Merge pull request #201 from CanDIG/develop

Develop

candig/server/datamodel/__init__.py

@@ -30,7 +30,7 @@ def __init__(self):
         self._cache = collections.deque()
         self._memoTable = dict()
         # Initialize the value even if it will be set up by the config
-        self._maxCacheSize = 50
+        self._maxCacheSize = 500
 
     def setMaxCacheSize(self, size):
         """

candig/server/datarepo.py

@@ -26,6 +26,8 @@
 
 import candig.schemas.protocol as protocol
 
+import peewee
+
 MODE_READ = 'r'
 MODE_WRITE = 'w'
 
@@ -793,6 +795,45 @@ def getPeers(self, offset=0, limit=1000):
             models.Peer.url).limit(limit).offset(offset)
         return [peers.Peer(p.url, record=p) for p in select]
 
+    def getSqlOntologyByName(self, name):
+        """
+        Returns the ontology set with the specified name.
+        """
+        select = list(models.Ontology.select().where(models.Ontology.name == name))
+
+        if len(select) == 0:
+            raise exceptions.OntologyNameNotFoundException(name)
+        else:
+            ontology = ontologies.Ontology(select[0].name)
+            ontology.populateFromRow(select[0])
+            return ontology
+
+    def getSqlReferenceSetByName(self, name):
+        """
+        Returns the reference set with the specified name.
+        """
+        select = list(models.Referenceset.select().where(models.Referenceset.name == name))
+
+        if len(select) == 0:
+            raise exceptions.ReferenceSetNameNotFoundException(name)
+        else:
+            referenceSet = references.HtslibReferenceSet(select[0].name)
+            referenceSet.populateFromRow(select[0])
+            return referenceSet
+
+    def getSqlDatasetByName(self, name):
+        """
+        Returns the dataset with the specified name.
+        """
+        select = list(models.Dataset.select().where(models.Dataset.name == name))
+
+        if len(select) == 0:
+            raise exceptions.DatasetNameNotFoundException(name)
+        else:
+            dataset = datasets.Dataset(select[0].name)
+            dataset.populateFromRow(select[0])
+            return dataset
+
     def tableToTsv(self, model):
         """
         Takes a model class and attempts to create a table in TSV format
@@ -1457,8 +1498,9 @@ def insertReadGroupSet(self, readGroupSet):
                 attributes=json.dumps(readGroupSet.getAttributes()))
             for readGroup in readGroupSet.getReadGroups():
                 self.insertReadGroup(readGroup)
-        except Exception as e:
-            raise exceptions.RepoManagerException(e)
+        except peewee.IntegrityError as e:
+            raise exceptions.DuplicateNameException(readGroupSet.getLocalId(),
+                                                    readGroupSet.getParentContainer().getLocalId())
 
     def removeReferenceSet(self, referenceSet):
         """
@@ -1584,8 +1626,9 @@ def insertVariantSet(self, variantSet):
                 patientId = variantSet.getPatientId(),
                 sampleId = variantSet.getSampleId(),
                 attributes=json.dumps(variantSet.getAttributes()))
-        except Exception as e:
-            raise exceptions.RepoManagerException(e)
+        except peewee.IntegrityError as e:
+            raise exceptions.DuplicateNameException(variantSet.getLocalId(),
+                                                    variantSet.getParentContainer().getLocalId())
         for callSet in variantSet.getCallSets():
             self.insertCallSet(callSet)
 
@@ -1619,8 +1662,9 @@ def insertFeatureSet(self, featureSet):
                 name=featureSet.getLocalId(),
                 dataurl=featureSet.getDataUrl(),
                 attributes=json.dumps(featureSet.getAttributes()))
-        except Exception as e:
-            raise exceptions.RepoManagerException(e)
+        except peewee.IntegrityError as e:
+            raise exceptions.DuplicateNameException(featureSet.getLocalId(),
+                                                    featureSet.getParentContainer().getLocalId())
 
     def _readFeatureSetTable(self):
         for featureSetRecord in models.Featureset.select():

candig/server/serverconfig.py

@@ -33,7 +33,7 @@ class BaseConfig(object):
     SIMULATED_BACKEND_NUM_RNA_QUANTIFICATION_SETS = 2
     SIMULATED_BACKEND_NUM_EXPRESSION_LEVELS_PER_RNA_QUANT_SET = 2
 
-    FILE_HANDLE_CACHE_MAX_SIZE = 50
+    FILE_HANDLE_CACHE_MAX_SIZE = 500
 
     LANDING_MESSAGE_HTML = "landing_message.html"
 

candig/server/static/.babelrc

@@ -0,0 +1,6 @@
+{
+  "presets": [["minify", {
+    "builtIns": false
+  }]],
+  "comments": false
+}

candig/server/static/src/gene_search.js

@@ -61,7 +61,6 @@ var statusCode = 0; // Initial value, table is empty
         statusCode = 0;
     }
 
-    document.getElementById("searchBtn").addEventListener("click", submit);
     document.getElementById("confirmRG").addEventListener("click", rg_submit);
 
     function submit() {

candig/server/templates/gene_search.html

@@ -19,10 +19,10 @@
          <div class="container-fluid">
             <h2 style="text-align: center; margin-bottom: 100px" class="title" id="title">Gene Search</h2>
 
-            <div class="wrapper" id="gene_search_parent">
-            <input type="text" id="request" name="search" placeholder="Search..">
+            <form class="wrapper" id="gene_search_parent" action="javascript:submit()">
+            <input type="text" id="request" name="search" placeholder="Search.."/>
             <button id="searchBtn" class="btn btn-primary" name="submit">Submit</button>
-            </div>
+            </form>
             <div class="loader mx-auto" id="loader" style="display: none"></div>
              <div id="geneTable_wrap" style="overflow: scroll; display: none"><table id="geneTable" class="table table-striped table-bordered nowrap"></table></div>