def migrate(db_path):
if db_path is None:
raise ConfigError("No database path is given.")
# make sure someone is not being funny
utils.is_pan_db(db_path)
# make sure the version is accurate
pan_db = db.DB(db_path, None, ignore_version = True)
if str(pan_db.get_version()) != current_version:
raise ConfigError("Version of this pan database is not %s (hence, this script cannot really do anything)." % current_version)
for table_name in ['layer_additional_data', 'item_additional_data']:
new_table = divide_stackedbar_to_multiple_entries(pan_db.get_table_as_dict(table_name))
pan_db._exec("DELETE FROM '%s'" % table_name)
new_entry_counter = 0
for entry_id in new_table:
pan_db.insert(table_name, (new_entry_counter, *new_table[entry_id].values()))
new_entry_counter += 1
# set the version
pan_db.remove_meta_key_value_pair('version')
pan_db.set_version(next_version)
# now bye for real!
pan_db.disconnect()
progress.end()
run.info_single('Your pan db is now %s.' % next_version, nl_after=1, nl_before=1, mc='green')
def migrate(db_path):
if db_path is None:
raise ConfigError("No database path is given.")
# make sure someone is not being funny
utils.is_pan_db(db_path)
# make sure the version is accurate
pan_db = db.DB(db_path, None, ignore_version = True)
if str(pan_db.get_version()) != current_version:
raise ConfigError("Version of this pan database is not %s (hence, this script cannot really do anything)." % current_version)
pan_db._exec('ALTER TABLE "item_additional_data" ADD COLUMN "data_group" text')
pan_db._exec('ALTER TABLE "layer_additional_data" ADD COLUMN "data_group" text')
pan_db._exec('UPDATE "item_additional_data" SET "data_group" = "default"')
pan_db._exec('UPDATE "layer_additional_data" SET "data_group" = "default"')
# set the version
pan_db.remove_meta_key_value_pair('version')
pan_db.set_version(next_version)
# now bye for real!
pan_db.disconnect()
progress.end()
run.info_single('Your pan db is now %s.' % next_version, nl_after=1, nl_before=1, mc='green')
def migrate(db_path):
if db_path is None:
raise ConfigError("No database path is given.")
# make sure someone is not being funny
utils.is_pan_db(db_path)
# make sure the version is accurate
pan_db = db.DB(db_path, None, ignore_version=True)
if str(pan_db.get_version()) != current_version:
raise ConfigError(
"Version of this pan database is not %s (hence, this script cannot really do anything)."
% current_version)
for table_name in ['layer_additional_data', 'item_additional_data']:
new_table = divide_stackedbar_to_multiple_entries(
pan_db.get_table_as_dict(table_name))
pan_db._exec("DELETE FROM '%s'" % table_name)
for entry_id in new_table:
pan_db.insert(table_name, tuple(new_table[entry_id].values()))
# set the version
pan_db.remove_meta_key_value_pair('version')
pan_db.set_version(next_version)
# now bye for real!
pan_db.disconnect()
progress.end()
run.info_single('Your pan db is now %s.' % next_version,
nl_after=1,
nl_before=1,
mc='green')
def migrate(db_path):
if db_path is None:
raise ConfigError("No database path is given.")
# make sure someone is not being funny
utils.is_pan_db(db_path)
# make sure the version is accurate
pan_db = db.DB(db_path, None, ignore_version = True)
if str(pan_db.get_version()) != current_version:
raise ConfigError("Version of this pan database is not %s (hence, this script cannot really do anything)." % current_version)
pan_db._exec('ALTER TABLE "item_orders" ADD COLUMN "additional" text')
pan_db._exec('UPDATE "item_orders" SET "additional" = "{}"')
# set the version
pan_db.remove_meta_key_value_pair('version')
pan_db.set_version(next_version)
# now bye for real!
pan_db.disconnect()
progress.end()
run.info_single('Your pan db is now %s.' % next_version, nl_after=1, nl_before=1, mc='green')
def migrate(db_path):
if db_path is None:
raise ConfigError("No database path is given.")
