o Nrf@sddlZddlZddlmZddlZddlZddlZddlm Z m Z m Z m Z m Z ddlmZeejddddejd d ddejd d dd edejddddejdddddejdddd edejddde dedddZdS)N) get_data_dir get_site_urlget_porthg_name_to_container_nameSQLITEDB)_stopz --old-hg-namezCThe name of the running higlass container that needs to be updated.F)helprequiredz--old-site-urlz_site-url at the old location. Provide this when higlass container to be updated is not running.z --old-portz[port at the old location. Provide this when higlass container to be updated is not running.80)r r defaulttypez--old-data-dirz|data directory of the higlass that is to be updated (usually 'hg-data'). Provide this when higlass container is not running.z--new-site-urlzhttp://localhostzsite-url at the new location.T)r r r z --new-portzport at the new locationz--db-backup-namezname of the database (db) backup file. db backup will be stored in the data directory provided explicitly or inferred from the running container.z.updatedc Cs|dur1zt|}t|}t|}Wn*tjjy0}ztjd|dWYd}~nd}~ww|dus9|dur=t d|dkrC|n|d|}|dkrP|n|d|} t |t } t ||} |durot |gdddzJzt| | Wnttfytjd| d | td YnwW|durtjd |d tjt} t|} | j| n%|durtjd |d tjt} t|} | j| wwd}zt| }Wn#tjy }ztjd | dtd WYd}~nd}~wwd|d| d}||}||Wdn 1s,wY|tjd| dt dtjtddS)aQUpdate stored viewconfs from one host to another The script allows one to update viewconfs saved in an existing higlass database. It does so by modifying references to tilesets that use old-site-url:old-port --> new-site-url:new-port old/new-site-urls must include schema (http, https): http://localhost http://old.host.org ... if 'old-hg-name' is provided and higlass is running, then 'old-site-url,old-port,old-data-dir' are inferred. if 'old-hg-name' is NOT provided then at least 'old-site-url'and 'old-data-dir' are required. This scenario should be invoked only when the container is not running, otherwise integrity of the DB-backup can not be guaranteed. Post 80 is default http port and both new-port and old-port defaults to it, if not specified otherwise. site-url:80 is equivalent to site-url Script keeps existing database unchanged, but modifies a backed up version located in the same path as the original one. Running higlass-container would be interrupted during database backup. NzInstance not running:  zlold-site-url and old-data-dir must be provided, when instance is not running and no old-hg-name is provided r :FzFailed to copy z to zRestarting container z ... zFailed to connect to zS UPDATE tilesets_viewconf SET viewconf = replace(viewconf,'z','z') z"Backed up version of the database z has been updated and ready for migration copy it to the new host along with the media folder rename the database file back to z and restart higlass. r)rrrdockererrorsZNotFoundsysstderrwrite ValueErroropjoinrrshutilcopyfileOSErrorIOErrorexitflushZfrom_envr containersgetZrestartsqlite3connectErrorcursorexecuteclose)Z old_hg_nameZ old_site_urlZold_portZ old_data_dirZ new_site_urlZnew_portZdb_backup_nameexorigin destinationZorigin_db_pathZupdate_db_pathclientZcontainer_nameconneZdb_querycurr.h/var/www/html/software/conda/envs/catlas/lib/python3.10/site-packages/higlass_manage/update_viewconfs.pyupdate_viewconfssb        r0)rZclickZos.pathpathrr!rrcommonrrrrrstoprcommandoptionstrr0r.r.r.r/sh