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

16 files changed, 340 insertions, 105 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 5d562871..cfba9104 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -93,7 +93,7 @@ Publish or ProbeSet. E.g.
         """
         self.redis_instance = redis_instance
         self.datasets = {}
-        data = redis_instance.get("dataset_structure")
+        data = self.redis_instance.get("dataset_structure")
         if data:
             self.datasets = json.loads(data)
         else:  # ZS: I don't think this should ever run unless Redis is emptied
@@ -115,73 +115,58 @@ Publish or ProbeSet. E.g.
             except:
                 pass
 
-            redis_instance.set("dataset_structure", json.dumps(self.datasets))
+            self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
 
-        # Set LOG_LEVEL_DEBUG=5 to see the following:
-        logger.debugf(5, "datasets", self.datasets)
+    def set_dataset_key(self, t, name):
+        """If name is not in the object's dataset dictionary, set it, and update
+        dataset_structure in Redis
+
+        args:
+          t: Type of dataset structure which can be: 'mrna_expr', 'pheno',
+             'other_pheno', 'geno'
+          name: The name of the key to inserted in the datasets dictionary
+
+        """
+        sql_query_mapping = {
+            'mrna_expr': ("""SELECT ProbeSetFreeze.Id FROM """ +
+                          """ProbeSetFreeze WHERE ProbeSetFreeze.Name = "{}" """),
+            'pheno': ("""SELECT InfoFiles.GN_AccesionId """ +
+                      """FROM InfoFiles, PublishFreeze, InbredSet """ +
+                      """WHERE InbredSet.Name = '{}' AND """ +
+                      """PublishFreeze.InbredSetId = InbredSet.Id AND """ +
+                      """InfoFiles.InfoPageName = PublishFreeze.Name"""),
+            'other_pheno': ("""SELECT PublishFreeze.Name """ +
+                            """FROM PublishFreeze, InbredSet """ +
+                            """WHERE InbredSet.Name = '{}' AND """ +
+                            """PublishFreeze.InbredSetId = InbredSet.Id"""),
+            'geno':  ("""SELECT GenoFreeze.Id FROM GenoFreeze WHERE """ +
+                      """GenoFreeze.Name = "{}" """)
+        }
+
+        dataset_name_mapping = {
+            "mrna_expr": "ProbeSet",
+            "pheno": "Publish",
+            "other_pheno": "Publish",
+            "geno": "Geno",
+        }
+
+        if t in ['pheno', 'other_pheno']:
+            name = name.replace("Publish", "")
+        if bool(len(g.db.execute(sql_query_mapping[t].format(name)))):
+            self.datasets[name] = dataset_name_mapping[t]
+            self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
+            return True
+
+        return None
 
     def __call__(self, name):
+
         if name not in self.datasets:
-            mrna_expr_query = """
-                            SELECT
-                                ProbeSetFreeze.Id
-                            FROM
-                                ProbeSetFreeze
-                            WHERE
-                                ProbeSetFreeze.Name = "{0}"
-                            """.format(name)
-
-            results = g.db.execute(mrna_expr_query).fetchall()
-            if len(results):
-                self.datasets[name] = "ProbeSet"
-                redis_instance.set("dataset_structure", json.dumps(self.datasets))
-                return self.datasets[name]
-
-            group_name = name.replace("Publish", "")
-
-            pheno_query = """SELECT InfoFiles.GN_AccesionId
-                             FROM InfoFiles, PublishFreeze, InbredSet
-                             WHERE InbredSet.Name = '{0}' AND
-                                   PublishFreeze.InbredSetId = InbredSet.Id AND
-                                   InfoFiles.InfoPageName = PublishFreeze.Name""".format(group_name)
-
-            results = g.db.execute(pheno_query).fetchall()
-            if len(results):
-                self.datasets[name] = "Publish"
-                redis_instance.set("dataset_structure", json.dumps(self.datasets))
-                return self.datasets[name]
-
-            # ZS: For when there isn't an InfoFiles ID; not sure if this and the preceding query are both necessary
-            other_pheno_query = """SELECT PublishFreeze.Name
-                                   FROM PublishFreeze, InbredSet
-                                   WHERE InbredSet.Name = '{}' AND
-                                         PublishFreeze.InbredSetId = InbredSet.Id""".format(group_name)
-
-            results = g.db.execute(other_pheno_query).fetchall()
-            if len(results):
-                self.datasets[name] = "Publish"
-                redis_instance.set("dataset_structure", json.dumps(self.datasets))
-                return self.datasets[name]
-
-            geno_query = """
-                                SELECT
-                                    GenoFreeze.Id
-                                FROM
-                                    GenoFreeze
-                                WHERE
-                                    GenoFreeze.Name = "{0}"
-                            """.format(name)
-
-            results = g.db.execute(geno_query).fetchall()
-            if len(results):
-                self.datasets[name] = "Geno"
-                self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
-                return self.datasets[name]
-
-            # ZS: It shouldn't ever reach this
-            return None
-        else:
-            return self.datasets[name]
+            for t in ["mrna_expr", "pheno", "other_pheno", "geno"]:
+                # This has side-effects, with the end result being a truth-y value
+                if(self.set_dataset_key(t, name)):
+                    break
+        return self.datasets.get(name, None)  # Return None if name has not been set
 
