forgot to add parser file

aiida_qeq/parsers/__init__.py

@@ -0,0 +1,7 @@
+# -*- coding: utf-8 -*-
+"""
+Parsers provided by aiida_qeq.
+
+Register parsers via the "aiida.parsers" entry point in setup.json.
+"""
+from __future__ import absolute_import

aiida_qeq/parsers/qeq.py

@@ -0,0 +1,86 @@
+# -*- coding: utf-8 -*-
+"""
+Parsers provided by aiida_qeq for QEQ calculations.
+
+Register parsers via the "aiida.parsers" entry point in setup.json.
+"""
+from __future__ import absolute_import
+
+from aiida.parsers.parser import Parser
+from aiida.parsers.exceptions import OutputParsingError
+
+from aiida.orm import CalculationFactory
+QeqCalculation = CalculationFactory('qeq.qeq')
+
+
+class QeqParser(Parser):
+    """
+    Parser class for parsing output of calculation.
+    """
+
+    def __init__(self, calculation):
+        """
+        Initialize Parser instance
+        """
+        super(QeqParser, self).__init__(calculation)
+
+        # check for valid input
+        if not isinstance(calculation, QeqCalculation):
+            raise OutputParsingError("Can only parse QeqCalculation")
+
+    # pylint: disable=protected-access
+    def parse_with_retrieved(self, retrieved):
+        """
+        Parse outputs, store results in database.
+
+        :param retrieved: a dictionary of retrieved nodes, where
+          the key is the link name
+        :returns: a tuple with two values ``(bool, node_list)``, 
+          where:
+
+          * ``bool``: variable to tell if the parsing succeeded
+          * ``node_list``: list of new nodes to be stored in the db
+            (as a list of tuples ``(link_name, node)``)
+        """
+        from aiida.orm import DataFactory
+
+        success = False
+        node_list = []
+
+        # Check that the retrieved folder is there
+        try:
+            out_folder = retrieved[self._calc._get_linkname_retrieved()]
+        except KeyError:
+            self.logger.error("No retrieved folder found")
+            return success, node_list
+
+        # Check the folder content is as expected
+        list_of_files = out_folder.get_folder_list()
+        output_files = self._calc.inp.configure.output_files
+        # Note: set(A) <= set(B) checks whether A is a subset
+        if set(output_files) <= set(list_of_files):
+            pass
+        else:
+            self.logger.error("Not all expected output files {} were found".
+                              format(output_files))
+
+        SinglefileData = DataFactory('singlefile')
+        CifData = DataFactory('cif')
+
+        for fname in output_files:
+            if fname == 'charges.cif':
+                # add cif file
+                cif = CifData(
+                    file=out_folder.get_abs_path(fname), parse_policy='lazy')
+                # Note: we might want to either contribute this attribute upstream
+                # or set up our own CifData class
+                cif._set_attr('partial_charge_method', 'qeq')
+                node_list.append(('structure_with_charges', cif))
+
+            else:
+                # add as singlefile
+                node = SinglefileData(file=out_folder.get_abs_path(fname))
+                node_list.append((fname, node))
+
+        success = True
+        return success, node_list