From aaf6b8d79396c8f77099a4fc01f9e69d01d6a903 Mon Sep 17 00:00:00 2001 From: Christian Date: Thu, 28 May 2020 17:31:27 -0500 Subject: Use the proxy in trait.py --- wqflask/base/trait.py | 100 +++++++++++++++++++++++++++----------------------- 1 file changed, 55 insertions(+), 45 deletions(-) (limited to 'wqflask/base') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index e454c593..a710f98f 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -179,7 +179,7 @@ class GeneralTrait(object): fmt += (' on the minus strand ') return fmt - + def retrieve_sample_data(trait, dataset, samplelist=None): if samplelist == None: samplelist = [] @@ -233,14 +233,14 @@ def get_sample_data(): trait_dict['pubmed_text'] = trait_ob.pubmed_text return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }]) - + def jsonable(trait): """Return a dict suitable for using as json Actual turning into json doesn't happen here though""" dataset = create_dataset(dataset_name = trait.dataset.name, dataset_type = trait.dataset.type, group_name = trait.dataset.group.name) - + if dataset.type == "ProbeSet": return dict(name=trait.name, symbol=trait.symbol, @@ -294,7 +294,7 @@ def jsonable_table_row(trait, dataset_name, index): Actual turning into json doesn't happen here though""" dataset = create_dataset(dataset_name) - + if dataset.type == "ProbeSet": if trait.mean == "": mean = "N/A" @@ -310,7 +310,7 @@ def jsonable_table_row(trait, dataset_name, index): trait.symbol, trait.description_display, trait.location_repr, - mean, + mean, trait.LRS_score_repr, trait.LRS_location_repr, additive] @@ -349,36 +349,43 @@ def jsonable_table_row(trait, dataset_name, index): def retrieve_trait_info(trait, dataset, get_qtl_info=False): assert dataset, "Dataset doesn't exist" - + if dataset.type == 'Publish': - query = """ - SELECT - PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID, - Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description, - Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean, - Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users, - Publication.Authors, Publication.Title, Publication.Abstract, - Publication.Journal, Publication.Volume, Publication.Pages, - Publication.Month, Publication.Year, PublishXRef.Sequence, - Phenotype.Units, PublishXRef.comments - FROM - PublishXRef, Publication, Phenotype, PublishFreeze, InbredSet - WHERE - PublishXRef.Id = %s AND - Phenotype.Id = PublishXRef.PhenotypeId AND - Publication.Id = PublishXRef.PublicationId AND - PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND - PublishXRef.InbredSetId = InbredSet.Id AND - PublishFreeze.Id = %s - """ % (trait.name, dataset.id) + resource_id = get_resource_id_by_data("dataset-publish", + {'dataset': dataset.id, + 'trait': trait.name}) + # If the user isn't logged in, + if g.user_session.record["user_type"] == 'anon': - logger.sql(query) - trait_info = g.db.execute(query).fetchone() + # we don't provide a user to the proxy, which means the proxy will + # use the default access level for the resource + request_fmt = 'http://localhost:8080/run-action/?resource={}&branch=data&action=view' + request_url = request_fmt.format(resource_id) + + trait_info = json.loads(requests.get(request_url)) + + # otherwise, we do provide the user ID to the proxy, and it looks at the user's group membership and the resource's access masks + user_id = g.user_session.record["user_id"] + + + request_fmt = 'http://localhost:8080/run-action/?resource={}&user={}&branch=data&action=view' + + request_url = request_fmt.format(resource_id, user_id) + + # trait_info will either be an array containing the single result, + # or the string "no-access". + + # thus, while the proxy on its own blocks access to the data, we'd + # want to branch on the value of trait_info to change the page to a + # 401 error or something -- but I don't know where or how to do + # that in GN + trait_info = json.loads(requests.get(request_url)) #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. elif dataset.type == 'ProbeSet': + display_fields_string = ', ProbeSet.'.join(dataset.display_fields) display_fields_string = 'ProbeSet.' + display_fields_string query = """ @@ -397,21 +404,24 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name # to avoid the problem of same marker name from different species. elif dataset.type == 'Geno': - display_fields_string = string.join(dataset.display_fields,',Geno.') - display_fields_string = 'Geno.' + display_fields_string - query = """ - SELECT %s - FROM Geno, GenoFreeze, GenoXRef - WHERE - GenoXRef.GenoFreezeId = GenoFreeze.Id AND - GenoXRef.GenoId = Geno.Id AND - GenoFreeze.Name = '%s' AND - Geno.Name = '%s' - """ % (escape(display_fields_string), - escape(dataset.name), - escape(trait.name)) - logger.sql(query) - trait_info = g.db.execute(query).fetchone() + + resource_id = get_resource_id_by_data("dataset-geno", + {'dataset': dataset.name}) + + if g.user_session.record["user_type"] == 'anon': + + request_fmt = 'http://localhost:8080/run-action/?resource={}&branch=data&action=view&trait={}' + request_url = request_fmt.format(resource_id, trait.name) + trait_info = json.loads(requests.get(request_url)) + else: + user_id = g.user_session.record["user_id"] + + request_fmt = 'http://localhost:8080/run-action/?resource={}&user={}&branch=data&action=view&trait={}' + + request_url = request_fmt.format(resource_id, user_id, trait.name) + + trait_info = json.loads(requests.get(request_url)) + else: #Temp type query = """SELECT %s FROM %s WHERE Name = %s""" logger.sql(query) @@ -578,5 +588,5 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs else: raise KeyError, `trait.name`+' information is not found in the database.' - - return trait \ No newline at end of file + + return trait -- cgit v1.2.3