User Story #2890 (new)
Opened 14 years ago
Last modified 12 years ago
RFE: cli scripts workflow weirdness
Reported by: | jamoore | Owned by: | |
---|---|---|---|
Priority: | minor | Milestone: | Unscheduled |
Component: | Scripting | Keywords: | n.a. |
Cc: | jburel, wmoore | Story Points: | n.a. |
Sprint: | n.a. | Importance: | n.a. |
Total Remaining Time: | n.a. | Estimated Remaining Time: | n.a. |
Description
Using session 0c388aa2-3419-49c7-9fc3-a268c71dc895 (root@localhost). Idle timeout: 10.0 min. Current group: system Traceback (most recent call last): File "bin/omero", line 152, in <module> rv = omero.cli.argv() File "/Users/moore/GlencoeSoftware.git/git/omero.git/dist/lib/python/omero/cli.py", line 1148, in argv cli.invoke(args[1:]) File "/Users/moore/GlencoeSoftware.git/git/omero.git/dist/lib/python/omero/cli.py", line 701, in invoke stop = self.onecmd(line, previous_args) File "/Users/moore/GlencoeSoftware.git/git/omero.git/dist/lib/python/omero/cli.py", line 770, in onecmd self.execute(line, previous_args) File "/Users/moore/GlencoeSoftware.git/git/omero.git/dist/lib/python/omero/cli.py", line 850, in execute args.func(args) File "/Users/moore/GlencoeSoftware.git/git/omero.git/dist/lib/python/omero/plugins/script.py", line 409, in params job_params = svc.getParams(script_id) File "/Users/moore/GlencoeSoftware.git/git/omero.git/dist/lib/python/omero_api_IScript_ice.py", line 138, in getParams return _M_omero.api.IScript._op_getParams.invoke(self, ((scriptID, ), _ctx)) omero.ValidationException: exception ::omero::ValidationException { serverStackTrace = serverExceptionClass = message = Can't find params for 19671. Stderr is in file 19672 ---stderr--- File "./script", line 34 version = "4.2.1", ^ IndentationError: unexpected indent } ~/code/git/dist $ vi lib/scripts/omero/analysis_scripts/Run_Matlab.py ~/code/git/dist $ bin/omero script params 19671 Using session 0c388aa2-3419-49c7-9fc3-a268c71dc895 (root@localhost). Idle timeout: 10.0 min. Current group: system Traceback (most recent call last): File "bin/omero", line 152, in <module> rv = omero.cli.argv() File "/Users/moore/GlencoeSoftware.git/git/omero.git/dist/lib/python/omero/cli.py", line 1148, in argv cli.invoke(args[1:]) File "/Users/moore/GlencoeSoftware.git/git/omero.git/dist/lib/python/omero/cli.py", line 701, in invoke stop = self.onecmd(line, previous_args) File "/Users/moore/GlencoeSoftware.git/git/omero.git/dist/lib/python/omero/cli.py", line 770, in onecmd self.execute(line, previous_args) File "/Users/moore/GlencoeSoftware.git/git/omero.git/dist/lib/python/omero/cli.py", line 850, in execute args.func(args) File "/Users/moore/GlencoeSoftware.git/git/omero.git/dist/lib/python/omero/plugins/script.py", line 409, in params job_params = svc.getParams(script_id) File "/Users/moore/GlencoeSoftware.git/git/omero.git/dist/lib/python/omero_api_IScript_ice.py", line 138, in getParams return _M_omero.api.IScript._op_getParams.invoke(self, ((scriptID, ), _ctx)) omero.InternalException: exception ::omero::InternalException { serverStackTrace = serverExceptionClass = message = Sha1s don't match! expected 57894b6fdfc03c42577f69e3e85b1ccb82ede8e4, found 143f40280bdb25b9002143fc5d325546c4831da6 } ~/code/git/dist $ bin/omero script disable 19671 Using session 0c388aa2-3419-49c7-9fc3-a268c71dc895 (root@localhost). Idle timeout: 10.0 min. Current group: system Disabled 19671 by setting mimetype to text/plain /code/git/dist $ bin/omero script replace 19671 lib/scripts/omero/analysis_scripts/Run_Matlab.py Using session 0c388aa2-3419-49c7-9fc3-a268c71dc895 (root@localhost). Idle timeout: 10.0 min. Current group: system ~/code/git/dist $ bin/omero script params 19671 Using session 0c388aa2-3419-49c7-9fc3-a268c71dc895 (root@localhost). Idle timeout: 10.0 min. Current group: system id: 19671 name: Run_Matlab.py version: 4.2.1 authors: institutions: description: PSLID/Matlab integration. namespaces: stdout: text/plain stderr: text/plain inputs: Image_ID - ID of a valid image Optional: False Type: ::omero::RLong Min: Max: Values: outputs:
