diff --git a/.bumpversion.cfg b/.bumpversion.cfg index fc2062d..e7cf612 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.8.15 +current_version = 0.8.16 commit = True tag = False diff --git a/CITATION.cff b/CITATION.cff index e21d395..d3b75bf 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -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 diff --git a/atomrdf/workflow/jobdict.yml b/atomrdf/workflow/jobdict.yml index c220b8a..e9eb973 100644 --- a/atomrdf/workflow/jobdict.yml +++ b/atomrdf/workflow/jobdict.yml @@ -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: @@ -19,6 +19,7 @@ outputs: - label: unit: value: + associate_to_sample: True workflow_manager: uri: software: diff --git a/atomrdf/workflow/workflow.py b/atomrdf/workflow/workflow.py index e69b26c..29cf660 100644 --- a/atomrdf/workflow/workflow.py +++ b/atomrdf/workflow/workflow.py @@ -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}") @@ -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) @@ -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) diff --git a/setup.py b/setup.py index 8b7d98d..b11c41b 100644 --- a/setup.py +++ b/setup.py @@ -6,7 +6,7 @@ setup( name='atomrdf', - version='0.8.15', + version='0.8.16', author='Abril Azocar Guzman, Sarath Menon', author_email='sarath.menon@pyscal.org', description='Ontology based structural manipulation and quering',