# make sure someone is not being funny
utils.is_pan_db(db_path)
# make sure the version is accurate
pan_db = db.DB(db_path, None, ignore_version=True)
if str(pan_db.get_version()) != current_version:
raise ConfigError(
"Version of this pan database is not %s (hence, this script cannot really do anything)."
% current_version)
progress.new("Trying to upgrade the pan database")
progress.update('...')
pan_db.set_meta_value('description', '_No description is found_')
# set the version
pan_db.remove_meta_key_value_pair('version')
pan_db.set_version(next_version)
# bye
pan_db.disconnect()
progress.end()
run.info_single('Your pan db is now %s.' % next_version,
nl_after=1,
nl_before=1,
mc='green')
def migrate(db_path):
if db_path is None:
raise ConfigError("No database path is given.")
# make sure someone is not being funny
utils.is_pan_db(db_path)
# make sure the version is accurate
pan_db = db.DB(db_path, None, ignore_version = True)
if str(pan_db.get_version()) != current_version:
raise ConfigError("Version of this pan database is not %s (hence, this script cannot really do anything)." % current_version)
# gene_clusters_ordered -> items_ordered
pan_db.set_meta_value('items_ordered', pan_db.get_meta_value('gene_clusters_ordered'))
pan_db.remove_meta_key_value_pair('gene_clusters_ordered')
pan_db.remove_meta_key_value_pair('gene_clusters_clustered')
# set the version
pan_db.remove_meta_key_value_pair('version')
pan_db.set_version(next_version)
# now bye for real!
pan_db.disconnect()
progress.end()
run.info_single('Your pan db is now %s (lucky you).' % next_version, nl_after=1, nl_before=1, mc='green')
def migrate(db_path):
if db_path is None:
raise ConfigError("No database path is given.")
# make sure someone is not being funny
utils.is_pan_db(db_path)
pan_db = db.DB(db_path, None, ignore_version=True)
if str(pan_db.get_version()) != current_version:
pan_db.disconnect()
raise ConfigError(
"Version of this pan database is not %s (hence, this script cannot really do anything)."
% current_version)
pan_db.disconnect()
# drop entry ids one by one
for table_name in tables:
drop_entry_id_column_from_table(db_path,
table_name,
table_properties=tables[table_name])
# set the version
pan_db = db.DB(db_path, None, ignore_version=True)
pan_db.remove_meta_key_value_pair('version')
pan_db.set_version(next_version)
pan_db.disconnect()
progress.end()
run.info_single(
"Your pan db is now version %s. There were %d tables in it that needed upatin'. "
"They're good now." % (next_version, len(tables)),
nl_after=1,
nl_before=1,
mc='green')
def migrate(db_path):
if db_path is None:
raise ConfigError("No database path is given.")
# make sure someone is not being funny
utils.is_pan_db(db_path)
# make sure the version is accurate
pan_db = db.DB(db_path, None, ignore_version = True)
if str(pan_db.get_version()) != current_version:
raise ConfigError("Version of this pan database is not %s (hence, this script cannot really do anything)." % current_version)
progress.new("Trying to upgrade the pan database")
progress.update('...')
pan_db.set_meta_value('description', '_No description is found_')
# set the version
pan_db.remove_meta_key_value_pair('version')
pan_db.set_version(next_version)
# bye
pan_db.disconnect()
progress.end()
run.info_single('Your pan db is now %s.' % next_version, nl_after=1, nl_before=1, mc='green')
def migrate(db_path):
if db_path is None:
raise ConfigError("No database path is given.")
# make sure someone is not being funny
utils.is_pan_db(db_path)
# make sure the version is accurate
pan_db = db.DB(db_path, None, ignore_version=True)
if str(pan_db.get_version()) != current_version:
raise ConfigError(
"Version of this pan database is not %s (hence, this script cannot really do anything)."
