Checking for orphaned files using pre-pull captured files... taking a really long time... any way to speed this up?

[anibal2j]

I am using 3.5.2 and the checking of orphaned files is taking a really long time.

In my case I'm using mirthsync to get a dump of all teh mirth configuration and then upload it all to github.

I'm not sure if I need to use the orphan checker or not.

[jessesaga]

If you're just pulling the config and uploading to Github you could probably just get by with pulling to a fresh clean empty directory each time and then committing to Github. In other words....just delete everything in your local Git checkout before the pull, then git add all the pulled files, and commit and push. It sounds like the orphaned detection logic could use some improvement, though. How many channels are you working with and how long does it take? Jesse Dowell Partner | Saga Healthcare IT https://www.saga-it.com <https://saga-it.com/> office: (888) 879-0132 x700 cell: (540) 327-8669

…

On Thu, Apr 9, 2026 at 7:26 PM anibal2j ***@***.***> wrote: I am using 3.5.2 and the checking of orphaned files is taking a really long time. In my case I'm using mirthsync to get a dump of all teh mirth configuration and then upload it all to github. I'm not sure if I need to use the orphan checker or not. — Reply to this email directly, view it on GitHub <#79>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGUTJ66DDOMTW2TH3TYKRDL4VBEUVAVCNFSM6AAAAACXTHDMBCVHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZZHA2TKNBTG4> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[anibal2j]

Hi, I'm not an expert in git, but if I do what you suggest wouldn't I lose the diffs between the changes? I use mirthsync to keep a copy of the configuration in gh but also to see what changed - even if I don't have a commit message, knowing what files changed and when has been a life saver for me; so I wouldn't want to lose that capability. I have 179 channels right now. here's the output of my script - let me know if you want to see it - which basically does the git thing and calls mirthsync - here's where you see that the orphan step starts at 22:30:16 and ends at 22:34:17 (4 minutes): (CMD) ***@***.***:/opt/scripts/mirthsync$ $SCRIPTS/mirthsync/git-cron-anibal.sh Already on 'last_backup' Your branch is up to date with 'origin/last_backup'. [2026-04-13 22:30:08] /usr/bin/java [2026-04-13 22:30:08] found java executable in PATH [2026-04-13 22:30:08] version 17.0.18 [2026-04-13 22:30:09] Authenticating to server at https://10.0.34.11:8443/api as backupuser [2026-04-13 22:30:10] Downloading from https://10.0.34.11:8443/api/server/configurationMap to /opt/scripts/mirthsync/backups/ [2026-04-13 22:30:11] Downloading from https://10.0.34.11:8443/api/server/globalScripts to /opt/scripts/mirthsync/backups/GlobalScripts [2026-04-13 22:30:11] Downloading from https://10.0.34.11:8443/api/server/resources to /opt/scripts/mirthsync/backups/ [2026-04-13 22:30:11] Downloading from https://10.0.34.11:8443/api/codeTemplateLibraries to /opt/scripts/mirthsync/backups/CodeTemplates [2026-04-13 22:30:11] Downloading from https://10.0.34.11:8443/api/codeTemplates to /opt/scripts/mirthsync/backups/CodeTemplates [2026-04-13 22:30:11] Downloading from https://10.0.34.11:8443/api/channelgroups to /opt/scripts/mirthsync/backups/Channels [2026-04-13 22:30:12] Downloading from https://10.0.34.11:8443/api/channels to /opt/scripts/mirthsync/backups/Channels [2026-04-13 22:30:16] Downloading from https://10.0.34.11:8443/api/alerts to /opt/scripts/mirthsync/backups/Alerts [2026-04-13 22:30:16] Checking for orphaned files using pre-pull captured files... [2026-04-13 22:34:17] No orphaned files found. [2026-04-13 22:34:17] Finished! [last_backup 7af09aa] Mirth changes found on 2026-04-13 22:30:08 24 files changed, 815 insertions(+), 285 deletions(-) create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From PACS - HX report to IO.xml create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From PACS - HX report to IO/DeployScript.js create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From PACS - HX report to IO/PostprocessingScript.js create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From PACS - HX report to IO/PreprocessingScript.js create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From PACS - HX report to IO/UndeployScript.js create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From PACS - HX report to IO/sourceConnector-transformer-step-0.js Enumerating objects: 57, done. Counting objects: 100% (57/57), done. Delta compression using up to 2 threads Compressing objects: 100% (33/33), done. Writing objects: 100% (33/33), 4.99 KiB | 4.99 MiB/s, done. Total 33 (delta 29), reused 0 (delta 0), pack-reused 0 remote: Resolving deltas: 100% (29/29), completed with 23 local objects. To github.com:anibal2j/mirth_sync.git 6cd5864..7af09aa last_backup -> last_backup Thanks, -- Anibal Jodorcovsky <https://www.linkedin.com/in/anibalj/> - Health Informatics Consultant ***@***.*** - 514-949-8028

