Merge pull request #630 from plantbreeding/brapi-V2.1

Merge in v2.1

Author: BrapiCoordinatorSelby

Scripts/buildBlueprint.py

@@ -32,7 +32,7 @@ def go():
 	headerHTML = ''
 	with open(headerPath, "r") as headerFile:
 		try:
-			fileObj = yaml.load(headerFile)
+			fileObj = yaml.safe_load(headerFile)
 			if 'info' in fileObj:
 				if 'description' in fileObj['info']:
 					headerHTML = parseHTMLToMD(fileObj['info']['description'])

Scripts/buildGlossaryFromOpenAPI.py

@@ -164,7 +164,7 @@ def main():
 	with open(rootPath + 'brapi_openapi.yaml', "r") as stream:
 		try:
 			global fullBrAPI
-			fullBrAPI = yaml.load(stream)
+			fullBrAPI = yaml.safe_load(stream)
 			stream.close()
 		except yaml.YAMLError as exc:
 			stream.close()

Scripts/buildOpenAPI.py

@@ -33,7 +33,7 @@ def go(rootPaths, metaFilePath = './swaggerMetaData.yaml'):
     for filename in filenames:
         with open(filename, "r") as stream:
             try:
-                fileObj = yaml.load(stream, Loader=Loader)
+                fileObj = yaml.safe_load(stream)
                 if 'paths' in fileObj:
                     paths.update(fileObj['paths'])
                 if 'components' in fileObj:
@@ -56,7 +56,7 @@ def go(rootPaths, metaFilePath = './swaggerMetaData.yaml'):
     out = {}
     with open(metaFilePath, "r") as metaFile:
         try:
-            out = yaml.load(metaFile, Loader=Loader)
+            out = yaml.safe_load(metaFile)
         except yaml.YAMLError as exc:
             print(exc)
 

Scripts/buildReadMes.py

@@ -254,7 +254,7 @@ def buildReadMe(dir, fullBrAPI):
 		fileObj = {}	
 		with open(filename, "r") as stream:
 			try:
-				fileObj = yaml.load(stream)
+				fileObj = yaml.safe_load(stream)
 				stream.close()
 			except yaml.YAMLError as exc:
 				print(exc)

Scripts/buildTermBrowserReference.py

@@ -9,7 +9,7 @@
 def buildTermBrowserData(specPath):
 	with open(specPath + '/brapi_openapi.yaml', "r") as stream:
 		try:
-			fullBrAPI = yaml.load(stream)
+			fullBrAPI = yaml.safe_load(stream)
 			stream.close()
 		except yaml.YAMLError as exc:
 			stream.close()

Scripts/buildWikiFiles.py

@@ -12,7 +12,7 @@ def getObject(filename):
 	fileObj = {}	
 	with open(filename, "r") as stream:
 		try:
-			fileObj = yaml.load(stream)
+			fileObj = yaml.safe_load(stream)
 			stream.close()
 		except yaml.YAMLError as exc:
 			print(exc)

Scripts/dereferenceAll.py

@@ -105,7 +105,7 @@ def dereferenceBrAPI(filePath = './brapi_openapi.yaml', verbose = False):
         print(filePath)
     with open(filePath, "r") as stream:
         try:
-            fileObj = yaml.load(stream)
+            fileObj = yaml.safe_load(stream)
             stream.close()
         except yaml.YAMLError as exc:
             stream.close()

Scripts/generateExamples.py

@@ -83,7 +83,7 @@ def readFileToDict(path):
 	fileObj = {}	
 	with open(path, "r") as stream:
 		try:
-			fileObj = yaml.load(stream)
+			fileObj = yaml.safe_load(stream)
 			stream.close()
 		except yaml.YAMLError as exc:
 			print(exc)

Specification/BrAPI-Core/Lists/Schemas/ListDetails.yaml

@@ -13,6 +13,6 @@ components:
         x-brapi-metadata:
           primaryModel: true
           module: BrAPI-Core
-          title: List
-          description: A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study.  
+        title: List
+        description: A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study.
         properties: {}

Specification/BrAPI-Core/Locations/Schemas/Location.yaml

@@ -12,8 +12,8 @@ components:
         x-brapi-metadata:
           primaryModel: true
           module: BrAPI-Core
-          title: Location
-          description: A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc. 
+        title: Location
+        description: A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc.
         properties:
           locationDbId:
             description: The unique identifier for a Location