diff options
Diffstat (limited to 'wqflask/base/trait.py')
| -rw-r--r-- | wqflask/base/trait.py | 89 |
1 files changed, 13 insertions, 76 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 41e2603c..d09cfd40 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -51,7 +51,7 @@ def create_trait(**kw): return None -class GeneralTrait(object): +class GeneralTrait: """ Trait class defines a trait in webqtl, can be either Microarray, Published phenotype, genotype, or user input trait @@ -337,74 +337,10 @@ def jsonable(trait): dataset_name=dataset.shortname, location=trait.location_repr ) - else: - return dict() - - -def jsonable_table_row(trait, dataset_name, index): - """Return a list suitable for json and intended to be displayed in a table - - Actual turning into json doesn't happen here though""" - - dataset = create_dataset(dataset_name) - - if dataset.type == "ProbeSet": - if trait.mean == "": - mean = "N/A" - else: - mean = "%.3f" % round(float(trait.mean), 2) - if trait.additive == "": - additive = "N/A" - else: - additive = "%.3f" % round(float(trait.additive), 2) - return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', - index, - '<a href="/show_trait?trait_id=' + - str(trait.name)+'&dataset='+dataset.name + - '">'+str(trait.name)+'</a>', - trait.symbol, - trait.description_display, - trait.location_repr, - mean, - trait.LRS_score_repr, - trait.LRS_location_repr, - additive] - elif dataset.type == "Publish": - if trait.additive == "": - additive = "N/A" - else: - additive = "%.2f" % round(float(trait.additive), 2) - if trait.pubmed_id: - return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', - index, - '<a href="/show_trait?trait_id=' + - str(trait.name)+'&dataset='+dataset.name + - '">'+str(trait.name)+'</a>', - trait.description_display, - trait.authors, - '<a href="' + trait.pubmed_link + '">' + trait.pubmed_text + '</href>', - trait.LRS_score_repr, - trait.LRS_location_repr, - additive] - else: - return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', - index, - '<a href="/show_trait?trait_id=' + - str(trait.name)+'&dataset='+dataset.name + - '">'+str(trait.name)+'</a>', - trait.description_display, - trait.authors, - trait.pubmed_text, - trait.LRS_score_repr, - trait.LRS_location_repr, - additive] - elif dataset.type == "Geno": - return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', - index, - '<a href="/show_trait?trait_id=' + - str(trait.name)+'&dataset='+dataset.name + - '">'+str(trait.name)+'</a>', - trait.location_repr] + elif dataset.name == "Temp": + return dict(name=trait.name, + dataset="Temp", + dataset_name="Temp") else: return dict() @@ -516,10 +452,11 @@ 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 - trait.description_display = "" + trait.description_display = "N/A" if not trait.pubmed_id: trait.abbreviation = trait.pre_publication_abbreviation - trait.description_display = trait.pre_publication_description + if trait.pre_publication_description: + trait.description_display = trait.pre_publication_description else: trait.abbreviation = trait.post_publication_abbreviation if description: @@ -542,9 +479,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): else: description_display = trait.symbol - if (str(description_display or "") != "" and - description_display != 'N/A' and - str(target_string or "") != "" and target_string != 'None'): + if (str(description_display or "") != "" + and description_display != 'N/A' + and str(target_string or "") != "" and target_string != 'None'): description_display = description_display + '; ' + target_string.strip() # Save it for the jinja2 template @@ -638,6 +575,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if str(trait.lrs or "") != "": trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs else: - raise KeyError(repr(trait.name) + - ' information is not found in the database.') + raise KeyError(repr(trait.name) + + ' information is not found in the database.') return trait |