db_genome_ids)
):
raise GenomeDatabaseError("User aborted database action.")
self.cur.execute("DELETE FROM aligned_markers " + "WHERE genome_id IN %s ", (tuple(db_genome_ids),))
self.cur.execute("DELETE FROM genome_list_contents " + "WHERE genome_id IN %s", (tuple(db_genome_ids),))
# Deletion of metadata
self.cur.execute("DELETE FROM metadata_genes " + "WHERE id IN %s", (tuple(db_genome_ids),))
self.cur.execute("DELETE FROM metadata_ncbi " + "WHERE id IN %s", (tuple(db_genome_ids),))
self.cur.execute("DELETE FROM metadata_nucleotide " + "WHERE id IN %s", (tuple(db_genome_ids),))
self.cur.execute("DELETE FROM metadata_taxonomy " + "WHERE id IN %s", (tuple(db_genome_ids),))
self.cur.execute("DELETE FROM metadata_rna " + "WHERE id IN %s", (tuple(db_genome_ids),))
self.cur.execute("DELETE FROM metadata_sequence " + "WHERE id IN %s", (tuple(db_genome_ids),))
self.cur.execute("DELETE FROM genomes " + "WHERE id IN %s", (tuple(db_genome_ids),))
self.cur.execute(
"UPDATE metadata_taxonomy set gtdb_genome_representative = NULL where "
+ "gtdb_genome_representative in %s",
(tuple(genomes_owners.keys()),),
)
for genome, info in genomes_owners.iteritems():
if str(username) != str(info.get("owner")):
logging.info(
"""Genome {0} has been deleted by {1} for the following reason '{2}'
WARNING: {1} is not the owner of this {0} (real owner {3} )
{0} needs to be moved manually to the deprecated folder""".format(
genome, username, reason, info.get("owner")
)
)
else:
if info.get("prefix") is "U":
target = os.path.dirname(os.path.join(self.deprecatedUserDir, info.get("relative_path")))
elif info.get("prefix") is "GB":
target = os.path.join(self.deprecatedGBKDir, info.get("relative_path"))
elif info.get("prefix") is "RS":
target = os.path.join(self.deprecatedRSQDir, info.get("relative_path"))
make_sure_path_exists(target)
os.rename(
os.path.dirname(Tools.fastaPathGenerator(info.get("relative_path"), info.get("prefix"))),
target,
)
logging.info(
"Genome {0} has been deleted by {1} for the following reason '{2}'".format(
genome, username, reason
)
)
except GenomeDatabaseError as e:
raise e
return True
def deleteGenomes(self, batchfile=None, db_genome_ids=None, reason=None):
'''
Delete Genomes
Returns True for success or False for fail
Parameters:
:param batchfile: text file listing a range of ids to delete
:param db_genome_ids: a list of ids can be written directly in the command line
'''
self._loggerSetup()
try:
if db_genome_ids is False:
raise GenomeDatabaseError(
"Unable to delete genomes. Unable to retrieve genome ids.")
# restrict deletion to genomes owned by user
has_permission, username, genomes_owners = self._hasPermissionToEditGenomes(
db_genome_ids)
if has_permission is None:
raise GenomeDatabaseError(
"Unable to delete genomes. Unable to retrieve permissions for genomes."
)
if has_permission is False:
raise GenomeDatabaseError(
"Unable to delete genomes. Insufficient permissions.")
if db_genome_ids:
if not confirm(
"Are you sure you want to delete %i genomes (this action cannot be undone)"
% len(db_genome_ids)):
raise GenomeDatabaseError("User aborted database action.")
self.cur.execute(
"DELETE FROM aligned_markers " + "WHERE genome_id IN %s ",
(tuple(db_genome_ids), ))
self.cur.execute(
"DELETE FROM genome_list_contents " +
"WHERE genome_id IN %s", (tuple(db_genome_ids), ))
# Deletion of metadata
self.cur.execute(
"DELETE FROM metadata_genes " + "WHERE id IN %s",
(tuple(db_genome_ids), ))
self.cur.execute(
"DELETE FROM metadata_ncbi " + "WHERE id IN %s",
(tuple(db_genome_ids), ))
self.cur.execute(
"DELETE FROM metadata_nucleotide " + "WHERE id IN %s",
(tuple(db_genome_ids), ))
self.cur.execute(
"DELETE FROM metadata_taxonomy " + "WHERE id IN %s",
(tuple(db_genome_ids), ))
self.cur.execute(
"DELETE FROM metadata_rna " + "WHERE id IN %s",
(tuple(db_genome_ids), ))
self.cur.execute(
"DELETE FROM metadata_sequence " + "WHERE id IN %s",
(tuple(db_genome_ids), ))
self.cur.execute("DELETE FROM genomes " + "WHERE id IN %s",
(tuple(db_genome_ids), ))
self.cur.execute(
"UPDATE metadata_taxonomy set gtdb_genome_representative = NULL where "
+ "gtdb_genome_representative in %s",
(tuple(genomes_owners.keys()), ))
for genome, info in genomes_owners.iteritems():
if str(username) != str(info.get("owner")):
logging.info(
'''Genome {0} has been deleted by {1} for the following reason '{2}'
WARNING: {1} is not the owner of this {0} (real owner {3} )
{0} needs to be moved manually to the deprecated folder'''
.format(genome, username, reason,
info.get("owner")))
else:
if info.get("prefix") is "U":
target = os.path.dirname(
os.path.join(self.deprecatedUserDir,
info.get("relative_path")))
elif info.get("prefix") is "GB":
target = os.path.join(self.deprecatedGBKDir,
info.get("relative_path"))
elif info.get("prefix") is "RS":
target = os.path.join(self.deprecatedRSQDir,
info.get("relative_path"))
make_sure_path_exists(target)
os.rename(
os.path.dirname(
Tools.fastaPathGenerator(
info.get("relative_path"),
info.get("prefix"))), target)
logging.info(
"Genome {0} has been deleted by {1} for the following reason '{2}'"
.format(genome, username, reason))
except GenomeDatabaseError as e:
raise e
return True