 
 # Do the intensive work at startup one time only
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index d8487f01..2844cedd 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -19,8 +19,7 @@
 # This module is used by GeneNetwork project (www.genenetwork.org)
 #
 # Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
+
 
 from utility.logger import getLogger
 logger = getLogger(__name__)
@@ -29,7 +28,7 @@ import utility.tools
 
 utility.tools.show_settings()
 
-class webqtlCaseData(object):
+class webqtlCaseData:
     """one case data in one trait"""
 
     def __init__(self, name, value=None, variance=None, num_cases=None, name2=None):
@@ -43,44 +42,40 @@ class webqtlCaseData(object):
         self.outlier = None   # Not set to True/False until later
 
     def __repr__(self):
-        str = "<webqtlCaseData> "
-        if self.value != None:
-            str += "value=%2.3f" % self.value
-        if self.variance != None:
-            str += " variance=%2.3f" % self.variance
+        case_data_string = "<webqtlCaseData> "
+        if self.value is not None:
+            case_data_string += "value=%2.3f" % self.value
+        if self.variance is not None:
+            case_data_string += " variance=%2.3f" % self.variance
         if self.num_cases:
-            str += " ndata=%s" % self.num_cases
+            case_data_string += " ndata=%s" % self.num_cases
         if self.name:
-            str += " name=%s" % self.name
+            case_data_string += " name=%s" % self.name
         if self.name2:
-            str += " name2=%s" % self.name2
-        return str
+            case_data_string += " name2=%s" % self.name2
+        return case_data_string
 
     @property
     def class_outlier(self):
         """Template helper"""
         if self.outlier:
             return "outlier"
-        else:
-            return ""
+        return ""
 
     @property
     def display_value(self):
-        if self.value != None:
+        if self.value is not None:
             return "%2.3f" % self.value
-        else:
-            return "x"
+        return "x"
 
     @property
     def display_variance(self):
-        if self.variance != None:
+        if self.variance is not None:
             return "%2.3f" % self.variance
-        else:
-            return "x"
+        return "x"
 
     @property
     def display_num_cases(self):
-        if self.num_cases != None:
+        if self.num_cases is not None:
             return "%s" % self.num_cases
-        else:
-            return "x"
+        return "x"
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 3d86bc22..862ac881 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -85,7 +85,7 @@ assert_writable_dir(GENERATED_TEXT_DIR)
 # Flat file directories
 GENODIR              = flat_files('genotype')+'/'
 assert_dir(GENODIR)
-assert_dir(GENODIR+'bimbam') # for gemma
+# assert_dir(GENODIR+'bimbam') # for gemma
 
