omero.api

Interface _IScriptOperations

All Superinterfaces:

_ServiceInterfaceOperations

All Known Subinterfaces:

IScript

All Known Implementing Classes:

_IScriptDisp, _IScriptTie, ScriptI

public interface _IScriptOperations
extends _ServiceInterfaceOperations

Utility service for managing and launching scripts for execution by the Processor API. Typical usage might include (PYTHON):

 
 sf = client.createSession()
 svc = sf.getScriptService()
 scripts = svc.getScripts()

 if len(scripts) >= 1:
 script_id = svc.keys()\[-1]
 else:
 script_id = svc.uploadScript('/test/my_script.py', SCRIPT_TEXT)

 params = svc.getParams(script_id)

 # You will need to parse the params to create the proper input
 inputs = {}

 # The last parameter is how long to wait as an RInt
 proc = svc.runScript(script_id, inputs, None)
 try:
 cb = omero.scripts.ProcessCallbackI(client, proc)
 while not cb.block(1000): # ms.
 pass
 cb.close()
 rv = proc.getResults(0)
 finally:
 proc.close(False)
 
 

See OMERO.scripts for more information.

Method Summary

Modifier and Type	Method and Description
void	canRunScript_async(AMD_IScript_canRunScript __cb, long scriptID, Ice.Current __current) Returns true if there is a processor which will run the given script.
void	deleteScript_async(AMD_IScript_deleteScript __cb, long scriptID, Ice.Current __current) Delete the script on the server with id.
void	editScript_async(AMD_IScript_editScript __cb, OriginalFile fileObject, java.lang.String scriptText, Ice.Current __current) Modify the text for the given script object.
void	getParams_async(AMD_IScript_getParams __cb, long scriptID, Ice.Current __current) Get the parameters that the script takes and returns, along with other metadata available from the script.
void	getScriptID_async(AMD_IScript_getScriptID __cb, java.lang.String path, Ice.Current __current) Get the id of an official script by the script path.
void	getScripts_async(AMD_IScript_getScripts __cb, Ice.Current __current) This method returns official server scripts as a list of OriginalFile objects.
void	getScriptsByMimetype_async(AMD_IScript_getScriptsByMimetype __cb, java.lang.String mimetype, Ice.Current __current) This method returns official server scripts identified with the specified extension as a list of OriginalFile objects.
void	getScriptText_async(AMD_IScript_getScriptText __cb, long scriptID, Ice.Current __current) Get the text from the server for the script with given id.
void	getScriptWithDetails_async(AMD_IScript_getScriptWithDetails __cb, long scriptID, Ice.Current __current) Get the script from the server with details from OriginalFile
void	getUserScripts_async(AMD_IScript_getUserScripts __cb, java.util.List<IObject> acceptsList, Ice.Current __current) Returns non-official scripts which have been uploaded by individual users.
void	runScript_async(AMD_IScript_runScript __cb, long scriptID, java.util.Map<java.lang.String,RType> inputs, RInt waitSecs, Ice.Current __current) If ResourceError is thrown, then no Processor is available.
void	uploadOfficialScript_async(AMD_IScript_uploadOfficialScript __cb, java.lang.String path, java.lang.String scriptText, Ice.Current __current) Like uploadScript but is only callable by administrators.
void	uploadScript_async(AMD_IScript_uploadScript __cb, java.lang.String path, java.lang.String scriptText, Ice.Current __current) Upload a user script to the server and return the id.
void	validateScript_async(AMD_IScript_validateScript __cb, Job j, java.util.List<IObject> acceptsList, Ice.Current __current) Used internally by processor.py to check if the script attached to the Job has a valid script attached, based on the acceptsList and the current security context.

Method Detail

getScripts_async

void getScripts_async(AMD_IScript_getScripts __cb,
                      Ice.Current __current)
               throws ServerError

This method returns official server scripts as a list of OriginalFile objects. These scripts will be executed by the server if submitted via runScript. The input parameters necessary for proper functioning can be retrieved via getParams. The OriginalFile.path value can be used in other official scripts via the language specific import command, since the script directory will be placed on the appropriate environment path variable.

 
 scripts = scriptService.getScripts()
 for script in scripts:
 text = scriptService.getScriptText(script.id.val)
 # First character is a "/" symbol
 path = script.path.val\[1:\]
 path = path.replace("/",".")
 print "Possible import: %s" % path
 
 

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ApiUsageException

SecurityViolation

ServerError

getScriptsByMimetype_async

void getScriptsByMimetype_async(AMD_IScript_getScriptsByMimetype __cb,
                                java.lang.String mimetype,
                                Ice.Current __current)
                         throws ServerError

This method returns official server scripts identified with the specified extension as a list of OriginalFile objects. These scripts will be executed by the server if submitted via runScript. The input parameters necessary for proper functioning can be retrieved via getParams. The OriginalFile.path value can be used in other official scripts via the language specific import command, since the script directory will be placed on the appropriate environment path variable.

 
 scripts = scriptService.getScripts("py")
 for script in scripts:
 text = scriptService.getScriptText(script.id.val)
 path = script.path.val\[1:\] # First symbol is a "/"
 path = path.replace("/",".")
 print "Possible import: %s" % path
 
 

Parameters:

__cb - The callback object for the operation.

mimetype - the mimetype identifying the scripts.