% current_version)
# gene_clusters_ordered -> items_ordered
pan_db.set_meta_value('items_ordered',
pan_db.get_meta_value('gene_clusters_ordered'))
pan_db.remove_meta_key_value_pair('gene_clusters_ordered')
pan_db.remove_meta_key_value_pair('gene_clusters_clustered')
# set the version
pan_db.remove_meta_key_value_pair('version')
pan_db.set_version(next_version)
# now bye for real!
pan_db.disconnect()
progress.end()
run.info_single('Your pan db is now %s (lucky you).' % next_version,
nl_after=1,
nl_before=1,
mc='green')
def __init__(self, db_path, run=run, progress=progress):
self.db_path = db_path
utils.is_pan_db(db_path)
self.run = run
self.progress = progress
Table.__init__(self, self.db_path, anvio.__pan__version__, run, progress)
self.entries = []
def __init__(self, db_path, run=run, progress=progress):
self.db_path = db_path
utils.is_pan_db(db_path)
self.run = run
self.progress = progress
Table.__init__(self, self.db_path, anvio.__pan__version__, run, progress)
self.set_next_available_id(t.pan_gene_clusters_table_name)
self.entries = []
def __init__(self, db_path, run=run, progress=progress):
self.db_path = db_path
utils.is_pan_db(db_path)
self.run = run
self.progress = progress
Table.__init__(self, self.db_path, anvio.__pan__version__, run,
progress)
self.set_next_available_id(t.pan_gene_clusters_table_name)
self.entries = []
def migrate(db_path):
if db_path is None:
raise ConfigError("No database path is given.")
# make sure someone is not being funny
utils.is_pan_db(db_path)
# make sure the version is accurate
pan_db = db.DB(db_path, None, ignore_version = True)
if str(pan_db.get_version()) != current_version:
raise ConfigError("Version of this pan database is not %s (hence, this script cannot really do anything)." % current_version)
# migrate item orders
item_orders = pan_db.get_table_as_dict(item_orders_table_name)
for order_name in item_orders:
if item_orders[order_name]['type'] == 'newick':
newick = Tree(item_orders[order_name]['data'], format=1)
newick = newick.write(format=2)
pan_db._exec("""UPDATE %s SET "data" = ? WHERE "name" LIKE ?""" % item_orders_table_name, (newick, order_name))
# migrate layer orders
layer_orders = pan_db.get_table_as_dict(layer_orders_table_name)
for order_name in layer_orders:
if layer_orders[order_name]['data_type'] == 'newick':
newick = Tree(layer_orders[order_name]['data_value'], format=1)
newick = newick.write(format=2)
pan_db._exec("""UPDATE %s SET "data_value" = ? WHERE "data_key" LIKE ?""" % layer_orders_table_name, (newick, order_name))
# set the version
pan_db.remove_meta_key_value_pair('version')
pan_db.set_version(next_version)
# now bye for real!
pan_db.disconnect()
progress.end()
run.info_single('Your pan db is now %s.' % next_version, nl_after=1, nl_before=1, mc='green')
def migrate(db_path):
if db_path is None:
raise ConfigError("No database path is given.")
# make sure someone is not being funny
utils.is_pan_db(db_path)
# make sure the version is accurate
pan_db = db.DB(db_path, None, ignore_version=True)
if str(pan_db.get_version()) != current_version:
raise ConfigError(
"Version of this pan database is not %s (hence, this script cannot really do anything)."
