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)
Пример #2
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()
Пример #3
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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()