__current - The Current object for the invocation.

Throws:

ApiUsageException

SecurityViolation

ServerError

getUserScripts_async

void getUserScripts_async(AMD_IScript_getUserScripts __cb,
                          java.util.List<IObject> acceptsList,
                          Ice.Current __current)
                   throws ServerError

Returns non-official scripts which have been uploaded by individual users. These scripts will not be run by the server, though a user can start a personal usermode processor which will allow the scripts to be executed. This is particularly useful for testing new scripts.

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError

getScriptID_async

void getScriptID_async(AMD_IScript_getScriptID __cb,
                       java.lang.String path,
                       Ice.Current __current)
                throws ServerError

Get the id of an official script by the script path. The script service ensures that all script paths are unique. Note: there is no similar method for user scripts (e.g. getUserScriptID) since the path is not guaranteed to be unique.

Parameters:

__cb - The callback object for the operation.

path - The name of the script.

__current - The Current object for the invocation.

Throws:

ApiUsageException

SecurityViolation

ServerError

getScriptText_async

void getScriptText_async(AMD_IScript_getScriptText __cb,
                         long scriptID,
                         Ice.Current __current)
                  throws ServerError

Get the text from the server for the script with given id.

Parameters:

__cb - The callback object for the operation.

scriptID - see above.

__current - The Current object for the invocation.

Throws:

ApiUsageException

ServerError

uploadScript_async

void uploadScript_async(AMD_IScript_uploadScript __cb,
                        java.lang.String path,
                        java.lang.String scriptText,
                        Ice.Current __current)
                 throws ServerError

Upload a user script to the server and return the id. This method checks that a script with that names does not exist and that the script has parameters if possible, i.e. a usermode processor is running which for the current user.

Parameters:

__cb - The callback object for the operation.

path - see above.

__current - The Current object for the invocation.

Throws:

ApiUsageException

SecurityViolation

ServerError

uploadOfficialScript_async

void uploadOfficialScript_async(AMD_IScript_uploadOfficialScript __cb,
                                java.lang.String path,
                                java.lang.String scriptText,
                                Ice.Current __current)
                         throws ServerError

Like uploadScript but is only callable by administrators. The parameters for the script are also checked.

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError

editScript_async

void editScript_async(AMD_IScript_editScript __cb,
                      OriginalFile fileObject,
                      java.lang.String scriptText,
                      Ice.Current __current)
               throws ServerError

Modify the text for the given script object.

Parameters:

__cb - The callback object for the operation.

fileObject - see above.

__current - The Current object for the invocation.

Throws:

ApiUsageException

SecurityViolation

ServerError

getScriptWithDetails_async

void getScriptWithDetails_async(AMD_IScript_getScriptWithDetails __cb,
                                long scriptID,
                                Ice.Current __current)
                         throws ServerError

Get the script from the server with details from OriginalFile

Parameters:

__cb - The callback object for the operation.

scriptID - see above

__current - The Current object for the invocation.

Throws:

ApiUsageException

ServerError

getParams_async

void getParams_async(AMD_IScript_getParams __cb,
                     long scriptID,
                     Ice.Current __current)
              throws ServerError

Get the parameters that the script takes and returns, along with other metadata available from the script.

Parameters:

__cb - The callback object for the operation.

scriptID - see above.

__current - The Current object for the invocation.

Throws:

ApiUsageException

ServerError

deleteScript_async

void deleteScript_async(AMD_IScript_deleteScript __cb,
                        long scriptID,
                        Ice.Current __current)
                 throws ServerError

Delete the script on the server with id. The file will also be removed from disk.

Parameters:

__cb - The callback object for the operation.

scriptID - Id of the script to delete.

__current - The Current object for the invocation.

Throws:

ApiUsageException

SecurityViolation

ServerError

runScript_async

void runScript_async(AMD_IScript_runScript __cb,
                     long scriptID,
                     java.util.Map<java.lang.String,RType> inputs,
                     RInt waitSecs,
                     Ice.Current __current)
              throws ServerError

If ResourceError is thrown, then no Processor is available. Use scheduleJob to create a ScriptJob in the Waiting state. A Processor may become available.

 
 try:
 proc = scriptService.runScript(1, {}, None)
 except ResourceError:
 job = scriptService.scheduleScript(1, {}, None)
 
 

The ScriptProcess proxy MUST be closed before exiting. If you would like the script execution to continue in the background, pass True as the argument.

 
 try:
 proc.poll()         # See if process is finished
 finally:
 proc.close(True)    # Detach and execution can continue
 # proc.close(False) # OR script is immediately stopped.
 
 

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError

canRunScript_async

void canRunScript_async(AMD_IScript_canRunScript __cb,
                        long scriptID,
                        Ice.Current __current)
                 throws ServerError

Returns true if there is a processor which will run the given script.

Either the script is an official script and this method will return true (though an individual invocation may fail with an ResourceError for some reason) or this is a user script, and a usermode processor must be active which takes the scripts user or group.

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError

validateScript_async

void validateScript_async(AMD_IScript_validateScript __cb,
                          Job j,
                          java.util.List<IObject> acceptsList,
                          Ice.Current __current)
                   throws ServerError

Used internally by processor.py to check if the script attached to the Job has a valid script attached, based on the acceptsList and the current security context. An example of an acceptsList might be

Experimenter(myUserId, False)

, meaning that only scripts belonging to me should be trusted. An empty list implies that the server should return what it would by default trust. A valid script will be returned if it exists; otherwise null.

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError