Fix parsers

edan-bainglass · Feb 7, 2024 · 217618b · 217618b
1 parent 3bfa248
commit 217618b
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Showing 11 changed files with 75 additions and 26 deletions.
diff --git a/examples/coulomb_blockade/tester.ipynb b/examples/coulomb_blockade/tester.ipynb
@@ -30,8 +30,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "DATA_DIR = Path(\"data\")\n",
-    "NPROCS = 4"
+    "DATA_DIR = Path(\"pentacene/data\")\n",
+    "NPROCS = 1"
    ]
   },
   {

diff --git a/src/aiida_quantum_transport/calculations/dft.py b/src/aiida_quantum_transport/calculations/dft.py
@@ -66,6 +66,12 @@ def define(cls, spec: CalcJobProcessSpec) -> None:
                 help=f"The {file} file",
             )
 
+        spec.exit_code(
+            400,
+            "ERROR_ACCESSING_OUTPUT_FILE",
+            "an issue occurred while accessing an expected retrieved file",
+        )
+
     def prepare_for_submission(self, folder: Folder) -> CalcInfo:
         """docstring"""
 

diff --git a/src/aiida_quantum_transport/calculations/dmft.py b/src/aiida_quantum_transport/calculations/dmft.py
@@ -134,6 +134,12 @@ def define(cls, spec: CalcJobProcessSpec) -> None:
             help="The sigma folder",
         )
 
+        spec.exit_code(
+            400,
+            "ERROR_ACCESSING_OUTPUT_FILE",
+            "an issue occurred while accessing an expected retrieved file",
+        )
+
     def prepare_for_submission(self, folder: Folder) -> CalcInfo:
         """docstring"""
 

diff --git a/src/aiida_quantum_transport/calculations/hybridize.py b/src/aiida_quantum_transport/calculations/hybridize.py
@@ -127,6 +127,12 @@ def define(cls, spec: CalcJobProcessSpec) -> None:
             help="The occupancies file",
         )
 
+        spec.exit_code(
+            400,
+            "ERROR_ACCESSING_OUTPUT_FILE",
+            "an issue occurred while accessing an expected retrieved file",
+        )
+
     def prepare_for_submission(self, folder: Folder) -> CalcInfo:
         """docstring"""
 

diff --git a/src/aiida_quantum_transport/calculations/localize.py b/src/aiida_quantum_transport/calculations/localize.py
@@ -73,6 +73,12 @@ def define(cls, spec: CalcJobProcessSpec) -> None:
             help="The transformed hamiltonian file",
         )
 
+        spec.exit_code(
+            400,
+            "ERROR_ACCESSING_OUTPUT_FILE",
+            "an issue occurred while accessing an expected retrieved file",
+        )
+
     def prepare_for_submission(self, folder: Folder) -> CalcInfo:
         """docstring"""
 

diff --git a/src/aiida_quantum_transport/calculations/transmission.py b/src/aiida_quantum_transport/calculations/transmission.py
@@ -97,6 +97,12 @@ def define(cls, spec: CalcJobProcessSpec) -> None:
             help="The transmission folder",
         )
 
+        spec.exit_code(
+            400,
+            "ERROR_ACCESSING_OUTPUT_FILE",
+            "an issue occurred while accessing an expected retrieved file",
+        )
+
     def prepare_for_submission(self, folder: Folder) -> CalcInfo:
         """docstring"""
 

diff --git a/src/aiida_quantum_transport/parsers/dft.py b/src/aiida_quantum_transport/parsers/dft.py
@@ -19,9 +19,12 @@ class DFTParser(Parser):
     def parse(self, **kwargs) -> ExitCode | None:
         """docstring"""
 
-        for label, filename in self._OUTPUT_FILE_MAPPING.items():
-            path = Path(self.node.get_remote_workdir()) / filename
-            output_label = f"{label}_file"
-            self.out(output_label, orm.SinglefileData(path))
+        try:
+            with self.retrieved.as_path() as retrieved_path:
+                for label, filename in self._OUTPUT_FILE_MAPPING.items():
+                    path = Path(retrieved_path) / filename
+                    self.out(f"{label}_file", orm.SinglefileData(path))
+        except OSError:
+            return self.exit_codes.ERROR_ACCESSING_OUTPUT_FILE
 
         return None
diff --git a/src/aiida_quantum_transport/parsers/dmft.py b/src/aiida_quantum_transport/parsers/dmft.py
@@ -13,16 +13,22 @@ class DMFTParser(Parser):
     def parse(self, **kwargs) -> ExitCode | None:
         """docstring"""
 
