diff --git a/LICENSE.txt b/LICENSE.txt index 318870ade..50ebcc3d8 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -1,6 +1,6 @@ The MIT License (MIT) -Copyright (c) 2014-2018 OpenWorm +Copyright (c) 2014-2019 OpenWorm Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in diff --git a/PyOpenWorm/data_trans/data_with_evidence_ds.py b/PyOpenWorm/data_trans/data_with_evidence_ds.py index 207476b85..923114971 100644 --- a/PyOpenWorm/data_trans/data_with_evidence_ds.py +++ b/PyOpenWorm/data_trans/data_with_evidence_ds.py @@ -38,17 +38,14 @@ def __init__(self, *args, **kwargs): self.__ad_hoc_contexts = dict() self.data_context = _DataContext.contextualize(self.context)(maker=self, - imported=(CONTEXT,), - conf=self.conf) + imported=(CONTEXT,)) self.evidence_context = _EvidenceContext.contextualize(self.context)(maker=self, - imported=(CONTEXT,), - conf=self.conf) + imported=(CONTEXT,)) self.combined_context = _CombinedContext.contextualize(self.context)(maker=self, imported=(self.data_context, - self.evidence_context), - conf=self.conf) + self.evidence_context)) def data_context_for(self, **kwargs): ctx = self.context_for(**kwargs) @@ -67,16 +64,14 @@ def context_for(self, **kwargs): def commit_augment(self): saved_contexts = set([]) self.data_context.save_context(inline_imports=True, saved_contexts=saved_contexts) - # self.data_context.save_imports() self.evidence_context.save_context(inline_imports=True, saved_contexts=saved_contexts) - # self.evidence_context.save_imports() - print(self.combined_context) self.combined_context.save_imports() class _SContext(Context): def __init__(self, maker, **kwargs): - super(_SContext, self).__init__(**kwargs) + conf = kwargs.pop('conf', maker.conf) + super(_SContext, self).__init__(conf=conf, **kwargs) self.maker = maker @property diff --git a/PyOpenWorm/data_trans/excel_ds.py b/PyOpenWorm/data_trans/excel_ds.py index bae1da3d9..067719c3e 100644 --- a/PyOpenWorm/data_trans/excel_ds.py +++ b/PyOpenWorm/data_trans/excel_ds.py @@ -7,6 +7,5 @@ class XLSXHTTPFileDataSource(HTTPFileDataSource): rdf_namespace = Namespace(DS_NS['XLSXHTTPFileDataSource#']) - # column_headers = Informational(display_name='Header column names', multiple=False) - # csv_field_delimiter = Informational(display_name='Field delimiter') +__yarom_mapped_classes__ = (XLSXHTTPFileDataSource,) diff --git a/PyOpenWorm/data_trans/sci_rna_seq.py b/PyOpenWorm/data_trans/sci_rna_seq.py index 245967dee..24fccbeed 100644 --- a/PyOpenWorm/data_trans/sci_rna_seq.py +++ b/PyOpenWorm/data_trans/sci_rna_seq.py @@ -1,5 +1,3 @@ -#!/home/ubuntu/env/bin/python - from rpy2.robjects.packages import importr from rpy2.robjects import r as R from PyOpenWorm.datasource import DataTranslator, DataSource, Informational