% current_version)
# update keys
for old_key, new_key in [('maxbit', 'minbit')]:
try:
pan_db.set_meta_value(new_key, pan_db.get_meta_value(old_key))
except:
pass
# remove stuff that are not irrelevant
try:
pan_db.remove_meta_key_value_pair('maxbit')
except:
pass
# learn additional_data_headers for later:
additional_data_headers = pan_db.get_meta_value(
'additional_data_headers').split(',')
# take care of the self table
self_table = pan_db.get_table_as_list_of_tuples('self')
pan_db.cursor.execute('ALTER TABLE self RENAME TO self_TEMP;')
pan_db.cursor.execute('CREATE TABLE self (key text, value text);')
for key, val in self_table:
new_key = key.replace('PC',
'gene_cluster').replace('pc', 'gene_cluster')
new_val = val.replace('PC',
'gene_cluster').replace('pc', 'gene_cluster')
pan_db.set_meta_value(new_key, new_val)
pan_db.cursor.execute('DROP TABLE self_TEMP;')
# take care of the views table
views_table = pan_db.get_table_as_list_of_tuples('views')
pan_db.cursor.execute('ALTER TABLE views RENAME TO views_TEMP;')
pan_db.cursor.execute(
'CREATE TABLE views (view_id str, target_table str);')
values = []
for view, target in views_table:
new_view = view.replace('PC',
'gene_cluster').replace('pc', 'gene_cluster')
new_target = target.replace('PC', 'gene_cluster').replace(
'pc', 'gene_cluster')
values.append((new_view, new_target), )
pan_db.insert_many('views', values)
pan_db.cursor.execute('DROP TABLE views_TEMP;')
# rename tables
pan_db._exec(
'ALTER TABLE PC_frequencies RENAME TO gene_cluster_frequencies;')
pan_db._exec(
'ALTER TABLE PC_presence_absence RENAME TO gene_cluster_presence_absence;'
)
pan_db._exec('ALTER TABLE protein_clusters RENAME TO gene_clusters;')
# protein_cluster_id -> gene_cluster_id in table gene_clusters.
pan_db.cursor.execute(
'ALTER TABLE gene_clusters RENAME TO gene_clusters_TEMP;')
pan_db.cursor.execute(
'CREATE TABLE gene_clusters (entry_id numeric, gene_caller_id numeric, gene_cluster_id str, genome_name str, alignment_summary str);'
)
pan_db.cursor.execute(
'INSERT INTO gene_clusters(entry_id, gene_caller_id, gene_cluster_id, genome_name, alignment_summary) SELECT entry_id, gene_caller_id, protein_cluster_id, genome_name, alignment_summary FROM gene_clusters_TEMP;'
)
pan_db.cursor.execute('DROP TABLE gene_clusters_TEMP;')
# commit
try:
pan_db._exec('COMMIT')
except:
pass
# we also added a totally new table to this version:
pan_db.create_table(item_additional_data_table_name,
item_additional_data_table_structure,
item_additional_data_table_types)
# set the version
pan_db.remove_meta_key_value_pair('version')
pan_db.set_version(next_version)
# we have one more thing to do: getting rid of the 'additional_data' table without losing data, by carrying
# its content into our new item_additional_data_table
additional_data_table_dict = pan_db.get_table_as_dict('additional_data')
# close the db temporarily
pan_db.disconnect()
# update the contents of the item_additional_data_table
args = argparse.Namespace(pan_db=db_path,
just_do_it=True,
ignore_db_version=True)
item_additional_data_table = TableForItemAdditionalData(args)
item_additional_data_table.add(additional_data_headers,
additional_data_table_dict)
# open the database again to remove stuff
pan_db = db.DB(db_path, None, ignore_version=True)
pan_db.remove_meta_key_value_pair('additional_data_headers')
pan_db._exec("DROP TABLE additional_data")
# now bye for real!
pan_db.disconnect()
progress.end()
run.info_single('Your pan db is now %s.' % next_version,
nl_after=1,
nl_before=1,
mc='green')
def migrate(db_path):
if db_path is None:
raise ConfigError("No database path is given.")
# make sure someone is not being funny
utils.is_pan_db(db_path)
# make sure the version is accurate
pan_db = db.DB(db_path, None, ignore_version = True)
if str(pan_db.get_version()) != current_version:
raise ConfigError("Version of this pan database is not %s (hence, this script cannot really do anything)." % current_version)
progress.new("Trying to upgrade the pan database")
progress.update('...')