-        path = Path(self.node.get_remote_workdir()) / "delta_folder"
-        self.out("delta_folder", orm.FolderData(tree=path))
+        try:
+            with self.retrieved.as_path() as retrieved_path:
+                root = Path(retrieved_path)
 
-        path = Path(self.node.get_remote_workdir()) / "sigma_folder"
-        self.out("sigma_folder", orm.FolderData(tree=path))
+                path = root / "delta_folder"
+                self.out("delta_folder", orm.FolderData(tree=path))
 
-        adjust_mu: orm.Bool = self.node.inputs.adjust_mu
+                path = root / "sigma_folder"
+                self.out("sigma_folder", orm.FolderData(tree=path))
 
-        if adjust_mu.value:
-            path = Path(self.node.get_remote_workdir()) / "mu.txt"
-            self.out("mu_file", orm.SinglefileData(path))
+                adjust_mu: orm.Bool = self.node.inputs.adjust_mu
+
+                if adjust_mu.value:
+                    path = root / "mu.txt"
+                    self.out("mu_file", orm.SinglefileData(path))
+        except OSError:
+            return self.exit_codes.ERROR_ACCESSING_OUTPUT_FILE
 
         return None
diff --git a/src/aiida_quantum_transport/parsers/hybridize.py b/src/aiida_quantum_transport/parsers/hybridize.py
@@ -10,7 +10,7 @@
 class HybridizationParser(Parser):
     """docstring"""
 
-    _OUTPUT_FILE_LIST = [
+    _OUTPUT_FILES = [
         "hybridization.bin",
         "energies.npy",
         "hamiltonian.npy",
@@ -23,10 +23,13 @@ class HybridizationParser(Parser):
     def parse(self, **kwargs) -> ExitCode | None:
         """docstring"""
 
-        for filename in self._OUTPUT_FILE_LIST:
-            path = Path(self.node.get_remote_workdir()) / filename
-            prefix = filename.split(".")[0]
-            output_label = f"{prefix}_file"
-            self.out(output_label, orm.SinglefileData(path))
+        try:
+            with self.retrieved.as_path() as retrieved_path:
+                for filename in self._OUTPUT_FILES:
+                    path = Path(retrieved_path) / filename
+                    prefix = filename.split(".")[0]
+                    self.out(f"{prefix}_file", orm.SinglefileData(path))
+        except OSError:
+            return self.exit_codes.ERROR_ACCESSING_OUTPUT_FILE
 
         return None
diff --git a/src/aiida_quantum_transport/parsers/localize.py b/src/aiida_quantum_transport/parsers/localize.py
@@ -18,9 +18,12 @@ class LocalizationParser(Parser):
     def parse(self, **kwargs) -> ExitCode | None:
         """docstring"""
 
-        for label, filename in self._OUTPUT_FILE_MAPPING.items():
-            path = Path(self.node.get_remote_workdir()) / filename
-            output_label = f"{label}_file"
-            self.out(output_label, orm.SinglefileData(path))
+        try:
+            with self.retrieved.as_path() as retrieved_path:
+                for label, filename in self._OUTPUT_FILE_MAPPING.items():
+                    path = Path(retrieved_path) / filename
+                    self.out(f"{label}_file", orm.SinglefileData(path))
+        except OSError:
+            return self.exit_codes.ERROR_ACCESSING_OUTPUT_FILE
 
         return None
diff --git a/src/aiida_quantum_transport/parsers/transmission.py b/src/aiida_quantum_transport/parsers/transmission.py
@@ -13,7 +13,11 @@ class TransmissionParser(Parser):
     def parse(self, **kwargs) -> ExitCode | None:
         """docstring"""
 
-        path = Path(self.node.get_remote_workdir()) / "transmission_folder"
-        self.out("transmission_folder", orm.FolderData(tree=path))
+        try:
+            with self.retrieved.as_path() as retrieved_path:
+                path = Path(retrieved_path) / "transmission_folder"
+                self.out("transmission_folder", orm.FolderData(tree=path))
+        except OSError:
+            return self.exit_codes.ERROR_ACCESSING_OUTPUT_FILE
 
         return None