 # JSON genotypes are OBSOLETE
 JSON_GENODIR         = flat_files('genotype/json')+'/'
diff --git a/wqflask/tests/base/data.py b/wqflask/tests/base/data.py
new file mode 100644
index 00000000..06a5a989
--- /dev/null
+++ b/wqflask/tests/base/data.py
@@ -0,0 +1,110 @@
+gen_menu_json = """
+{
+  "datasets": {
+    "human": {
+      "HLC": {
+        "Liver mRNA": [
+          [
+            "320",
+            "HLC_0311",
+            "GSE9588 Human Liver Normal (Mar11) Both Sexes"
+          ]
+        ],
+        "Phenotypes": [
+          [
+            "635",
+            "HLCPublish",
+            "HLC Published Phenotypes"
+          ]
+        ]
+      }
+    },
+    "mouse": {
+      "BXD": {
+        "Genotypes": [
+          [
+            "600",
+            "BXDGeno",
+            "BXD Genotypes"
+          ]
+        ],
+        "Hippocampus mRNA": [
+          [
+            "112",
+            "HC_M2_0606_P",
+            "Hippocampus Consortium M430v2 (Jun06) PDNN"
+          ]
+        ],
+        "Phenotypes": [
+          [
+            "602",
+            "BXDPublish",
+            "BXD Published Phenotypes"
+          ]
+        ]
+      }
+    }
+  },
+  "groups": {
+    "human": [
+      [
+        "HLC",
+        "Liver: Normal Gene Expression with Genotypes (Merck)",
+        "Family:None"
+      ]
+    ],
+    "mouse": [
+      [
+        "BXD",
+        "BXD",
+        "Family:None"
+      ]
+    ]
+  },
+  "species": [
+    [
+      "human",
+      "Human"
+    ],
+    [
+      "mouse",
+      "Mouse"
+    ]
+  ],
+  "types": {
+    "human": {
+      "HLC": [
+        [
+          "Phenotypes",
+          "Traits and Cofactors",
+          "Phenotypes"
+        ],
+        [
+          "Liver mRNA",
+          "Liver mRNA",
+          "Molecular Trait Datasets"
+        ]
+      ]
+    },
+    "mouse": {
+      "BXD": [
+        [
+          "Phenotypes",
+          "Traits and Cofactors",
+          "Phenotypes"
+        ],
+        [
+          "Genotypes",
+          "DNA Markers and SNPs",
+          "Genotypes"
+        ],
+        [
+          "Hippocampus mRNA",
+          "Hippocampus mRNA",
+          "Molecular Trait Datasets"
+        ]
+      ]
+    }
+  }
+}
+"""
diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py
index 44a54c7e..94780a5d 100644
--- a/wqflask/tests/base/test_data_set.py
+++ b/wqflask/tests/base/test_data_set.py
@@ -1,25 +1,18 @@
+"""Tests for wqflask/base/data_set.py"""
+
 import unittest
 import mock
 
 from wqflask import app
-
+from data import gen_menu_json
 from base.data_set import DatasetType
 
-    
-class TestDataSetTypes(unittest.TestCase):
-    def setUp(self):
-        self.app_context = app.app_context()
-        self.app_context.push()
 
-    def tearDown(self):
-        self.app_context.pop()
+class TestDataSetTypes(unittest.TestCase):
+    """Tests for the DataSetType class"""
 