~/code/git/dist $ bin/omero script edit 19671 lib/scripts/omero/analysis_scripts/Run_Matlab.py usage: bin/omero script edit [-h] original_file bin/omero script edit: error: unrecognized arguments: lib/scripts/omero/analysis_scripts/Run_Matlab.py ~/code/git/dist $ bin/omero script edit 19671 Using session 0c388aa2-3419-49c7-9fc3-a268c71dc895 (root@localhost). Idle timeout: 10.0 min. Current group: system Failed to find script: 19671 (exception ::omero::ValidationException { serverStackTrace = serverExceptionClass = message = Can't find params for 19671. Stderr is in file 19677 ---stderr--- Traceback (most recent call last): File "./script", line 193, in <module> client = setup() File "./script", line 36, in setup optional = true, NameError: global name 'true' is not defined }) ~/code/git/dist $ bin/omero script edit 19671 Using session 0c388aa2-3419-49c7-9fc3-a268c71dc895 (root@localhost). Idle timeout: 10.0 min. Current group: system Failed to find script: 19671 (exception ::omero::ValidationException { serverStackTrace = serverExceptionClass = message = Can't find params for 19671. No stderr }) ~/code/git/dist $ bin/omero script edit 19671 Using session 0c388aa2-3419-49c7-9fc3-a268c71dc895 (root@localhost). Idle timeout: 10.0 min. Current group: system Failed to find script: 19671 (exception ::omero::ValidationException { serverStackTrace = serverExceptionClass = message = Can't find params for 19671. No stderr }) ~/code/git/dist $ vi lib/scripts/omero/analysis_scripts/Run_Matlab.py ~/code/git/dist $
Change History (5)
comment:1 Changed 12 years ago by jmoore
- Milestone changed from Unscheduled to OMERO-Beta4.4
- Owner set to jmoore
- Remaining Time set to 0.25
- Sprint set to 2012-01-17 (6)
- Status changed from new to accepted
comment:2 Changed 12 years ago by jmoore
- Cc jburel wmoore added
Similar to #2845, this would be helped somewhat if either we mentioned a warning (e.g. "You're file has changed. Do X to refresh it") If we do a refresh automatically, then the id will no longer be present, and a "No processor available" will be thrown. If we do an in-place refresh, then the user will not be getting the script they think they are getting. Thoughts?
comment:3 Changed 12 years ago by jmoore
- Owner jmoore deleted
- Status changed from accepted to new
comment:4 Changed 12 years ago by jmoore
- Milestone changed from OMERO-Beta4.4 to Unscheduled
- Sprint 2012-01-17 (6) deleted
- Summary changed from Bug: cli scripts workflow weirdness to RFE: cli scripts workflow weirdness
- Type changed from Task to User Story
After looking into #2845, it's clear that for the workflow to be more usable, there need to be a few features added to the service:
- list --all to display non-script files
- edit --overwrite to fix bad files
- possibly some kind of "status", including which files have params, etc.
comment:5 Changed 12 years ago by jmoore <josh@…>
(In [5cd136469e7860291011f97947c04b8213087c56/ome.git] on branch develop) Add help message on bad edit (Fix #2845, See #2890)
Investigating...