Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing

7 files changed, 44 insertions, 62 deletions

diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
index 48bad39b..af60c290 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -8,27 +8,21 @@ assignees: ''
 ---
 
 **Describe the bug**
-
 <!-- A clear and concise description of what the bug is. -->
 
 **To Reproduce**
-
 <!-- Steps to reproduce the behavior -->
 
 **Expected behavior**
-
 <!-- A clear and concise description of what you expected to happen. -->
 
 **Screenshots**
-
 <!-- If applicable, add screenshots to help explain your problem. -->
 
 **Environment setup (please complete the following information):**
-
 <!-- - OS: [e.g. Linux] -->
 <!-- - Guix Version (optional) -->
 <!-- - [Anything else you think is relevant] -->
 
 **Additional context**
-
 <!-- Add any other context about the problem here. -->
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
index eb6c3e4b..813974c1 100644
--- a/.github/ISSUE_TEMPLATE/feature_request.md
+++ b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -8,34 +8,23 @@ assignees: ''
 ---
 
 ## Is your feature request related to a problem? Please describe.
-
 <!-- A clear and concise description of what the problem is. -->
-
 <!-- Example: I'm always frustrated when [...] -->
 
 ## Describe the solution you'd like
-
 <!-- A clear and concise description of what you want to happen. -->
 
 ## Describe alternatives you've considered
-
 <!-- A clear and concise description of any alternative solutions or features you've considered. -->
 
 ## User Stories (optional)
-
 <!-- Example: -->
-
 <!-- As a _[role or persona]_, I want _[goal/ need]_ so that _[why]_ -->
-
 <!-- **Feature:** _[Brief description of feature]_ -->
-
 <!-- _[Any additional descriptions on feature]_ -->
-
 <!-- **Scenario:**
-
 Please use _[Gherkin](https://cucumber.io/docs/gherkin/reference/)_
 here -->
 
 ## Additional context
-
 <!-- Add any other context or screenshots about the feature request here. -->
diff --git a/.github/ISSUE_TEMPLATE/user_story.md b/.github/ISSUE_TEMPLATE/user_story.md
index 52ae775d..d46976ba 100644
--- a/.github/ISSUE_TEMPLATE/user_story.md
+++ b/.github/ISSUE_TEMPLATE/user_story.md
@@ -6,11 +6,7 @@ labels: ''
 assignees: ''
 
 ---
-
 <!-- As a _[role or persona]_, I want _[goal/ need]_ so that _[why]_ -->
-
 <!-- **Feature:** _[Brief description of feature]_ -->
-
 <!-- _[Any additional descriptions on feature]_ -->
-
 <!-- **Scenario:** Please use _[Gherkin](https://cucumber.io/docs/gherkin/reference/)_ here -->
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index f3371183..926b0548 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -6,15 +6,12 @@
 assurance checks that should be done. What are the expectations -->
 
 #### Any background context you want to provide?
-
 <!-- Anything the reviewer should be aware of ahead of testing -->
 
 #### What are the relevant pivotal tracker stories?
-
 <!-- Does this PR track anything anywhere? -->
 
 #### Screenshots (if appropriate)
 
 #### Questions
-
 <!-- Are there any questions for the reviewer -->
diff --git a/wqflask/tests/unit/wqflask/test_pbkdf2.py b/wqflask/tests/unit/wqflask/test_pbkdf2.py
index a33fbd4f..7ad6c83e 100644
--- a/wqflask/tests/unit/wqflask/test_pbkdf2.py
+++ b/wqflask/tests/unit/wqflask/test_pbkdf2.py
@@ -11,43 +11,43 @@ class TestPbkdf2(unittest.TestCase):
         """
 
