def main():
if len(sys.argv) < 2:
print "Usage: python %s <Tool shed config file>" % sys.argv[0]
sys.exit(0)
now = strftime("%Y-%m-%d %H:%M:%S")
print " "
print "##########################################"
print "%s - Migrating current tool archives to new tool repositories" % now
# tool_shed_wsgi.ini file
ini_file = sys.argv[1]
conf_parser = ConfigParser.ConfigParser({'here': os.getcwd()})
conf_parser.read(ini_file)
try:
db_conn_str = conf_parser.get("app:main", "database_connection")
except ConfigParser.NoOptionError:
db_conn_str = conf_parser.get("app:main", "database_file")
print 'DB Connection: ', db_conn_str
# Instantiate app
configuration = {}
for key, value in conf_parser.items("app:main"):
configuration[key] = value
app = galaxy.webapps.tool_shed.app.UniverseApplication(global_conf=dict(__file__=ini_file), **configuration)
sa_session = app.model.context
# Remove the hgweb.config file if it exists
hgweb_config = "%s/hgweb.config" % os.getcwd()
if os.path.exists(hgweb_config):
print "Removing old file: ", hgweb_config
os.remove(hgweb_config)
repo_records = 0
rca_records = 0
rra_records = 0
for repo in sa_session.query(app.model.Repository):
# Remove the hg repository from disk. We have to be careful here, because old
# tool files exist in app.config.file_path/tools and we don't want to delete them
dir = os.path.join(app.config.file_path, *directory_hash_id(repo.id))
if os.path.exists(dir):
print "Removing old repository file directory: ", dir
shutil.rmtree(dir)
# Delete all records from db tables:
# repository_category_association, repository_rating_association, repository
print "Deleting db records for repository: ", repo.name
for rca in repo.categories:
sa_session.delete(rca)
rca_records += 1
for rra in repo.ratings:
sa_session.delete(rra)
rra_records += 1
sa_session.delete(repo)
repo_records += 1
sa_session.flush()
print "Deleted %d rows from the repository table" % repo_records
print "Deleted %d rows from the repository_category_association table" % rca_records
print "Deleted %d rows from the repository_rating_association table" % rra_records
# Migrate database tool, tool category and tool rating records to new
# database repository, repository category and repository rating records
# and create the hg repository on disk for each.
for tool in get_approved_tools(app, sa_session):
create_repository_from_tool(app, sa_session, tool)
# Add, commit and push all valid versions of each approved tool to the
# associated hg repository.
for tool in get_approved_tools(app, sa_session):
add_tool_files_to_repository(app, sa_session, tool)
app.shutdown()
print ' '
print 'Migration to next gen tool shed complete...'
print "##########################################"
sys.exit(0)
for rca in repo.categories:
sa_session.delete(rca)
rca_records += 1
for rra in repo.ratings:
sa_session.delete(rra)
rra_records += 1
sa_session.delete(repo)
repo_records += 1
sa_session.flush()
print "Deleted %d rows from the repository table" % repo_records
print "Deleted %d rows from the repository_category_association table" % rca_records
print "Deleted %d rows from the repository_rating_association table" % rra_records
# Migrate database tool, tool category and tool rating records to new
# database repository, repository category and repository rating records
# and create the hg repository on disk for each.
for tool in get_approved_tools(app, sa_session):
create_repository_from_tool(app, sa_session, tool)
# Add, commit and push all valid versions of each approved tool to the
# associated hg repository.
for tool in get_approved_tools(app, sa_session):
add_tool_files_to_repository(app, sa_session, tool)
app.shutdown()
print ' '
print 'Migration to next gen tool shed complete...'
print "##########################################"
sys.exit(0)
if __name__ == "__main__":
main()
def main():
if len(sys.argv) < 2:
print("Usage: python %s <Tool shed config file>" % sys.argv[0])
sys.exit(0)
now = strftime("%Y-%m-%d %H:%M:%S")
print()
print("##########################################")
print("%s - Migrating current tool archives to new tool repositories" % now)
# tool_shed_wsgi.ini file
ini_file = sys.argv[1]
conf_parser = configparser.ConfigParser({'here': os.getcwd()})
conf_parser.read(ini_file)
try:
db_conn_str = conf_parser.get("app:main", "database_connection")
except configparser.NoOptionError:
db_conn_str = conf_parser.get("app:main", "database_file")
print('DB Connection: ', db_conn_str)
# Instantiate app
configuration = {}
for key, value in conf_parser.items("app:main"):
configuration[key] = value
app = galaxy.webapps.tool_shed.app.UniverseApplication(global_conf=dict(__file__=ini_file), **configuration)
sa_session = app.model.context
# Remove the hgweb.config file if it exists
hgweb_config = "%s/hgweb.config" % os.getcwd()
if os.path.exists(hgweb_config):
print("Removing old file: ", hgweb_config)
os.remove(hgweb_config)
repo_records = 0
rca_records = 0
rra_records = 0
for repo in sa_session.query(app.model.Repository):
# Remove the hg repository from disk. We have to be careful here, because old
# tool files exist in app.config.file_path/tools and we don't want to delete them
dir = os.path.join(app.config.file_path, *directory_hash_id(repo.id))
if os.path.exists(dir):
print("Removing old repository file directory: ", dir)
shutil.rmtree(dir)
# Delete all records from db tables:
# repository_category_association, repository_rating_association, repository
print("Deleting db records for repository: ", repo.name)
for rca in repo.categories:
sa_session.delete(rca)
rca_records += 1
for rra in repo.ratings:
sa_session.delete(rra)
rra_records += 1
sa_session.delete(repo)
repo_records += 1
sa_session.flush()
print("Deleted %d rows from the repository table" % repo_records)
print("Deleted %d rows from the repository_category_association table" % rca_records)
print("Deleted %d rows from the repository_rating_association table" % rra_records)
# Migrate database tool, tool category and tool rating records to new
# database repository, repository category and repository rating records
# and create the hg repository on disk for each.
for tool in get_approved_tools(app, sa_session):
create_repository_from_tool(app, sa_session, tool)
# Add, commit and push all valid versions of each approved tool to the
# associated hg repository.
for tool in get_approved_tools(app, sa_session):
add_tool_files_to_repository(app, sa_session, tool)
app.shutdown()
print()
print('Migration to next gen tool shed complete...')
print("##########################################")
sys.exit(0)
print "Deleting db records for repository: ", repo.name
for rca in repo.categories:
sa_session.delete( rca )
rca_records += 1
for rra in repo.ratings:
sa_session.delete( rra )
rra_records += 1
sa_session.delete( repo )
repo_records += 1
sa_session.flush()
print "Deleted %d rows from the repository table" % repo_records
print "Deleted %d rows from the repository_category_association table" % rca_records
print "Deleted %d rows from the repository_rating_association table" % rra_records
# Migrate database tool, tool category and tool rating records to new
# database repository, repository category and repository rating records
# and create the hg repository on disk for each.
for tool in get_approved_tools( app, sa_session ):
create_repository_from_tool( app, sa_session, tool )
# Add, commit and push all valid versions of each approved tool to the
# associated hg repository.
for tool in get_approved_tools( app, sa_session ):
add_tool_files_to_repository( app, sa_session, tool )
app.shutdown()
print ' '
print 'Migration to next gen tool shed complete...'
print "##########################################"
sys.exit(0)
if __name__ == "__main__":
main()