…

On Mon, Apr 13, 2026 at 1:06 PM jessesaga ***@***.***> wrote: If you're just pulling the config and uploading to Github you could probably just get by with pulling to a fresh clean empty directory each time and then committing to Github. In other words....just delete everything in your local Git checkout before the pull, then git add all the pulled files, and commit and push. It sounds like the orphaned detection logic could use some improvement, though. How many channels are you working with and how long does it take? Jesse Dowell Partner | Saga Healthcare IT https://www.saga-it.com <https://saga-it.com/> office: (888) 879-0132 x700 cell: (540) 327-8669 On Thu, Apr 9, 2026 at 7:26 PM anibal2j ***@***.***> wrote: > I am using 3.5.2 and the checking of orphaned files is taking a really > long time. > > In my case I'm using mirthsync to get a dump of all teh mirth > configuration and then upload it all to github. > > I'm not sure if I need to use the orphan checker or not. > > — > Reply to this email directly, view it on GitHub > <#79>, or > unsubscribe > < https://github.com/notifications/unsubscribe-auth/AGUTJ66DDOMTW2TH3TYKRDL4VBEUVAVCNFSM6AAAAACXTHDMBCVHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZZHA2TKNBTG4> > . > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> > — Reply to this email directly, view it on GitHub <#79 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKBSGDJK2IFL6X7UIG3A2UD4VUNARAVCNFSM6AAAAACXTHDMBCVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTMNJUGY4DSOA> . You are receiving this because you authored the thread.Message ID: ***@***.*** com>

[jessesaga]

As long as the mirthsync target directory isn't used for any other purpose (README files or any other files not originally created by mirthsync) and as long as you're careful not to delete the .git index directory, you should be fine with the approach I described. Git will notice any differences in the pulled files and ignore unchanged files (even though they were deleted and then re-added). 4 minutes seems excessive. Let's keep this issue open and I'll look into ways to improve performance.

