Changes for ESS-DIVE suite v1.1.0

Merge branch 'develop'

build.properties

@@ -1,7 +1,7 @@
 # Ant build properties files for the metadig-checks build
 
 # MetaDIG checks version
-metadig-checks.version=0.2.6
+metadig-checks.version=0.4.0
 
 build=build
 dist=dist
@@ -12,4 +12,5 @@ data=data
 stagescript=stageFiles.py
 # The suites to include in the distribution tar file
 #suites=arctic-data-center.xml,ess-dive.xml,FAIR-suite.xml,knb-suite.xml
-suites=FAIR-suite.xml
+#suites=FAIR-suite.xml
+suites=ess-dive-1.1.0.xml

src/checks/coverage.contentType.present.xml → src/checks/entity.attributeCoverageContentType.present.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <mdq:check xmlns:mdq="https://nceas.ucsb.edu/mdqe/v1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://nceas.ucsb.edu/mdqe/v1 ../schemas/schema1.xsd">
-   <id>coverage.contentType.present.1</id>
-   <name>Coverage Content Type</name>
+   <id>entity.attributeCoverageContentType.present.1</id>
+   <name>Attribute Coverage Content Type</name>
    <description>Check that a coverage content type exists.</description>
    <type>Interoperable</type>
    <level>REQUIRED</level>
@@ -17,7 +17,7 @@ def call():
 
   # A coverage content type is not present
   if 'coverageContentType' not in globals() or coverageContentType is None:
-    output = "A coverage content type was not found."
+    output = "No coverage content type was found."
     status = "FAILURE"
     return False
         
@@ -48,13 +48,9 @@ def call():
       </xpath>
    </selector>
    <dialect>
-      <name>DataCite 3.1</name>
+      <name>DataCite 4</name>
       <xpath>boolean(/*[local-name() = 'resource'])</xpath>
    </dialect>
-   <dialect>
-      <name>Dryad Data Package and Data File Modules</name>
-      <xpath>boolean(/*[local-name() = 'DryadDataFile' or local-name() = 'DryadDataPackage'])</xpath>
-   </dialect>
    <dialect>
       <name>Ecological Metadata Language</name>
       <xpath>boolean(/*[local-name() = 'eml'])</xpath>

src/checks/entity.attributeDefinition.present.xml

@@ -19,7 +19,7 @@ def call():
   
   # Check if definitions are present for each attribute.
   if not attributeDefinitionPresent:
-    output = "No attributes definitions are present."
+    output = "No attributes were found so unable to check attribute defintions."
     status = "FAILURE"
     return False
     
@@ -111,13 +111,9 @@ def call():
      </subSelector>
    </selector>
    <dialect>
-      <name>DataCite 3.1</name>
+      <name>DataCite 4</name>
       <xpath>boolean(/*[local-name() = 'resource'])</xpath>
    </dialect>
-   <dialect>
-      <name>Dryad Data Package and Data File Modules</name>
-      <xpath>boolean(/*[local-name() = 'DryadDataFile' or local-name() = 'DryadDataPackage'])</xpath>
-   </dialect>
    <dialect>
       <name>Ecological Metadata Language</name>
       <xpath>boolean(/*[local-name() = 'eml'])</xpath>

src/checks/entity.attributeDefinition.sufficient.xml

@@ -22,7 +22,7 @@ def call():
   
   # Check if definitions are present for each attribute.
   if not attributeDefinitionPresent:
-    output = "No attribute definitions are present, so unable to check if definitions are sufficient."
+    output = "No attribute definitions were found, so unable to check if definitions are sufficient."
     status = "FAILURE"
     return False
     