try:
pan_db.create_table(item_orders_table_name, item_orders_table_structure, item_orders_table_types)
except:
pass
clusterings = pan_db.get_table_as_dict('clusterings')
# move clustering data into the new table
for clustering in clusterings:
newick = clusterings[clustering]['newick']
pan_db._exec('''INSERT INTO %s VALUES (?,?,?)''' % item_orders_table_name, tuple([clustering, 'newick', newick]))
# update keys
for old_key, new_key in [('pc_min_occurrence', 'gene_cluster_min_occurrence'),
('num_protein_clusters', 'num_gene_clusters'),
('num_genes_in_protein_clusters', 'num_genes_in_gene_clusters'),
('available_clusterings', 'available_item_orders'),
('PCs_clustered', 'PCs_ordered'),
('default_clustering', 'default_item_order')]:
try:
pan_db.set_meta_value(new_key, pan_db.get_meta_value(old_key))
except:
pass
# remove stuff that are not irrelevant
try:
pan_db._exec('DROP TABLE clusterings;')
pan_db.remove_meta_key_value_pair('available_clusterings')
pan_db.remove_meta_key_value_pair('PCs_clustered')
pan_db.remove_meta_key_value_pair('default_clustering')
pan_db.remove_meta_key_value_pair('num_protein_clusters')
pan_db.remove_meta_key_value_pair('num_genes_in_protein_clusters')
pan_db.remove_meta_key_value_pair('pc_min_occurrence')
except:
pass
# commit
try:
pan_db._exec('COMMIT')
except:
pass
# cleanup
try:
pan_db._exec('vacuum')
except:
pass
# set the version
pan_db.remove_meta_key_value_pair('version')
pan_db.set_version(next_version)
# bye
pan_db.disconnect()
progress.end()
run.info_single('Your pan db is now %s.' % next_version, nl_after=1, nl_before=1, mc='green')
def migrate(db_path):
if db_path is None:
raise ConfigError("No database path is given.")
# make sure someone is not being funny
utils.is_pan_db(db_path)
# make sure the version is accurate
pan_db = db.DB(db_path, None, ignore_version=True)
if str(pan_db.get_version()) != current_version:
raise ConfigError(
"Version of this pan database is not %s (hence, this script cannot really do anything)."
% current_version)
progress.new("Trying to upgrade the pan database")
progress.update('...')
try:
pan_db.create_table(t.item_orders_table_name,
t.item_orders_table_structure,
t.item_orders_table_types)
except:
pass
clusterings = pan_db.get_table_as_dict('clusterings')
# move clustering data into the new table
for clustering in clusterings:
newick = clusterings[clustering]['newick']
pan_db._exec(
'''INSERT INTO %s VALUES (?,?,?)''' % t.item_orders_table_name,
tuple([clustering, 'newick', newick]))
# update keys
for old_key, new_key in [
('pc_min_occurrence', 'gene_cluster_min_occurrence'),
('num_protein_clusters', 'num_gene_clusters'),
('num_genes_in_protein_clusters', 'num_genes_in_gene_clusters'),
('available_clusterings', 'available_item_orders'),
('PCs_clustered', 'PCs_ordered'),
('default_clustering', 'default_item_order')
]:
try:
pan_db.set_meta_value(new_key, pan_db.get_meta_value(old_key))
except:
pass
# remove stuff that are not irrelevant
try:
pan_db._exec('DROP TABLE clusterings;')
pan_db.remove_meta_key_value_pair('available_clusterings')
pan_db.remove_meta_key_value_pair('PCs_clustered')
pan_db.remove_meta_key_value_pair('default_clustering')
pan_db.remove_meta_key_value_pair('num_protein_clusters')
pan_db.remove_meta_key_value_pair('num_genes_in_protein_clusters')
pan_db.remove_meta_key_value_pair('pc_min_occurrence')
except:
pass
# commit
try:
pan_db._exec('COMMIT')
except:
pass
# cleanup
try:
pan_db._exec('vacuum')
except:
pass
# set the version
pan_db.remove_meta_key_value_pair('version')
pan_db.set_version(next_version)
# bye
pan_db.disconnect()
progress.end()
run.info_single('Your pan db is now %s.' % next_version,
nl_after=1,
nl_before=1,
mc='green')
def migrate(db_path):
if db_path is None:
raise ConfigError("No database path is given.")
