Assay improvements - issues #369, #370

.travis.yml

@@ -11,9 +11,9 @@ install:
 - pip install --upgrade pip && pip install -r requirements.txt
 - pip install tox-travis
 script:
-#- flake8 --show-source --exclude=.svn,CVS,.bzr,.hg,.git,isatab_configurator.py,study_design_wizard.py isatools
+#- flake8 --show-source --exclude=.svn,CVS,.bzr,.hg,.git,isatab_configurator.py isatools
 - behave --no-capture --no-capture-stderr --format=progress features/isa-file-handler.feature
-- python -m unittest discover -s tests/
+- travis_wait python -m unittest discover -s tests/
 - coverage run -m unittest discover -s tests/
 - coverage report -m
 branches:

isatools/create/assay_templates.py

@@ -1,4 +1,4 @@
-from isatools.create.models import *
+from isatools.create.model import *
 
 NAME = 'name'
 

isatools/create/connectors.py

@@ -1,5 +1,5 @@
 from isatools.model import OntologyAnnotation, OntologySource, FactorValue, Characteristic
-from isatools.create.models import StudyDesign, NonTreatment, Treatment, StudyCell, StudyArm, SampleAndAssayPlan
+from isatools.create.model import StudyDesign, NonTreatment, Treatment, StudyCell, StudyArm, SampleAndAssayPlan
 from isatools.create.constants import SCREEN, INTERVENTIONS, BASE_FACTORS, SAMPLE, ORGANISM_PART
 from collections import OrderedDict
 
@@ -209,7 +209,7 @@ def _generate_characteristics_from_observational_factor(observational_factor_dic
 
 def generate_assay_ord_dict_from_config(datascriptor_assay_config, arm_name, epoch_no):
     res = OrderedDict()
-    res['name'] = datascriptor_assay_config['name']
+    res['id'], res['name'] = datascriptor_assay_config['id'], datascriptor_assay_config['name']
     res['measurement_type'] = _map_ontology_annotation(
         datascriptor_assay_config['measurement_type'], expand_strings=True
     )