diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/GeneralObject.py | 2 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 29 |
2 files changed, 17 insertions, 14 deletions
diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py index 0122ee32..249195e2 100644 --- a/wqflask/base/GeneralObject.py +++ b/wqflask/base/GeneralObject.py @@ -28,7 +28,7 @@ class GeneralObject: """ Base class to define an Object. a = [Spam(1, 4), Spam(9, 3), Spam(4,6)] - a.sort(lambda x, y: cmp(x.eggs, y.eggs)) + a.sort(key = lambda x: x.eggs) """ def __init__(self, *args, **kw): diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index cfc02f8b..50bd8874 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -25,19 +25,19 @@ def create_trait(**kw): assert bool(kw.get('dataset')) != bool( kw.get('dataset_name')), "Needs dataset ob. or name" - if kw.get('name'): - if kw.get('dataset_name'): - if kw.get('dataset_name') != "Temp": - dataset = create_dataset(kw.get('dataset_name')) - else: - dataset = kw.get('dataset') + assert bool(kw.get('name')), "Needs trait name" + if kw.get('dataset_name'): if kw.get('dataset_name') != "Temp": - if dataset.type == 'Publish': - permissions = check_resource_availability( - dataset, kw.get('name')) - else: - permissions = check_resource_availability(dataset) + dataset = create_dataset(kw.get('dataset_name')) + else: + dataset = kw.get('dataset') + + if dataset.type == 'Publish': + permissions = check_resource_availability( + dataset, kw.get('name')) + else: + permissions = check_resource_availability(dataset) if "view" in permissions['data']: the_trait = GeneralTrait(**kw) @@ -265,14 +265,17 @@ def get_sample_data(): trait_dict['species'] = trait_ob.dataset.group.species trait_dict['url'] = url_for( 'show_trait_page', trait_id=trait, dataset=dataset) - trait_dict['description'] = trait_ob.description_display if trait_ob.dataset.type == "ProbeSet": trait_dict['symbol'] = trait_ob.symbol trait_dict['location'] = trait_ob.location_repr + trait_dict['description'] = trait_ob.description_display elif trait_ob.dataset.type == "Publish": + trait_dict['description'] = trait_ob.description_display if trait_ob.pubmed_id: trait_dict['pubmed_link'] = trait_ob.pubmed_link trait_dict['pubmed_text'] = trait_ob.pubmed_text + else: + trait_dict['location'] = trait_ob.location_repr return json.dumps([trait_dict, {key: value.value for key, value in list( @@ -513,7 +516,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): # If the dataset is confidential and the user has access to confidential # phenotype traits, then display the pre-publication description instead # of the post-publication description - if trait.confidential: + if not trait.pubmed_id: trait.abbreviation = trait.pre_publication_abbreviation trait.description_display = trait.pre_publication_description else: |