# make sure someone is not being funny
utils.is_pan_db(db_path)
# make sure the version is accurate
pan_db = db.DB(db_path, None, ignore_version = True)
if str(pan_db.get_version()) != current_version:
raise ConfigError("Version of this pan database is not %s (hence, this script cannot really do anything)." % current_version)
# update keys
for old_key, new_key in [('maxbit', 'minbit')]:
try:
pan_db.set_meta_value(new_key, pan_db.get_meta_value(old_key))
except:
pass
# remove stuff that are not irrelevant
try:
pan_db.remove_meta_key_value_pair('maxbit')
except:
pass
# learn additional_data_headers for later:
additional_data_headers = pan_db.get_meta_value('additional_data_headers').split(',')
# take care of the self table
self_table = pan_db.get_table_as_list_of_tuples('self')
pan_db.cursor.execute('ALTER TABLE self RENAME TO self_TEMP;')
pan_db.cursor.execute('CREATE TABLE self (key text, value text);')
for key, val in self_table:
new_key = key.replace('PC', 'gene_cluster').replace('pc', 'gene_cluster')
new_val = val.replace('PC', 'gene_cluster').replace('pc', 'gene_cluster')
pan_db.set_meta_value(new_key, new_val)
pan_db.cursor.execute('DROP TABLE self_TEMP;')
# take care of the views table
views_table = pan_db.get_table_as_list_of_tuples('views')
pan_db.cursor.execute('ALTER TABLE views RENAME TO views_TEMP;')
pan_db.cursor.execute('CREATE TABLE views (view_id str, target_table str);')
values = []
for view, target in views_table:
new_view = view.replace('PC', 'gene_cluster').replace('pc', 'gene_cluster')
new_target = target.replace('PC', 'gene_cluster').replace('pc', 'gene_cluster')
values.append((new_view, new_target),)
pan_db.insert_many('views', values)
pan_db.cursor.execute('DROP TABLE views_TEMP;')
# rename tables
pan_db._exec('ALTER TABLE PC_frequencies RENAME TO gene_cluster_frequencies;')
pan_db._exec('ALTER TABLE PC_presence_absence RENAME TO gene_cluster_presence_absence;')
pan_db._exec('ALTER TABLE protein_clusters RENAME TO gene_clusters;')
# protein_cluster_id -> gene_cluster_id in table gene_clusters.
pan_db.cursor.execute('ALTER TABLE gene_clusters RENAME TO gene_clusters_TEMP;')
pan_db.cursor.execute('CREATE TABLE gene_clusters (entry_id numeric, gene_caller_id numeric, gene_cluster_id str, genome_name str, alignment_summary str);')
pan_db.cursor.execute('INSERT INTO gene_clusters(entry_id, gene_caller_id, gene_cluster_id, genome_name, alignment_summary) SELECT entry_id, gene_caller_id, protein_cluster_id, genome_name, alignment_summary FROM gene_clusters_TEMP;')
pan_db.cursor.execute('DROP TABLE gene_clusters_TEMP;')
# commit
try:
pan_db._exec('COMMIT')
except:
pass
# we also added a totally new table to this version:
pan_db.create_table(item_additional_data_table_name, item_additional_data_table_structure, item_additional_data_table_types)
# set the version
pan_db.remove_meta_key_value_pair('version')
pan_db.set_version(next_version)
# we have one more thing to do: getting rid of the 'additional_data' table without losing data, by carrying
# its content into our new item_additional_data_table
additional_data_table_dict = pan_db.get_table_as_dict('additional_data')
# close the db temporarily
pan_db.disconnect()
# update the contents of the item_additional_data_table
args = argparse.Namespace(pan_db=db_path, just_do_it=True, ignore_db_version=True)
item_additional_data_table = TableForItemAdditionalData(args)
item_additional_data_table.add(additional_data_headers, additional_data_table_dict)
# open the database again to remove stuff
pan_db = db.DB(db_path, None, ignore_version = True)
pan_db.remove_meta_key_value_pair('additional_data_headers')
pan_db._exec("DROP TABLE additional_data")
# now bye for real!
pan_db.disconnect()
progress.end()
run.info_single('Your pan db is now %s.' % next_version, nl_after=1, nl_before=1, mc='green')