         for password, salt, iterations, keylen, expected_value in [
-                ('password', 'salt', 1, 20,
+                ('password', b'salt', 1, 20,
                  '0c60c80f961f0e71f3a9b524af6012062fe037a6'),
-                ('password', 'salt', 2, 20,
+                ('password', b'salt', 2, 20,
                  'ea6c014dc72d6f8ccd1ed92ace1d41f0d8de8957'),
-                ('password', 'salt', 4096, 20,
+                ('password', b'salt', 4096, 20,
                  '4b007901b765489abead49d926f721d065a429c1'),
                 ('passwordPASSWORDpassword',
-                 'saltSALTsaltSALTsaltSALTsaltSALTsalt',
+                 b'saltSALTsaltSALTsaltSALTsaltSALTsalt',
                  4096, 25,
                  '3d2eec4fe41c849b80c8d83662c0e44a8b291a964cf2f07038'),
-                ('pass\x00word', 'sa\x00lt', 4096, 16,
+                ('pass\x00word', b'sa\x00lt', 4096, 16,
                  '56fa6aa75548099dcc37d7f03425e0c3'),
-                ('password', 'ATHENA.MIT.EDUraeburn', 1, 16,
+                ('password', b'ATHENA.MIT.EDUraeburn', 1, 16,
                  'cdedb5281bb2f801565a1122b2563515'),
-                ('password', 'ATHENA.MIT.EDUraeburn', 1, 32,
+                ('password', b'ATHENA.MIT.EDUraeburn', 1, 32,
                  ('cdedb5281bb2f80'
                   '1565a1122b256351'
                   '50ad1f7a04bb9f3a33'
                   '3ecc0e2e1f70837')),
-                ('password', 'ATHENA.MIT.EDUraeburn', 2, 16,
+                ('password', b'ATHENA.MIT.EDUraeburn', 2, 16,
                  '01dbee7f4a9e243e988b62c73cda935d'),
-                ('password', 'ATHENA.MIT.EDUraeburn', 2, 32,
+                ('password', b'ATHENA.MIT.EDUraeburn', 2, 32,
                  ('01dbee7f4a9e243e9'
                   '88b62c73cda935da05'
                   '378b93244ec8f48a99'
                   'e61ad799d86')),
-                ('password', 'ATHENA.MIT.EDUraeburn', 1200, 32,
+                ('password', b'ATHENA.MIT.EDUraeburn', 1200, 32,
                  ('5c08eb61fdf71e'
                   '4e4ec3cf6ba1f55'
                   '12ba7e52ddbc5e51'
                   '42f708a31e2e62b1e13')),
-                ('X' * 64, 'pass phrase equals block size', 1200, 32,
+                ('X' * 64, b'pass phrase equals block size', 1200, 32,
                  ('139c30c0966bc32ba'
                   '55fdbf212530ac9c5'
                   'ec59f1a452f5cc9ad'
                   '940fea0598ed1')),
-                ('X' * 65, 'pass phrase exceeds block size', 1200, 32,
+                ('X' * 65, b'pass phrase exceeds block size', 1200, 32,
                  ('9ccad6d468770cd'
                   '51b10e6a68721be6'
                   '11a8b4d282601db3'
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 9e46c0c5..2b8d4bc1 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -1,4 +1,6 @@
 import json
+import datetime as dt
+from types import SimpleNamespace
 
 from flask import Flask, g
 from base.data_set import create_dataset
@@ -9,8 +11,9 @@ from base import webqtlConfig
 
 from utility import hmac
 
-from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
 from utility.benchmark import Bench
+from utility.authentication_tools import check_resource_availability
+from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
 
