Merge pull request #230 from ICRAR/liu-354

Added parser fields to doxygen of apps

daliuge-engine/dlg/apps/archiving.py

@@ -58,7 +58,6 @@ class ExternalStoreApp(BarrierAppDROP):
     )
 
     def run(self):
-
         # Check that the constrains are correct
         if self.outputs:
             raise Exception(
@@ -85,6 +84,8 @@ def store(self, inputDrop):
 # @param category PythonApp
 # @param tag daliuge
 # @param appclass Application Class/dlg.apps.archiving.NgasArchivingApp/String/ComponentParameter/readonly//False/False/Application class
+# @param input_parser Input Parser/pickle/Select/ApplicationArgument/readwrite/raw,pickle,eval,npy,path,dataurl/False/False/Input port parsing technique
+# @param output_parser Output Parser/pickle/Select/ApplicationArgument/readwrite/raw,pickle,eval,npy,path,dataurl/False/False/Output port parsing technique
 # @param execution_time Execution Time/5/Float/ComponentParameter/readonly//False/False/Estimated execution time
 # @param num_cpus No. of CPUs/1/Integer/ComponentParameter/readonly//False/False/Number of cores used
 # @param group_start Group start/False/Boolean/ComponentParameter/readwrite//False/False/Is this node the start of a group?

daliuge-engine/dlg/apps/bash_shell_app.py

@@ -387,6 +387,8 @@ def execute(self, data):
 # @param command_line_arguments Command Line Arguments//String/ComponentParameter/readwrite//False/False/Additional command line arguments to be added to the command line to be executed
 # @param paramValueSeparator Param value separator/ /String/ComponentParameter/readwrite//False/False/Separator character(s) between parameters on the command line
 # @param argumentPrefix Argument prefix/"--"/String/ComponentParameter/readwrite//False/False/Prefix to each keyed argument on the command line
+# @param input_parser Input Parser/pickle/Select/ApplicationArgument/readwrite/raw,pickle,eval,npy,path,dataurl/False/False/Input port parsing technique
+# @param output_parser Output Parser/pickle/Select/ApplicationArgument/readwrite/raw,pickle,eval,npy,path,dataurl/False/False/Output port parsing technique
 # @param execution_time Execution Time/5/Float/ComponentParameter/readonly//False/False/Estimated execution time
 # @param num_cpus No. of CPUs/1/Integer/ComponentParameter/readonly//False/False/Number of cores used
 # @param group_start Group start/False/Boolean/ComponentParameter/readwrite//False/False/Is this node the start of a group?

daliuge-engine/dlg/apps/branch.py

@@ -2,13 +2,16 @@
 from dlg.apps.app_base import BarrierAppDROP
 from dlg.exceptions import InvalidDropException
 
+
 ##
 # @brief Branch
 # @details A conditional branch to control flow
 # @par EAGLE_START
 # @param category Branch
 # @param tag template
 # @param appclass Application Class/dlg.apps.simple.SimpleBranch/String/ComponentParameter/readonly//False/False/Application class
+# @param input_parser Input Parser/pickle/Select/ApplicationArgument/readwrite/raw,pickle,eval,npy,path,dataurl/False/False/Input port parsing technique
+# @param output_parser Output Parser/pickle/Select/ApplicationArgument/readwrite/raw,pickle,eval,npy,path,dataurl/False/False/Output port parsing technique
 # @param execution_time Execution Time/5/Float/ComponentParameter/readonly//False/False/Estimated execution time
 # @param num_cpus No. of CPUs/1/Integer/ComponentParameter/readonly//False/False/Number of cores used
 # @param group_start Group start/False/Boolean/ComponentParameter/readwrite//False/False/Is this node the start of a group?

daliuge-engine/dlg/apps/crc.py

@@ -87,6 +87,8 @@ def run(self):
 # @param category PythonApp
 # @param tag daliuge
 # @param appclass Application Class/dlg.apps.crc.CRCStreamApp/String/ComponentParameter/readonly//False/False/Application class
+# @param input_parser Input Parser/pickle/Select/ApplicationArgument/readwrite/raw,pickle,eval,npy,path,dataurl/False/False/Input port parsing technique
+# @param output_parser Output Parser/pickle/Select/ApplicationArgument/readwrite/raw,pickle,eval,npy,path,dataurl/False/False/Output port parsing technique
 # @param execution_time Execution Time/5/Float/ComponentParameter/readonly//False/False/Estimated execution time
 # @param num_cpus No. of CPUs/1/Integer/ComponentParameter/readonly//False/False/Number of cores used
 # @param group_start Group start/False/Boolean/ComponentParameter/readwrite//False/False/Is this node the start of a group?