…

On Mon, Apr 13, 2026 at 8:35 PM anibal2j ***@***.***> wrote: Hi, I'm not an expert in git, but if I do what you suggest wouldn't I lose the diffs between the changes? I use mirthsync to keep a copy of the configuration in gh but also to see what changed - even if I don't have a commit message, knowing what files changed and when has been a life saver for me; so I wouldn't want to lose that capability. I have 179 channels right now. here's the output of my script - let me know if you want to see it - which basically does the git thing and calls mirthsync - here's where you see that the orphan step starts at 22:30:16 and ends at 22:34:17 (4 minutes): (CMD) ***@***.***:/opt/scripts/mirthsync$ $SCRIPTS/mirthsync/git-cron-anibal.sh Already on 'last_backup' Your branch is up to date with 'origin/last_backup'. [2026-04-13 22:30:08] /usr/bin/java [2026-04-13 22:30:08] found java executable in PATH [2026-04-13 22:30:08] version 17.0.18 [2026-04-13 22:30:09] Authenticating to server at https://10.0.34.11:8443/api as backupuser [2026-04-13 22:30:10] Downloading from https://10.0.34.11:8443/api/server/configurationMap to /opt/scripts/mirthsync/backups/ [2026-04-13 22:30:11] Downloading from https://10.0.34.11:8443/api/server/globalScripts to /opt/scripts/mirthsync/backups/GlobalScripts [2026-04-13 22:30:11] Downloading from https://10.0.34.11:8443/api/server/resources to /opt/scripts/mirthsync/backups/ [2026-04-13 22:30:11] Downloading from https://10.0.34.11:8443/api/codeTemplateLibraries to /opt/scripts/mirthsync/backups/CodeTemplates [2026-04-13 22:30:11] Downloading from https://10.0.34.11:8443/api/codeTemplates to /opt/scripts/mirthsync/backups/CodeTemplates [2026-04-13 22:30:11] Downloading from https://10.0.34.11:8443/api/channelgroups to /opt/scripts/mirthsync/backups/Channels [2026-04-13 22:30:12] Downloading from https://10.0.34.11:8443/api/channels to /opt/scripts/mirthsync/backups/Channels [2026-04-13 22:30:16] Downloading from https://10.0.34.11:8443/api/alerts to /opt/scripts/mirthsync/backups/Alerts [2026-04-13 22:30:16] Checking for orphaned files using pre-pull captured files... [2026-04-13 22:34:17] No orphaned files found. [2026-04-13 22:34:17] Finished! [last_backup 7af09aa] Mirth changes found on 2026-04-13 22:30:08 24 files changed, 815 insertions(+), 285 deletions(-) create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From PACS - HX report to IO.xml create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From PACS - HX report to IO/DeployScript.js create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From PACS - HX report to IO/PostprocessingScript.js create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From PACS - HX report to IO/PreprocessingScript.js create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From PACS - HX report to IO/UndeployScript.js create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From PACS - HX report to IO/sourceConnector-transformer-step-0.js Enumerating objects: 57, done. Counting objects: 100% (57/57), done. Delta compression using up to 2 threads Compressing objects: 100% (33/33), done. Writing objects: 100% (33/33), 4.99 KiB | 4.99 MiB/s, done. Total 33 (delta 29), reused 0 (delta 0), pack-reused 0 remote: Resolving deltas: 100% (29/29), completed with 23 local objects. To github.com:anibal2j/mirth_sync.git 6cd5864..7af09aa last_backup -> last_backup Thanks, -- Anibal Jodorcovsky <https://www.linkedin.com/in/anibalj/> - Health Informatics Consultant ***@***.*** - 514-949-8028 On Mon, Apr 13, 2026 at 1:06 PM jessesaga ***@***.***> wrote: > If you're just pulling the config and uploading to Github you could > probably just get by with pulling to a fresh clean empty directory each > time and then committing to Github. In other words....just delete > everything in your local Git checkout before the pull, then git add all > the > pulled files, and commit and push. > > It sounds like the orphaned detection logic could use some improvement, > though. How many channels are you working with and how long does it take? > > Jesse Dowell > > Partner | Saga Healthcare IT > > https://www.saga-it.com <https://saga-it.com/> > > office: (888) 879-0132 x700 > > cell: (540) 327-8669 > > > On Thu, Apr 9, 2026 at 7:26 PM anibal2j ***@***.***> wrote: > > > I am using 3.5.2 and the checking of orphaned files is taking a really > > long time. > > > > In my case I'm using mirthsync to get a dump of all teh mirth > > configuration and then upload it all to github. > > > > I'm not sure if I need to use the orphan checker or not. > > > > — > > Reply to this email directly, view it on GitHub > > <#79>, or > > unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/AGUTJ66DDOMTW2TH3TYKRDL4VBEUVAVCNFSM6AAAAACXTHDMBCVHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZZHA2TKNBTG4> > > > . > > You are receiving this because you are subscribed to this thread.Message > > ID: ***@***.***> > > > > — > Reply to this email directly, view it on GitHub > < #79 (comment)>, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AKBSGDJK2IFL6X7UIG3A2UD4VUNARAVCNFSM6AAAAACXTHDMBCVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTMNJUGY4DSOA> > . > You are receiving this because you authored the thread.Message ID: > ***@***.*** > com> > — Reply to this email directly, view it on GitHub <#79 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGUTJ64ZMKK64DQ7YEWRYND4VWPWTAVCNFSM6AAAAACXTHDMBCVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTMNJVGEYDMMY> . You are receiving this because you commented.Message ID: ***@***.*** com>

[anibal2j]

Hi, I'll leave my side setup as is for now, with everything the same and let me know as soon as you have a new version that I can test with, and I can try it in side-by-side with the current one. If you notice there's not much gains then I'll consider a re-write with your proposal. Thanks, -- Anibal Jodorcovsky <https://www.linkedin.com/in/anibalj/> - Health Informatics Consultant ***@***.*** - 514-949-8028

…

On Tue, Apr 14, 2026 at 12:42 PM jessesaga ***@***.***> wrote: As long as the mirthsync target directory isn't used for any other purpose (README files or any other files not originally created by mirthsync) and as long as you're careful not to delete the .git index directory, you should be fine with the approach I described. Git will notice any differences in the pulled files and ignore unchanged files (even though they were deleted and then re-added). 4 minutes seems excessive. Let's keep this issue open and I'll look into ways to improve performance. On Mon, Apr 13, 2026 at 8:35 PM anibal2j ***@***.***> wrote: > Hi, > > I'm not an expert in git, but if I do what you suggest wouldn't I lose the > diffs between the changes? I use mirthsync to keep a copy of the > configuration in gh but also to see what changed - even if I don't have a > commit message, knowing what files changed and when has been a life saver > for me; so I wouldn't want to lose that capability. > > I have 179 channels right now. > > here's the output of my script - let me know if you want to see it - which > basically does the git thing and calls mirthsync - here's where you see > that the orphan step starts at 22:30:16 and ends at 22:34:17 (4 minutes): > > (CMD) ***@***.***:/opt/scripts/mirthsync$ > $SCRIPTS/mirthsync/git-cron-anibal.sh > Already on 'last_backup' > Your branch is up to date with 'origin/last_backup'. > [2026-04-13 22:30:08] /usr/bin/java > [2026-04-13 22:30:08] found java executable in PATH > [2026-04-13 22:30:08] version 17.0.18 > [2026-04-13 22:30:09] Authenticating to server at > https://10.0.34.11:8443/api as backupuser > [2026-04-13 22:30:10] Downloading from > https://10.0.34.11:8443/api/server/configurationMap to > /opt/scripts/mirthsync/backups/ > [2026-04-13 22:30:11] Downloading from > https://10.0.34.11:8443/api/server/globalScripts to > /opt/scripts/mirthsync/backups/GlobalScripts > [2026-04-13 22:30:11] Downloading from > https://10.0.34.11:8443/api/server/resources to > /opt/scripts/mirthsync/backups/ > [2026-04-13 22:30:11] Downloading from > https://10.0.34.11:8443/api/codeTemplateLibraries to > /opt/scripts/mirthsync/backups/CodeTemplates > [2026-04-13 22:30:11] Downloading from > https://10.0.34.11:8443/api/codeTemplates to > /opt/scripts/mirthsync/backups/CodeTemplates > [2026-04-13 22:30:11] Downloading from > https://10.0.34.11:8443/api/channelgroups to > /opt/scripts/mirthsync/backups/Channels > [2026-04-13 22:30:12] Downloading from > https://10.0.34.11:8443/api/channels > to /opt/scripts/mirthsync/backups/Channels > [2026-04-13 22:30:16] Downloading from https://10.0.34.11:8443/api/alerts > to /opt/scripts/mirthsync/backups/Alerts > [2026-04-13 22:30:16] Checking for orphaned files using pre-pull captured > files... > [2026-04-13 22:34:17] No orphaned files found. > [2026-04-13 22:34:17] Finished! > [last_backup 7af09aa] Mirth changes found on 2026-04-13 22:30:08 > 24 files changed, 815 insertions(+), 285 deletions(-) > create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From > PACS - HX report to IO.xml > create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From > PACS - HX report to IO/DeployScript.js > create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From > PACS - HX report to IO/PostprocessingScript.js > create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From > PACS - HX report to IO/PreprocessingScript.js > create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From > PACS - HX report to IO/UndeployScript.js > create mode 100644 Channels/Intelerad (PACS %2F InteleOrchestrator)/From > PACS - HX report to IO/sourceConnector-transformer-step-0.js > Enumerating objects: 57, done. > Counting objects: 100% (57/57), done. > Delta compression using up to 2 threads > Compressing objects: 100% (33/33), done. > Writing objects: 100% (33/33), 4.99 KiB | 4.99 MiB/s, done. > Total 33 (delta 29), reused 0 (delta 0), pack-reused 0 > remote: Resolving deltas: 100% (29/29), completed with 23 local objects. > To github.com:anibal2j/mirth_sync.git > 6cd5864..7af09aa last_backup -> last_backup > > Thanks, > -- > Anibal Jodorcovsky <https://www.linkedin.com/in/anibalj/> - Health > Informatics Consultant > ***@***.*** - 514-949-8028 > > > On Mon, Apr 13, 2026 at 1:06 PM jessesaga ***@***.***> wrote: > > > If you're just pulling the config and uploading to Github you could > > probably just get by with pulling to a fresh clean empty directory each > > time and then committing to Github. In other words....just delete > > everything in your local Git checkout before the pull, then git add all > > the > > pulled files, and commit and push. > > > > It sounds like the orphaned detection logic could use some improvement, > > though. How many channels are you working with and how long does it > take? > > > > Jesse Dowell > > > > Partner | Saga Healthcare IT > > > > https://www.saga-it.com <https://saga-it.com/> > > > > office: (888) 879-0132 x700 > > > > cell: (540) 327-8669 > > > > > > On Thu, Apr 9, 2026 at 7:26 PM anibal2j ***@***.***> wrote: > > > > > I am using 3.5.2 and the checking of orphaned files is taking a really > > > long time. > > > > > > In my case I'm using mirthsync to get a dump of all teh mirth > > > configuration and then upload it all to github. > > > > > > I'm not sure if I need to use the orphan checker or not. > > > > > > — > > > Reply to this email directly, view it on GitHub > > > <#79>, or > > > unsubscribe > > > < > > > https://github.com/notifications/unsubscribe-auth/AGUTJ66DDOMTW2TH3TYKRDL4VBEUVAVCNFSM6AAAAACXTHDMBCVHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZZHA2TKNBTG4> > > > > > > . > > > You are receiving this because you are subscribed to this > thread.Message > > > ID: ***@***.***> > > > > > > > — > > Reply to this email directly, view it on GitHub > > < > #79 (comment)>, > > > or unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/AKBSGDJK2IFL6X7UIG3A2UD4VUNARAVCNFSM6AAAAACXTHDMBCVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTMNJUGY4DSOA> > > > . > > You are receiving this because you authored the thread.Message ID: > > ***@***.*** > > com> > > > > — > Reply to this email directly, view it on GitHub > < #79 (comment)>, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AGUTJ64ZMKK64DQ7YEWRYND4VWPWTAVCNFSM6AAAAACXTHDMBCVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTMNJVGEYDMMY> > . > You are receiving this because you commented.Message ID: > ***@***.*** > com> > — Reply to this email directly, view it on GitHub <#79 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKBSGDMZWZGY6DIOC3RIYPL4VZS7JAVCNFSM6AAAAACXTHDMBCVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTMNJVHE2DINY> . You are receiving this because you authored the thread.Message ID: ***@***.*** com>