@@ -124,13 +124,9 @@ def call():
      </subSelector>
    </selector>
    <dialect>
-      <name>DataCite 3.1</name>
+      <name>DataCite 4</name>
       <xpath>boolean(/*[local-name() = 'resource'])</xpath>
    </dialect>
-   <dialect>
-      <name>Dryad Data Package and Data File Modules</name>
-      <xpath>boolean(/*[local-name() = 'DryadDataFile' or local-name() = 'DryadDataPackage'])</xpath>
-   </dialect>
    <dialect>
       <name>Ecological Metadata Language</name>
       <xpath>boolean(/*[local-name() = 'eml'])</xpath>

src/checks/entity.attributeDomain.present.xml

@@ -18,7 +18,7 @@ def call():
   NoneType = type(None)
   # Check if a measurementScale is present for each attribute.
   if not attributesPresent:
-    output = "No attributes are present so attribute measurement domain cannot be checked."
+    output = "No attributes were found so attribute measurement domain cannot be checked."
     status = "FAILURE"
     return False
     
@@ -108,13 +108,9 @@ def call():
      </subSelector>
    </selector>
    <dialect>
-      <name>DataCite 3.1</name>
+      <name>DataCite 4</name>
       <xpath>boolean(/*[local-name() = 'resource'])</xpath>
    </dialect>
-   <dialect>
-      <name>Dryad Data Package and Data File Modules</name>
-      <xpath>boolean(/*[local-name() = 'DryadDataFile' or local-name() = 'DryadDataPackage'])</xpath>
-   </dialect>
    <dialect>
       <name>Ecological Metadata Language</name>
       <xpath>boolean(/*[local-name() = 'eml'])</xpath>

src/checks/entity.attributeEnumeratedDomains.present.xml

@@ -12,6 +12,10 @@ library(metadig)
 # Find the <attribute> elements that have enumerated domains in them
 idxs <- which(!is.na(enumerated_domains))
 
+if(length(idxs) == 0) {
+    failure(paste0("No entity attribute enumerated domains found."))
+}
+
 for (i in idxs) {
   # Check the <code> element
   for (code in codes[i]) {
@@ -66,4 +70,16 @@ success("All enumerated domain descriptions found had codes and definitions.")
       <xpath>./measurementScale/nominal/nonNumericDomain/enumeratedDomain/codeDefinition/definition</xpath>
     </subSelector>
   </selector>
+   <dialect>
+      <name>DataCite 4</name>
+      <xpath>boolean(/*[local-name() = 'resource'])</xpath>
+   </dialect>
+   <dialect>
+      <name>Ecological Metadata Language</name>
+      <xpath>boolean(/*[local-name() = 'eml'])</xpath>
+   </dialect>
+   <dialect>
+      <name>ISO 19115 and ISO 19115-2 / ISO 19139 and ISO 19139-2</name>
+      <xpath>boolean(/*[local-name() = 'MI_Metadata' or local-name() = 'MD_Metadata'])</xpath>
+   </dialect>
 </mdq:check>

src/checks/entity.attributeMeasurementScale.present.xml

@@ -18,7 +18,7 @@ def call():
 
   # Check if a measurementScale is present for each attribute.
   if not attributesPresent:
-    output = "No attributes present, unable to check if attributes have a measurement scale defined."
+    output = "No attributes were found so unable to check if attributes have a measurement scale defined."
     status = "FAILURE"
     return False
     
@@ -86,13 +86,9 @@ def call():
      </subSelector>
    </selector>
    <dialect>
-      <name>DataCite 3.1</name>
+      <name>DataCite 4</name>
       <xpath>boolean(/*[local-name() = 'resource'])</xpath>
    </dialect>
-   <dialect>
-      <name>Dryad Data Package and Data File Modules</name>
-      <xpath>boolean(/*[local-name() = 'DryadDataFile' or local-name() = 'DryadDataPackage'])</xpath>
-   </dialect>
    <dialect>
       <name>Ecological Metadata Language</name>
       <xpath>boolean(/*[local-name() = 'eml'])</xpath>

src/checks/entity.attributeName.differs.xml

@@ -20,7 +20,7 @@ def call():
   
   # For each entity, check that the attributes defined for it have unique names
   if(not attributeDefinitionPresent):
-    output = "No attribute definitions found, unable to check if attribute names differ from definitions."
+    output = "No attributes were found, unable to check if attribute names differ from definitions."
     status = "FAILURE"
     return False
   