-    @mock.patch('base.data_set.g')
-    def test_data_set_type(self, db_mock):
-        with app.app_context():
-            db_mock.get = mock.Mock()
-            r = mock.Mock()
-            r.get.return_value = """
+    def setUp(self):
+        self.test_dataset = """
             {
                 "AD-cases-controls-MyersGeno": "Geno",
                 "AD-cases-controls-MyersPublish": "Publish",
@@ -32,4 +25,116 @@ class TestDataSetTypes(unittest.TestCase):
                 "B139_K_1206_R": "ProbeSet"
             }
             """
-            self.assertEqual(DatasetType(r)("All Phenotypes"), "Publish")
+        self.app_context = app.app_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+
+    @mock.patch('base.data_set.g')
+    def test_data_set_type(self, db_mock):
+        """Test that DatasetType returns correctly if the Redis Instance is not empty
+        and the name variable exists in the dictionary
+
+        """
+        with app.app_context():
+            db_mock.get = mock.Mock()
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = self.test_dataset
+            self.assertEqual(DatasetType(redis_mock)
+                             ("All Phenotypes"), "Publish")
+            redis_mock.get.assert_called_once_with("dataset_structure")
+
+    @mock.patch('base.data_set.requests.get')
+    def test_data_set_type_with_empty_redis(self, request_mock):
+        """Test that DatasetType returns correctly if the Redis Instance is empty and
+        the name variable exists in the dictionary
+
+        """
+        with app.app_context():
+            request_mock.return_value.content = gen_menu_json
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = None
+            data_set = DatasetType(redis_mock)
+            self.assertEqual(data_set("BXDGeno"), "Geno")
+            self.assertEqual(data_set("BXDPublish"), "Publish")
+            self.assertEqual(data_set("HLC_0311"), "ProbeSet")
+            redis_mock.set.assert_called_once_with(
+                "dataset_structure",
+                '{"BXDGeno": "Geno", "BXDPublish": "Publish", "HLCPublish": "Publish", "HLC_0311": "ProbeSet", "HC_M2_0606_P": "ProbeSet"}')
+
+    @mock.patch('base.data_set.g')
+    def test_set_dataset_key_mrna(self, db_mock):
+        with app.app_context():
+            db_mock.db.execute.return_value = [1, 2, 3]
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = self.test_dataset
+            data_set = DatasetType(redis_mock)
+            data_set.set_dataset_key("mrna_expr", "Test")
+            self.assertEqual(data_set("Test"), "ProbeSet")
+            redis_mock.set.assert_called_once_with(
+                "dataset_structure",
+                '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "ProbeSet", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
+            expected_db_call = """"""
+            db_mock.db.execute.assert_called_with(
+                ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze " +
+                 "WHERE ProbeSetFreeze.Name = \"Test\" ")
+            )
+
+    @mock.patch('base.data_set.g')
+    def test_set_dataset_key_pheno(self, db_mock):
+        with app.app_context():
+            db_mock.db.execute.return_value = [1, 2, 3]
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = self.test_dataset
+            data_set = DatasetType(redis_mock)
+            data_set.set_dataset_key("pheno", "Test")
+            self.assertEqual(data_set("Test"), "Publish")
+            redis_mock.set.assert_called_once_with(
+                "dataset_structure",
+                '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
+            expected_db_call = """"""
+            db_mock.db.execute.assert_called_with(
+                ("SELECT InfoFiles.GN_AccesionId " +
+                 "FROM InfoFiles, PublishFreeze, InbredSet " +
+                 "WHERE InbredSet.Name = 'Test' AND "
+                 "PublishFreeze.InbredSetId = InbredSet.Id AND " +
+                 "InfoFiles.InfoPageName = PublishFreeze.Name")
+            )
+
+    @mock.patch('base.data_set.g')
+    def test_set_dataset_other_pheno(self, db_mock):
+        with app.app_context():
+            db_mock.db.execute.return_value = [1, 2, 3]
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = self.test_dataset
+            data_set = DatasetType(redis_mock)
+            data_set.set_dataset_key("other_pheno", "Test")
+            self.assertEqual(data_set("Test"), "Publish")
+            redis_mock.set.assert_called_once_with(
+                "dataset_structure",
+                '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
+            expected_db_call = """"""
+            db_mock.db.execute.assert_called_with(
+                ("SELECT PublishFreeze.Name " +
+                 "FROM PublishFreeze, InbredSet " +
+                 "WHERE InbredSet.Name = 'Test' AND "
+                 "PublishFreeze.InbredSetId = InbredSet.Id")
+            )
+
+    @mock.patch('base.data_set.g')
+    def test_set_dataset_geno(self, db_mock):
+        with app.app_context():
+            db_mock.db.execute.return_value = [1, 2, 3]
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = self.test_dataset
+            data_set = DatasetType(redis_mock)
+            data_set.set_dataset_key("geno", "Test")
+            self.assertEqual(data_set("Test"), "Geno")
+            redis_mock.set.assert_called_once_with(
+                "dataset_structure",
+                '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Geno", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
+            expected_db_call = """"""
+            db_mock.db.execute.assert_called_with(
+                ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE GenoFreeze.Name = \"Test\" ")
+            )
diff --git a/wqflask/tests/base/test_webqtl_case_data.py b/wqflask/tests/base/test_webqtl_case_data.py
new file mode 100644
index 00000000..8e8ba482
--- /dev/null
+++ b/wqflask/tests/base/test_webqtl_case_data.py
@@ -0,0 +1,39 @@
+"""Tests for wqflask/base/webqtlCaseData.py"""
+import unittest
+
+from wqflask import app  # Required because of utility.tools in webqtlCaseData.py
+from base.webqtlCaseData import webqtlCaseData
+
+class TestWebqtlCaseData(unittest.TestCase):
+    """Tests for WebqtlCaseData class"""
+
+    def setUp(self):
+        self.w = webqtlCaseData(name="Test",
+                           value=0,
+                           variance=0.0,
+                           num_cases=10,
+                           name2="Test2")
+
+    def test_webqtl_case_data_repr(self):
+        self.assertEqual(
+            repr(self.w),
+            "<webqtlCaseData> value=0.000 variance=0.000 ndata=10 name=Test name2=Test2"
+        )
+
+    def test_class_outlier(self):
+        self.assertEqual(self.w.class_outlier, "")
+
+    def test_display_value(self):
+        self.assertEqual(self.w.display_value, "0.000")
+        self.w.value = None
+        self.assertEqual(self.w.display_value, "x")
+
+    def test_display_variance(self):
+        self.assertEqual(self.w.display_variance, "0.000")
+        self.w.variance = None
+        self.assertEqual(self.w.display_variance, "x")
+
+    def test_display_num_cases(self):
+        self.assertEqual(self.w.display_num_cases, "10")
+        self.w.num_cases = None
+        self.assertEqual(self.w.display_num_cases, "x")
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index deddaec3..9a2a5ccd 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -45,7 +45,7 @@ def check_resource_availability(dataset, trait_id=None):
 
