Merge branch 'master' into datatables

.gitignore

@@ -1,3 +1,4 @@
 *.pyc
 code/credentials.py
 *credentials.py
+database/metadata.db

code/templates/layout.html

@@ -38,6 +38,9 @@
         <li class="nav-item">
           <a class="nav-link" href="/datalookup">File Query - Sample Information</a>
         </li>
+        <li class="nav-item">
+            <a class="nav-link" href="ftp://massive.ucsd.edu/MSV000084206/other/ReDU_all_identifications.tsv">Download Annotations</a>
+        </li>    
       </ul>
 
     </nav>

code/test/test_redu_integration.py

@@ -4,32 +4,24 @@
 import json
 
 BASE_URL = "https://redu.ucsd.edu/"
-URL_ONE = "displayglobalmultivariate"
-URL_TWO = "processcomparemultivariate"
 SAMPLE_TASK_ID = "ffa003f6c4d844188f1f751d34c649b0"
-URL_THREE = "ReDUValidator" #optional
-URL_FIVE = "compoundfilename"
 TEST_COMPOUND = "2,5-Dimethoxyphenethylamine"
-URL_SIX = "compoundenrichment"
-URL_FOUR  = "/attributes"
-URL_SEVEN = "attribute/MassSpectrometer/attributeterms?filters=%5B%5D"
-URL_EIGHT = "dump"
 
-def test_pca_library_search(self):
+def test_pca_library_search():
     query_url = BASE_URL + "processcomparemultivariate?task={}".format("f39c94cb7afe4568950bf61cdb8fee0d")
     r = requests.get(query_url)
     r.raise_for_status()
 
     return 0
 
-def test_pca_metabolomics_snets(self):
+def test_pca_metabolomics_snets():
     query_url = BASE_URL + "processcomparemultivariate?task={}".format("1ad7bc366aef45ce81d2dfcca0a9a5e7")
     r = requests.get(query_url)
     r.raise_for_status()
 
     return 0
 
-def test_pca_feature_based(self):
+def test_pca_feature_based():
     query_url = BASE_URL + "processcomparemultivariate?task={}".format("bb49a839face44cbb5ec3e6f855e7285")
     r = requests.get(query_url)
     r.raise_for_status()
@@ -38,56 +30,57 @@ def test_pca_feature_based(self):
 
 
 def test_data_dump():
-    query_url = BASE_URL + URL_EIGHT
+    query_url = BASE_URL + "dump"
     response = requests.get(query_url)
     data = response.content
     file_size = sys.getsizeof(data)
 
     if file_size < 17762000:
-        sys.exit(1)
+        return 1
+
+    return 0
 
 def test_attribute_filtration():
-    query_url = BASE_URL + URL_SEVEN
+    query_url = BASE_URL + "attribute/MassSpectrometer/attributeterms?filters=%5B%5D"
     response = requests.get(query_url)
     data = json.loads(response.content)
     key_value = list(data[0].keys())
-    print(key_value)
     expected_keys = ["attributename", "attributeterm", "ontologyterm", "countfiles"]
 
     if (key_value != expected_keys):
-        sys.exit(1)
+        return 1
 
     return 0
 
 
 def test_attribute_terms_display():
-    query_url = BASE_URL + URL_FOUR
+    query_url = BASE_URL + "/attributes"
     response = requests.get(query_url)
     data = json.loads(response.content)
     key_value = list(data[0].keys())
 
     expected_keys = ["attributename", "attributedisplay", "countterms"]
 
     if (key_value != expected_keys):
-        sys.exit(1)
+        return 1
 
     return 0
 
 def test_file_enrichment():
-    query_url = BASE_URL + URL_FIVE
+    query_url = BASE_URL + "compoundfilename"
     params = {'compoundname' :  TEST_COMPOUND}
     response = requests.get(query_url, params = params)
     data = json.loads(response.content)
 
     key_value = next(iter(data[0]))
 
     if (key_value != 'filepath'):
-       sys.exit(1)
+       return 1
 
     return 0
 
 def test_compound_enrichment():
-    query_url = BASE_URL + URL_SIX  
+    query_url = BASE_URL + "compoundenrichment"  
     params = {'compoundname' : TEST_COMPOUND}
     response = requests.post(query_url, params )
     data = json.loads(response.content)  
@@ -96,29 +89,29 @@ def test_compound_enrichment():
     expected_keys = ["attribute_name", "attribute_term", "totalfiles", "compoundfiles", "percentage"]
 
     if key_value != expected_keys:
-        sys.exit(1)
+        return 1
 
     return 0
 
 def test_your_pca():
     params = {'task': SAMPLE_TASK_ID}
-    query_url = BASE_URL + URL_TWO
+    query_url = BASE_URL + "processcomparemultivariate"
     response = requests.get(query_url, params = params)
     data = response.content
     file_size = sys.getsizeof(data) 
 
     if (file_size < 28000000):
-       sys.exit(1)
+       return 1
 
     return 0
 
 
 def test_global_pca():
-    response = requests.get(BASE_URL + URL_ONE)
+    response = requests.get(BASE_URL + "displayglobalmultivariate")
     data = response.content
-    file_size = sys.getsizeof(data)
-            
-    if (file_size < 27762100):
-        sys.exit(1)
+    file_size = sys.getsizeof(data)    
+
+    if (file_size < 27760000):
+        return 1
 
     return 0