daliuge-engine/dlg/apps/dockerapp.py

@@ -88,6 +88,8 @@ def waitForIp(self, timeout=None):
 # @param command_line_arguments Command Line Arguments//String/ComponentParameter/readwrite//False/False/Additional command line arguments to be added to the command line to be executed
 # @param paramValueSeparator Param value separator/ /String/ComponentParameter/readwrite//False/False/Separator character(s) between parameters and their respective values on the command line
 # @param argumentPrefix Argument prefix/"--"/String/ComponentParameter/readwrite//False/False/Prefix to each keyed argument on the command line
+# @param input_parser Input Parser/pickle/Select/ApplicationArgument/readwrite/raw,pickle,eval,npy,path,dataurl/False/False/Input port parsing technique
+# @param output_parser Output Parser/pickle/Select/ApplicationArgument/readwrite/raw,pickle,eval,npy,path,dataurl/False/False/Output port parsing technique
 # @param execution_time Execution Time/5/Float/ComponentParameter/readonly//False/False/Estimated execution time
 # @param num_cpus No. of CPUs/1/Integer/ComponentParameter/readonly//False/False/Number of cores used
 # @param group_start Group start/False/Boolean/ComponentParameter/readwrite//False/False/Is this node the start of a group?
@@ -239,6 +241,8 @@ def initialize(self, **kwargs):
 
         self._image = self._popArg(kwargs, "image", None)
         self._env = self._popArg(kwargs, "env", None)
+        self._inputRedirect = self._popArg(kwargs, "input_redirection", "")
+        self._outputRedirect = self._popArg(kwargs, "output_redirection", "")
         self._cmdLineArgs = self._popArg(kwargs, "command_line_arguments", "")
         self._applicationArgs = self._popArg(kwargs, "applicationArgs", {})
         self._argumentPrefix = self._popArg(kwargs, "argumentPrefix", "--")
@@ -564,6 +568,13 @@ def run(self):
                 cmd = droputils.replace_dataurl_placeholders(
                     cmd, dataURLInputs, dataURLOutputs
                 )
+                # if "output_redirection" in self._applicationArgs:
+                #     logger.debug(">>>> outport_names: %s", outport_names)
+                #     out_name = outport_names["output_redirection"]
+                #     cmd = f"{cmd} > {out_name}"
+                # if "input_redirection" in self._applicationArgs:
+                #     in_name = inport_names["input_redirection"]
+                #     cmd = f"cat {in_name} > {cmd}"
             else:
                 cmd = ""
             ###############

daliuge-engine/dlg/apps/mpi.py

@@ -31,6 +31,7 @@
 
 logger = logging.getLogger(__name__)
 
+
 ##
 # @brief MPI
 # @details An application component using the Message Passing Interface (MPI)
@@ -44,6 +45,8 @@
 # @param command_line_arguments Command Line Arguments//String/ComponentParameter/readwrite//False/False/Additional command line arguments to be added to the command line to be executed
 # @param paramValueSeparator Param value separator/ /String/ComponentParameter/readwrite//False/False/Separator character(s) between parameters on the command line
 # @param argumentPrefix Argument prefix/"--"/String/ComponentParameter/readwrite//False/False/Prefix to each keyed argument on the command line
+# @param input_parser Input Parser/pickle/Select/ApplicationArgument/readwrite/raw,pickle,eval,npy,path,dataurl/False/False/Input port parsing technique
+# @param output_parser Output Parser/pickle/Select/ApplicationArgument/readwrite/raw,pickle,eval,npy,path,dataurl/False/False/Output port parsing technique
 # @param execution_time Execution Time/5/Float/ComponentParameter/readonly//False/False/Estimated execution time
 # @param num_cpus No. of CPUs/1/Integer/ComponentParameter/readonly//False/False/Number of cores used
 # @param group_end Group end/False/Boolean/ComponentParameter/readwrite//False/False/Is this node the end of a group?

daliuge-engine/dlg/apps/scp.py

@@ -43,6 +43,8 @@
 # @param category PythonApp
 # @param tag daliuge
 # @param appclass Application Class/dlg.apps.scp.ScpApp/String/ComponentParameter/readonly//False/False/Application class
+# @param input_parser Input Parser/pickle/Select/ApplicationArgument/readwrite/raw,pickle,eval,npy,path,dataurl/False/False/Input port parsing technique
+# @param output_parser Output Parser/pickle/Select/ApplicationArgument/readwrite/raw,pickle,eval,npy,path,dataurl/False/False/Output port parsing technique
 # @param execution_time Execution Time/5/Float/ComponentParameter/readonly//False/False/Estimated execution time
 # @param num_cpus No. of CPUs/1/Integer/ComponentParameter/readonly//False/False/Number of cores used
 # @param group_start Group start/False/Boolean/ComponentParameter/readwrite//False/False/Is this node the start of a group?
@@ -110,7 +112,6 @@ def initialize(self, **kwargs):
         BarrierAppDROP.initialize(self, **kwargs)
 
     def run(self):
-
         # Check inputs/outputs are of a valid type
         for i in self.inputs + self.outputs:
             # The current only way to check if we are handling a FileDROP