 def add_new_resource(dataset, trait_id=None):
     resource_ob = {
-        'owner_id'    : "None",
+        'owner_id'    : "none", # webqtlConfig.DEFAULT_OWNER_ID,
         'default_mask': webqtlConfig.DEFAULT_PRIVILEGES,
         'group_masks' : {}
     }
@@ -84,6 +84,7 @@ def check_admin(resource_id=None):
     try:
         response = json.loads(requests.get(the_url).content)['admin']
     except:
+        logger.debug(resource_info)
         response = resource_info['default_mask']['admin']
 
     if 'edit-admins' in response:
@@ -124,4 +125,4 @@ def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
         else:
             return check_admin(resource_id)
 
-    return "not-admin"
\ No newline at end of file
+    return "not-admin"
diff --git a/wqflask/wqflask/static/gif/error/m001.gif b/wqflask/wqflask/static/gif/error/m001.gif
new file mode 100644
index 00000000..81c8ba26
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/m001.gif
diff --git a/wqflask/wqflask/static/gif/error/m002.gif b/wqflask/wqflask/static/gif/error/m002.gif
new file mode 100644
index 00000000..7232c58b
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/m002.gif
diff --git a/wqflask/wqflask/static/gif/error/m003.gif b/wqflask/wqflask/static/gif/error/m003.gif
new file mode 100644
index 00000000..2384ceb6
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/m003.gif
diff --git a/wqflask/wqflask/static/gif/error/m004.gif b/wqflask/wqflask/static/gif/error/m004.gif
new file mode 100644
index 00000000..d77c708d
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/m004.gif
diff --git a/wqflask/wqflask/static/gif/error/m005.gif b/wqflask/wqflask/static/gif/error/m005.gif
new file mode 100644
index 00000000..1b2de7ec
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/m005.gif
diff --git a/wqflask/wqflask/static/gif/error/m006.gif b/wqflask/wqflask/static/gif/error/m006.gif
new file mode 100644
index 00000000..f354a4cc
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/m006.gif
diff --git a/wqflask/wqflask/static/gif/error/m007.gif b/wqflask/wqflask/static/gif/error/m007.gif
new file mode 100644
index 00000000..ba2eeb37
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/m007.gif
diff --git a/wqflask/wqflask/static/gif/error/m008.gif b/wqflask/wqflask/static/gif/error/m008.gif
new file mode 100644
index 00000000..4cdec5cb
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/m008.gif
diff --git a/wqflask/wqflask/static/gif/error/mouse-wheel.gif b/wqflask/wqflask/static/gif/error/mouse-wheel.gif
new file mode 100644
index 00000000..164220e7
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/mouse-wheel.gif