Merge pull request #409 from djarecka/mnt/wf_run

[mnt] changes in the run methods

Author: djarecka

pydra/engine/core.py

@@ -433,15 +433,15 @@ def _run(self, rerun=False, **kwargs):
         lockfile = self.cache_dir / (checksum + ".lock")
         # Eagerly retrieve cached - see scenarios in __init__()
         self.hooks.pre_run(self)
-        # adding info file with the checksum in case the task was cancelled
-        # and the lockfile has to be removed
-        with open(self.cache_dir / f"{self.uid}_info.json", "w") as jsonfile:
-            json.dump({"checksum": self.checksum}, jsonfile)
         with SoftFileLock(lockfile):
             if not (rerun or self.task_rerun):
                 result = self.result()
                 if result is not None:
                     return result
+            # adding info file with the checksum in case the task was cancelled
+            # and the lockfile has to be removed
+            with open(self.cache_dir / f"{self.uid}_info.json", "w") as jsonfile:
+                json.dump({"checksum": self.checksum}, jsonfile)
             # Let only one equivalent process run
             odir = self.output_dir
             if not self.can_resume and odir.exists():
@@ -965,11 +965,6 @@ async def _run(self, submitter=None, rerun=False, **kwargs):
                 "Workflow output cannot be None, use set_output to define output(s)"
             )
         checksum = self.checksum
-        # Eagerly retrieve cached
-        if not (rerun or self.task_rerun):
-            result = self.result()
-            if result is not None:
-                return result
         # creating connections that were defined after adding tasks to the wf
         for task in self.graph.nodes:
             # if workflow has task_rerun=True and propagate_rerun=True,
@@ -981,15 +976,18 @@ async def _run(self, submitter=None, rerun=False, **kwargs):
                     task.propagate_rerun = self.propagate_rerun
             task.cache_locations = task._cache_locations + self.cache_locations
             self.create_connections(task)
-        # TODO add signal handler for processes killed after lock acquisition
-        # adding info file with the checksum in case the task was cancelled
-        # and the lockfile has to be removed
-        with open(self.cache_dir / f"{self.uid}_info.json", "w") as jsonfile:
-            json.dump({"checksum": checksum}, jsonfile)
         lockfile = self.cache_dir / (checksum + ".lock")
         self.hooks.pre_run(self)
         with SoftFileLock(lockfile):
-            # # Let only one equivalent process run
+            # retrieve cached results
+            if not (rerun or self.task_rerun):
+                result = self.result()
+                if result is not None:
+                    return result
+            # adding info file with the checksum in case the task was cancelled
+            # and the lockfile has to be removed
+            with open(self.cache_dir / f"{self.uid}_info.json", "w") as jsonfile:
+                json.dump({"checksum": checksum}, jsonfile)
             odir = self.output_dir
             if not self.can_resume and odir.exists():
                 shutil.rmtree(odir)
@@ -1015,6 +1013,8 @@ async def _run(self, submitter=None, rerun=False, **kwargs):
                 (self.cache_dir / f"{self.uid}_info.json").unlink()
                 os.chdir(cwd)
         self.hooks.post_run(self, result)
+        if result is None:
+            raise Exception("This should never happen, please open new issue")
         return result
 
     async def _run_task(self, submitter, rerun=False):

pydra/engine/helpers.py

@@ -109,6 +109,8 @@ def load_result(checksum, cache_locations):
     """
     if not cache_locations:
         return None
+    # TODO: if there are issues with loading, we might need to
+    # TODO: sleep and repeat loads (after checkin that there are no lock files!)
     for location in cache_locations:
         if (location / checksum).exists():
             result_file = location / checksum / "_result.pklz"