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
--
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