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Merge pull request #129 from pyscal/update_data_readin
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Update data readin
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srmnitc authored Jun 24, 2024
2 parents 2afeb4a + c9a0264 commit 1a42866
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Showing 5 changed files with 13 additions and 8 deletions.
2 changes: 1 addition & 1 deletion .bumpversion.cfg
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
[bumpversion]
current_version = 0.8.15
current_version = 0.8.16
commit = True
tag = False

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2 changes: 1 addition & 1 deletion CITATION.cff
Original file line number Diff line number Diff line change
Expand Up @@ -19,4 +19,4 @@ url: 'https://atomrdf.pyscal.org'
license: "MIT"
repository-code: https://github.com/pyscal/atomRDF
type: software
version: 0.8.15
version: 0.8.16
7 changes: 4 additions & 3 deletions atomrdf/workflow/jobdict.yml
Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,9 @@ intermediate: False
method: MolecularStatics/MolecularDynamics/DensityFunctionalTheory/EquationOfState/QuasiHarmonicModel
path: job path folder
dof:
- AtomicPosition
- CellVolume
- CellShape
- AtomicPositionRelaxation
- CellVolumeRelaxation
- CellShapeRelaxation
inputs:
- label:
unit:
Expand All @@ -19,6 +19,7 @@ outputs:
- label:
unit:
value:
associate_to_sample: True
workflow_manager:
uri:
software:
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8 changes: 6 additions & 2 deletions atomrdf/workflow/workflow.py
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Expand Up @@ -52,7 +52,7 @@ def inform_graph(self, pr, workflow_environment=None, workflow_module=None):
workflow_module.inform_graph(pr, self.kg)


def to_graph(self, job, workflow_environment=None, workflow_module=None, job_dicts=None, add_intermediate_jobs=False):
def to_graph(self, job=None, workflow_environment=None, workflow_module=None, job_dicts=None, add_intermediate_jobs=False):

if workflow_environment is not None:
workflow_module = importlib.import_module(f"atomrdf.workflow.{workflow_environment}.{workflow_environment}")
Expand All @@ -64,8 +64,11 @@ def to_graph(self, job, workflow_environment=None, workflow_module=None, job_dic
job_dicts = np.atleast_1d(job_dicts)

#print(job_dict)

#now we call the functions in order
for job_dict in job_dicts:
if not 'intermediate' in job_dict.keys():
job_dict['intermediate'] = False
if (not add_intermediate_jobs) and job_dict['intermediate']:
continue
job_dict = self._add_structure(job_dict)
Expand Down Expand Up @@ -310,7 +313,8 @@ def _add_method(
# add that structure was generated
self.kg.add((activity, ASMO.hasComputationalMethod, method))
self.kg.add((job_dict['sample']['final'], PROV.wasGeneratedBy, activity))
self.kg.add((activity, CMSO.hasPath, Literal(job_dict['path'], datatype=XSD.string)))
if 'path' in job_dict.keys():
self.kg.add((activity, CMSO.hasPath, Literal(job_dict['path'], datatype=XSD.string)))
self._add_inputs(job_dict, activity)
self._add_outputs(job_dict, activity)
self._add_software(job_dict, method)
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -6,7 +6,7 @@

setup(
name='atomrdf',
version='0.8.15',
version='0.8.16',
author='Abril Azocar Guzman, Sarath Menon',
author_email='[email protected]',
description='Ontology based structural manipulation and quering',
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