Merge branch 'fix-file-parser' into 'develop'

Fix previous merge

See merge request !2076

nomad/parsing/file_parser/text_parser.py

@@ -605,7 +605,7 @@ class DataTextParser(TextParser):
                     data = np.loadtxt(self.mainfile)
                 else:
                     if not self._mainfile_contents and self.mainfile_obj:
-                        with self.mainfile_obj as mainfile_obj:
+                        with self.open_mainfile_obj() as mainfile_obj:
                             self._mainfile_contents = mainfile_obj.read()
                     if self._mainfile_contents:
                         buffer = self._mainfile_contents

nomad/parsing/file_parser/vasp_parser.py

-import numpy as np
-
-import runschema
-from nomad.parsing.file_parser.mapping_parser import MappingAnnotationModel, XMLParser
-
-
-class Program(runschema.run.Program):
-    version = runschema.run.Program.version
-    version.m_annotations = dict(
-        xml=MappingAnnotationModel(
-            # path=[".i[?_name=='version']"],
-            operator=(
-                'get_version',
-                [
-                    ".i[?_name=='version']",
-                    ".i[?_name=='subversion']",
-                    ".i[?_name=='platform']",
-                ],
-            ),
-        )
-    )
-
-    # compilation_datetime = runschema.run.Program.compilation_datetime
-    # compilation_datetime.m_annotations = dict(
-    #     xml=XMLAnnotation(operator=[('get_compilation_datetime', ["i[?_name=='']"])])
-    # )
-
-
-class BandEnergies(runschema.calculation.BandEnergies):
-    n_spin_channels = runschema.calculation.BandEnergies.n_spin_channels
-    n_spin_channels.m_annotations = dict(
-        xml=MappingAnnotationModel(path='length(.array.set.set)')
-    )
-
-    n_kpoints = runschema.calculation.BandEnergies.n_kpoints
-    n_kpoints.m_annotations = dict(
-        xml=MappingAnnotationModel(path='length(.array.set.set[0].set)')
-    )
-
-    energies = runschema.calculation.BandEnergies.energies
-    energies.m_annotations = dict(
-        xml=MappingAnnotationModel(
-            operator=(
-                'get_eigenvalues_energies',
-                [
-                    '.array.set.set[].set[].r',
-                    'length(.array.set.set)',
-                    'length(.array.set.set[0].set)',
-                ],
-            ),
-        )
-    )
-
-
-class Calculation(runschema.calculation.Calculation):
-    eigenvalues = runschema.calculation.Calculation.eigenvalues
-    eigenvalues.m_annotations = dict(xml=MappingAnnotationModel(path='.eigenvalues'))
-
-
-class Run(runschema.run.Run):
-    program = runschema.run.Run.program
-    program.m_annotations = dict(xml=MappingAnnotationModel(path='.generator'))
-
-    calculation = runschema.run.Run.calculation
-    calculation.m_annotations = dict(xml=MappingAnnotationModel(path='.calculation'))
-
-
-runschema.run.Run.m_def.m_annotations = dict(
-    xml=MappingAnnotationModel(path='modeling')
-)
-
-
-class VASPXMLParser(XMLParser):
-    @staticmethod
-    def get_eigenvalues_energies(value, n_spin, n_kpoints):
-        array = np.transpose(value)[0].T
-        return np.reshape(array, (n_spin, n_kpoints, len(array[0])))
-
-    @staticmethod
-    def get_version(version, sub_version, platform):
-        return ' '.join([' '.join(s.split()) for s in [version, sub_version, platform]])
-
-    @staticmethod
-    def slice(value):
-        return np.array(value)[2:]