From a40538d382b334b2fcb52c1f9bccbe0533ddbaba Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 11 Nov 2020 12:55:36 -0600 Subject: Switched checking if a trait is confidential to checking if it has a pubmed ID for the purposes of showing pre-publication abbreviation/description --- wqflask/base/trait.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask/base/trait.py') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index cfc02f8b..e0afa915 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -513,7 +513,7 @@ 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: -- cgit v1.2.3 From 7a2a59f3d225f94bda5a9bc51a958d3203ea690c Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 18 Nov 2020 12:48:43 -0600 Subject: Fixed issue that was causing scatterplot cofactors to not work if the cofactors were genotypes (because it tried to get the "description_display" which doesn't exist for genotype traits) --- wqflask/base/trait.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'wqflask/base/trait.py') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index cfc02f8b..7763dbe8 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -265,11 +265,12 @@ 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 -- cgit v1.2.3 From 6ed037083f0b2bac95021e5fb00c0c8877422a47 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 18 Nov 2020 14:06:27 -0600 Subject: Fixed issue where the cofactor trait descriptions didn't work correctly for genotype/snp cofactors (the code previously only accounted for probeset/phenotype cofactors, so it was treating genotypes/snps like phenotype traits) --- wqflask/base/trait.py | 2 ++ .../new/javascript/get_traits_from_collection.js | 24 ++++++++++++++++------ 2 files changed, 20 insertions(+), 6 deletions(-) (limited to 'wqflask/base/trait.py') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 7763dbe8..0f8f937c 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -274,6 +274,8 @@ def get_sample_data(): 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( diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js index a55ab356..626357d4 100644 --- a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js +++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js @@ -201,13 +201,17 @@ populate_cofactor_info = function(trait_info) { if (trait_info['type'] == "ProbeSet"){ $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name']) $('#cofactor1_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) - } else { + } else if (trait_info['type'] == "Publish") { $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) if ('pubmed_link' in trait_info) { $('#cofactor1_description').html('PubMed: ' + trait_info['pubmed_text'] + '
' + trait_info['description']) } else { - $('#cofactor1_description').html('PubMed: ' + trait_info['pubmed_text'] + '
' + trait_info['description']) + $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor1_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) } + } else { + $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor1_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n") } $('#select_cofactor1').text("Change Cofactor 1"); $('#cofactor1_info_container').css("display", "inline"); @@ -217,13 +221,17 @@ populate_cofactor_info = function(trait_info) { if (trait_info['type'] == "ProbeSet"){ $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name']) $('#cofactor2_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) - } else { + } else if (trait_info['type'] == "Publish") { $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) if ('pubmed_link' in trait_info) { $('#cofactor2_description').html('PubMed: ' + trait_info['pubmed_text'] + '
' + trait_info['description']) } else { - $('#cofactor2_description').html('PubMed: ' + trait_info['pubmed_text'] + '
' + trait_info['description']) + $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor2_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) } + } else { + $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor2_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n") } $('#select_cofactor2').text("Change Cofactor 2"); $('#cofactor2_info_container').css("display", "inline"); @@ -233,13 +241,17 @@ populate_cofactor_info = function(trait_info) { if (trait_info['type'] == "ProbeSet"){ $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name']) $('#cofactor3_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) - } else { + } else if (trait_info['type'] == "Publish") { $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) if ('pubmed_link' in trait_info) { $('#cofactor3_description').html('PubMed: ' + trait_info['pubmed_text'] + '
' + trait_info['description']) } else { - $('#cofactor3_description').html('PubMed: ' + trait_info['pubmed_text'] + '
' + trait_info['description']) + $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor3_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) } + } else { + $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor3_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n") } $('#select_cofactor3').text("Change Cofactor 3"); $('#cofactor3_info_container').css("display", "inline"); -- cgit v1.2.3 From d0a3db3851bc2895a8775b1dc7c01a92f9c8c85c Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 7 Dec 2020 14:22:54 -0600 Subject: Changed the logic in create_trait so that permissions should always be set, and added an assert that 'name' is passed instead of using if/else, since it should always be passed --- wqflask/base/trait.py | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) (limited to 'wqflask/base/trait.py') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index ec8c40a0..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) -- cgit v1.2.3