Dear Patryk, Mathias As promised, I had some free time today after the talks, so here is the initial sample script to sync patients and studies from an Orthanc that can be run in a cronjob at operating system level.
We'll work more on health_orthanc, to get more return codes, and details and pass them to the script, but is a good start :) Once you have your Orthanc server label setup, you can invoke the script as follow: Usage : sync_orthanc_server <hostname> <port> <user> <password> <dbname> <orthanc_server_label> For example: python ./sync_orthanc_server.py localhost 8000 admin gnusolidario health42 FAA (where "FAA" correspond to the given label at GNU Health. The expected output would be something like... Connecting to GNU Health Server http://admin:gnusolidario@localhost:8000/health42/ Connected ! Last index: 2843 Last Synced on: 2023-05-24 21:39:58 Orthanc Server URL: https://demo.orthanc-server.com At GNU Health HMIS Tryton server, you would get this type of output. 2255 37818935296 [2023-05-24 21:39:47,263] INFO apiron.client GET https://demo.orthanc-server.com/changes/?since=2200&limit=100 2255 37818935296 [2023-05-24 21:39:47,857] INFO apiron.client 200 ... trytond.modules.health_orthanc.health_orthanc <FAA> at newest change 2255 37818935296 [2023-05-24 21:39:50,048] INFO apiron.client GET https://demo.orthanc-server.com/patients/46e6332c-677825b6-202fcf7c-f787bc5f-7b07c382/ 2255 37818935296 [2023-05-24 21:39:52,800] INFO apiron.client 200 https://demo.orthanc-server.com/patients/0946fcb6-cf12ab43-bad958c1-bf057ad5-0fc6f54c/ 2255 37818935296 [2023-05-24 21:39:52,804] INFO apiron.client GET ... 2255 37818935296 [2023-05-24 21:39:58,972] INFO And at the end of the run, the result: <FAA> sync complete: 8 new patients, 0 update patients, 8 new studies, 0 updated studies You can find the latest version of the script at our GNU Savannah mercurial repository (development branch): https://hg.savannah.gnu.org/hgweb/health/file/tip/tryton/doc/samples/interfaces/orthanc Let me know how it went Have a great day! Luis On Fri, 19 May 2023 11:37:58 +0200 p.ro...@stud.uni-hannover.de <p.ro...@stud.uni-hannover.de> wrote: > Hello Mathias, > > there were 2 reasons why I decided to use low-level programming. In > the module "health_orthanc" a button for the one-time manual > synchronisation is already provided and therefore I thought it would > be useful to have the synchronisation in one place to increase the > usability. The other reason is that I saw in the wiki > (https://en.wikibooks.org/wiki/GNU_Health/Imaging) that there should > already be a tryton cronjob by activating the module. But since this > is not the case, I thought that maybe there were problems with the > execution of the cronjob. If you think that the solution with the use > of the cronjob should actually be feasible, I would be grateful for > feedback. > > Best regards > Patryk > > > > * p.ro...@stud.uni-hannover.de: " [Health-dev] Integration of Orthanc > (module health_orthanc)" (Wed, 17 May 2023 16:53:01 +0200): > > Hello Patryk, > > is there any special reason to do this via low level programming? > > Usually regular returning tasks are performed with the included > scheduler (cron). It also offers to run the task manually once. You > can have a look at the Tryton core modules 'stock' or > 'account_payment_stripe' to find examples. > > Best > Mathias > > > > Hello dear GNU Health community , > > > > I am currently writing my master thesis and trying to implement a > > periodic synchronisation of the Orthanc and GNU Health DB. > > Unfortunately I run into some problems. I create a background > > thread in which the synchronisation should be done periodically. My > > idea was to initialise the variable "sync_thread = None" in the > > class "OrthancServerConfig" in order to be able to start and stop > > the synchronisation via a start and stop button. In addition, I use > > the already implemented method "sync" of the same class. I have > > already tried this: > > > > class SyncThread(threading.Thread): > > """A background thread that periodically synchronizes data with > > an Orthanc server.""" def __init__(self, servers=None, timeout=180): > > """ > > Initialize the SyncThread object as a background service. > > :param servers: A list of Orthanc servers. > > :type servers: list > > :param timeout: The time interval (in seconds) between each > > synchronization. :type timeout: int > > """ > > threading.Thread.__init__(self, > > name="OrthancPeriodicSyncronizationThread") self.daemon = True > > self.servers = servers > > self.timeout = timeout > > self.stop_event = threading.Event() > > > > def run(self): > > """Call loop with timeout to synchronize the Orthanc DB > > with the GNU Health DB.""" with Transaction().start(): <-- > > (line in which error 1 occurs) while not self.stop_event.is_set(): > > OrthancServerConfig.sync(self.servers) > > self.stop_event.wait(self.timeout) > > > > def stop(self): > > """Stop the synchronization thread.""" > > self.stop_event.set() > > > > > > Class OrthancServerConfig(ModelSQL, ModelView): > > sync_thread = None > > ... > > @classmethod > > @ModelView.button > > def start_periodic_sync(cls, servers): > > """ > > Initializes the synchronization of data with Orthanc as a > > background service. :param servers: A list of Orthanc servers. > > :type servers: list > > """ > > if cls.sync_thread is not None: > > raise UserWarning("Synchronization is already running!") > > else: > > cls.sync_thread = SyncThread(servers=servers) > > cls.sync_thread.start() > > > > @classmethod > > @ModelView.button > > def stop_periodic_sync(cls): <-- (error 2 occurs here, when > > "stop"-button is pressed) """ > > Stop the synchronization thread. > > """ > > if cls.sync_thread is None: > > raise UserWarning("No synchronization is performed!") > > else: > > cls.sync_thread.stop() > > cls.sync_thread.join() > > cls.sync_thread = None > > > > 2 errors occur, for which I unfortunately don't know an answer to > > fix them. Error 1 occurs, when the "start" button is pressed and > > the "run"-method of the class "SyncThread" is triggered: > > orthanc/health_orthanc.py", line 66, in run with > > Transaction().start(): TypeError: Transaction.start() missing 2 > > required positional arguments: 'database_name' and 'user' I'm not > > sure, if "with Transaction.start():" is necessary here, but i tried > > this, because i got this error before: orthanc/health_orthanc.py", > > line 269, in sync pool = Pool() File > > "/opt/gnuhealth/venv/lib/python3.10/site-packages/trytond/pool.py", > > line 61, in __new__ database_name = Transaction().database.name > > AttributeError: 'NoneType' object has no attribute 'name' If "with > > Transaction.start():" is required, unfortunately I wasn't able to > > figure out which are the two required arguments or if the solution > > is generally in a completely different direction. > > > > The second error occurs, when the "stop" button is pressed: > > TypeError: OrthancServerConfig.stop_periodic_sync() takes 1 > > positional argument but 2 were given Here I was also not able to > > interpret the error, because both my button and the stop method are > > not passed 2 arguments. > > > > I would be grateful for any help and am available for queries! > > > > Best regards, > > Patryk > > > > > > -- > > Mathias Behrle > MBSolutions > Gilgenmatten 10 A > D-79114 Freiburg > > Tel: +49(761)471023 > Fax: +49(761)4770816 > http://www.m9s.biz > UStIdNr: DE 142009020 > PGP/GnuPG key availabable from any keyserver, ID: 0xD6D09BE48405BBF6 > AC29 7E5C 46B9 D0B6 1C71 7681 D6D0 9BE4 8405 BBF6 > >