 from utility.logger import getLogger
 logger = getLogger(__name__)
@@ -42,15 +45,19 @@ class GSearch(object):
                 ProbeSetXRef.LRS AS lrs,
                 ProbeSetXRef.`Locus` AS locus,
                 ProbeSetXRef.`pValue` AS pvalue,
-                ProbeSetXRef.`additive` AS additive
-                FROM Species, InbredSet, ProbeSetXRef, ProbeSet, ProbeFreeze, ProbeSetFreeze, Tissue
-                WHERE InbredSet.`SpeciesId`=Species.`Id`
-                AND ProbeFreeze.InbredSetId=InbredSet.`Id`
-                AND ProbeFreeze.`TissueId`=Tissue.`Id`
-                AND ProbeSetFreeze.ProbeFreezeId=ProbeFreeze.Id
-                AND ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias,GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) )
-                AND ProbeSet.Id = ProbeSetXRef.ProbeSetId
-                AND ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id
+                ProbeSetXRef.`additive` AS additive,
+                ProbeSetFreeze.Id AS probesetfreeze_id,
+                Geno.Chr as geno_chr,
+                Geno.Mb as geno_mb
+                FROM Species 
+                INNER JOIN InbredSet ON InbredSet.`SpeciesId`=Species.`Id` 
+                INNER JOIN ProbeFreeze ON ProbeFreeze.InbredSetId=InbredSet.`Id` 
+                INNER JOIN Tissue ON ProbeFreeze.`TissueId`=Tissue.`Id` 
+                INNER JOIN ProbeSetFreeze ON ProbeSetFreeze.ProbeFreezeId=ProbeFreeze.Id 
+                INNER JOIN ProbeSetXRef ON ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id 
+                INNER JOIN ProbeSet ON ProbeSet.Id = ProbeSetXRef.ProbeSetId 
+                LEFT JOIN Geno ON ProbeSetXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id
+                WHERE ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,ProbeSet.alias,ProbeSet.GenbankId, ProbeSet.UniGeneId, ProbeSet.Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) )
                 AND ProbeSetFreeze.confidentiality < 1
                 AND ProbeSetFreeze.public > 0
                 ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name
@@ -61,6 +68,7 @@ class GSearch(object):
                 re = g.db.execute(sql).fetchall()
 
             trait_list = []
+            dataset_to_permissions = {}
             with Bench("Creating trait objects"):
                 for i, line in enumerate(re):
                     this_trait = {}
@@ -90,16 +98,22 @@ class GSearch(object):
                     this_trait['additive'] = "N/A"
                     if line[14] != "" and line[14] != None:
                         this_trait['additive'] = '%.3f' % line[14]
-
-                    #dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
-                    #trait_id = line[4]
-                    #with Bench("Building trait object"):
-                    trait_ob = create_trait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False)
-                    if not trait_ob:
+                    this_trait['dataset_id'] = line[15]
+                    this_trait['locus_chr'] = line[16]
+                    this_trait['locus_mb'] = line[17]
+
+                    dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="ProbeSet",species=this_trait["species"])
+                    if dataset_ob.id not in dataset_to_permissions:
+                        permissions = check_resource_availability(dataset_ob)
+                        dataset_to_permissions[dataset_ob.id] = permissions
+                    else:
+                        pemissions = dataset_to_permissions[dataset_ob.id]
+                    if "view" not in permissions['data']:
                         continue
+
                     max_lrs_text = "N/A"
-                    if trait_ob.locus_chr != "" and trait_ob.locus_mb != "":
-                        max_lrs_text = "Chr" + str(trait_ob.locus_chr) + ": " + str(trait_ob.locus_mb)
+                    if this_trait['locus_chr'] != None and this_trait['locus_mb'] != None:
+                        max_lrs_text = "Chr" + str(this_trait['locus_chr']) + ": " + str(this_trait['locus_mb'])
                     this_trait['max_lrs_text'] = max_lrs_text
 
                     trait_list.append(this_trait)
diff --git a/wqflask/wqflask/templates/facilities.html b/wqflask/wqflask/templates/facilities.html
index dc8d0ded..56b127f9 100644
--- a/wqflask/wqflask/templates/facilities.html
+++ b/wqflask/wqflask/templates/facilities.html
@@ -4,14 +4,6 @@
 
 {% block css %}
 <link rel="stylesheet" type="text/css" href="/static/new/css/markdown.css" />
-
-<style>
-	 img[src="https://github.com/genenetwork/gn-docs/raw/master/general/help/octopus.jpg"] {
-    width:100%;
-    margin:20px 0px;
-}
-</style>
-
 {% endblock %}
 
 {% block content %}