Rename CmdlineTask's entry method runDataRef

Prepare Tasks for Gen3 PipelineTask conversion by:
* Renaming CmdlineTask's entry method to `runDataRef`.  The default
  CmdlineTask.TaskRunner now calls a Task's `runDataRef` method on the
  parsed command line inputs.
  `runDataRef` method can take any Gen2 Butler data products.
* Renaming CmdlineTasks previous core methods (e.g. assemble,
  characterize) to `run` when they exist.

python/lsst/meas/mosaic/calibrate.py

@@ -24,7 +24,7 @@ def _makeArgumentParser(cls):
                                ContainerClass=PerTractCcdDataIdContainer)
         return parser
 
-    def run(self, dataRef):
+    def runDataRef(self, dataRef):
         catalog = dataRef.get("src", immediate=True)
         calexp_md = dataRef.get('calexp_md', immediate=True)
         # Check if we are looking at HSC stack outputs
@@ -59,7 +59,7 @@ def _makeArgumentParser(cls):
                                ContainerClass=PerTractCcdDataIdContainer)
         return parser
 
-    def run(self, dataRef):
+    def runDataRef(self, dataRef):
         results = applyMosaicResultsExposure(dataRef)
         dataRef.put(results.exposure, "calibrated_exp")
 

python/lsst/meas/mosaic/checkMosaicTask.py

@@ -424,7 +424,7 @@ def writeCatalog(self, allSource, wcsDic, calibDic, ffpDic):
         outHdu.writeto("catalog_check.fits", clobber=True)
 
 
-    def check(self, dataRefList, ct=None, debug=False, verbose=False):
+    def run(self, dataRefList, ct=None, debug=False, verbose=False):
         ccdSet = self.readCcd(dataRefList)
         self.removeNonExistCcd(dataRefList, ccdSet)
 
@@ -548,7 +548,7 @@ def check(self, dataRefList, ct=None, debug=False, verbose=False):
         self.plotPosAsMag(m0_s, dx_s, dy_s)
         self.writeCatalog(allSource, wcsDic, calibDic, ffpDic)
 
-    def run(self, camera, butler, tract, dataRefList, debug):
+    def runDataRef(self, dataRefList, camera, butler, tract, debug):
 
         colorterms = ColortermLibrary()
         name = os.path.join(os.environ["OBS_SUBARU_DIR"], "config", camera, "colorterms.py")
@@ -566,7 +566,7 @@ def run(self, camera, butler, tract, dataRefList, debug):
 
         ct = colorterms.getColorterm(butler.mapper.filters[filters[0]], self.config.photoCatName)
 
-        return self.check(dataRefList, ct, debug)
+        return self.run(dataRefList, ct, debug)
 
 if __name__ == '__main__':
 

python/lsst/meas/mosaic/mosaicTask.py

@@ -46,11 +46,11 @@
 class MosaicRunner(pipeBase.TaskRunner):
     """Subclass of TaskRunner for MosaicTask
 
-    MosaicTask.run() takes a number of arguments, one of which is a list of dataRefs
-    extracted from the command line (whereas most CmdLineTasks' run methods take
+    MosaicTask.runDataRef() takes a number of arguments, one of which is a list of dataRefs
+    extracted from the command line (whereas most CmdLineTasks' runDataRef methods take
     single dataRef, are are called repeatedly).  This class transforms the processed
     arguments generated by the ArgumentParser into the arguments expected by
-    MosaicTask.run().
+    MosaicTask.runDataRef().
 
     See pipeBase.TaskRunner for more information, but note that the multiprocessing
     code path does not apply, because MosaicTask.canMultiprocess == False.
@@ -63,10 +63,10 @@ def getTargetList(parsedCmd, **kwargs):
         for ref in parsedCmd.id.refList:
             refListDict.setdefault(ref.dataId["tract"], []).append(ref)
         # we call run() once with each tract
-        return [(parsedCmd.camera,
+        return [(refListDict[tract],
+                 parsedCmd.camera,
                  parsedCmd.butler,
                  tract,
-                 refListDict[tract],
                  parsedCmd.debug,
                  parsedCmd.diagDir,
                  parsedCmd.diagnostics,
@@ -77,7 +77,7 @@ def getTargetList(parsedCmd, **kwargs):
 
     def __call__(self, args):
         task = self.TaskClass(config=self.config, log=self.log)
-        result = task.run(*args)
+        result = task.runDataRef(*args)
         return pipeBase.Struct(exitStatus=0)
 
 class MosaicConfig(pexConfig.Config):
@@ -849,8 +849,8 @@ def checkOverlapWithTract(self, tractInfo, dataRefList, verbose=False):
 
         return dataRefListOverlapWithTract, dataRefListToUse
 
-    def mosaic(self, dataRefList, tractInfo, ct=None, debug=False, diagDir=".",
-               diagnostics=False, snapshots=False, numCoresForReadSource=1, readTimeout=9999, verbose=False):
+    def run(self, dataRefList, tractInfo, ct=None, debug=False, diagDir=".",
+            diagnostics=False, snapshots=False, numCoresForReadSource=1, readTimeout=9999, verbose=False):
 
         self.log.info(str(self.config))
 
@@ -1025,8 +1025,9 @@ def mosaic(self, dataRefList, tractInfo, ct=None, debug=False, diagDir=".",
         return list(wcsDic.keys())
 
 
-    def run(self, camera, butler, tract, dataRefList, debug, diagDir=".",
-            diagnostics=False, snapshots=False, numCoresForReadSource=1, readTimeout=9999, verbose=False):
+    def runDataRef(self, dataRefList, camera, butler, tract, debug, diagDir=".",
+                   diagnostics=False, snapshots=False, numCoresForReadSource=1,
+                   readTimeout=9999, verbose=False):
         self.log.info("Running self-calibration for tract %d" % tract)
         skyMap = butler.get("deepCoadd_skyMap", immediate=True)
         tractInfo = skyMap[tract]
@@ -1050,5 +1051,5 @@ def run(self, camera, butler, tract, dataRefList, debug, diagDir=".",
             ct = None
             self.log.info("Not applying color term")
 
-        return self.mosaic(dataRefList, tractInfo, ct, debug, diagDir, diagnostics, snapshots,
-                           numCoresForReadSource, readTimeout, verbose)
+        return self.run(dataRefList, tractInfo, ct, debug, diagDir, diagnostics, snapshots,
+                        numCoresForReadSource, readTimeout, verbose)