@@ -113,6 +113,10 @@ def call():
             </xpath>
         </subSelector>
       </selector>
+   <dialect>
+      <name>DataCite 4</name>
+      <xpath>boolean(/*[local-name() = 'resource'])</xpath>
+   </dialect>
    <dialect>
       <name>Ecological Metadata Language</name>
       <xpath>boolean(/*[local-name() = 'eml'])</xpath>

src/checks/entity.attributeNames.unique.xml

@@ -39,7 +39,7 @@ def call():
   
   # The check fails if no attributes are found.
   if(len(entities) == 0):
-    output = "No attributes found, unable to check for duplicate attribute names."
+    output = "No attributes were found, unable to check for duplicate attribute names."
     status = "FAILURE"
     return False
   
@@ -93,6 +93,10 @@ def call():
           </xpath>
       </subSelector>
    </selector>
+   <dialect>
+      <name>DataCite 4</name>
+      <xpath>boolean(/*[local-name() = 'resource'])</xpath>
+   </dialect>
    <dialect>
       <name>Ecological Metadata Language</name>
       <xpath>boolean(/*[local-name() = 'eml'])</xpath>

src/checks/entity.attributePrecision.present.xml

@@ -20,7 +20,7 @@ def call():
   
   # Check if a measurement precision is present for each attribute.
   if not attributesPresent:
-    output = "No attributes present, unable to check if attribute measurement precision is defined."
+    output = "No attributes were found so unable to check if attribute measurement precision is defined."
     status = "FAILURE"
     return False
     
@@ -111,13 +111,9 @@ def call():
      </subSelector>
    </selector>
    <dialect>
-      <name>DataCite 3.1</name>
+      <name>DataCite 4</name>
       <xpath>boolean(/*[local-name() = 'resource'])</xpath>
    </dialect>
-   <dialect>
-      <name>Dryad Data Package and Data File Modules</name>
-      <xpath>boolean(/*[local-name() = 'DryadDataFile' or local-name() = 'DryadDataPackage'])</xpath>
-   </dialect>
    <dialect>
       <name>Ecological Metadata Language</name>
       <xpath>boolean(/*[local-name() = 'eml'])</xpath>

src/checks/entity.attributeStorageType.present.xml

@@ -20,13 +20,13 @@ def call():
   # Check if an attribute storage type is present for each attribute.
   
   if not attributesPresent:
-    output = "No attributes are present, so unable to check for attribute storage type."
+    output = "No attributes were found, so unable to check for attribute storage type."
     status = "FAILURE"
     return False
     
   # If attributes are present, they can have a storage type (in EML), so fail if none are found.
   if not attributeStorageTypePresent:
-    output = "No attribute storage types are present."
+    output = "No attribute storage types were found."
     status = "FAILURE"
     return False
 
@@ -100,13 +100,9 @@ def call():
      </subSelector>
    </selector>
    <dialect>
-      <name>DataCite 3.1</name>
+      <name>DataCite 4</name>
       <xpath>boolean(/*[local-name() = 'resource'])</xpath>
    </dialect>
-   <dialect>
-      <name>Dryad Data Package and Data File Modules</name>
-      <xpath>boolean(/*[local-name() = 'DryadDataFile' or local-name() = 'DryadDataPackage'])</xpath>
-   </dialect>
    <dialect>
       <name>Ecological Metadata Language</name>
       <xpath>boolean(/*[local-name() = 'eml'])</xpath>

src/checks/entity.attributeUnits.present.xml

@@ -19,7 +19,7 @@ def call():
   # Check if measurement units are present for each attribute.
   
   if not attributesPresent:
-    output = "No attributes present."
+    output = "No attributes were found so unable to check attribute units."
     status = "FAILURE"
     return False
     
@@ -113,13 +113,9 @@ def call():
      </subSelector>
    </selector>
    <dialect>
-      <name>DataCite 3.1</name>
+      <name>DataCite 4</name>
       <xpath>boolean(/*[local-name() = 'resource'])</xpath>
    </dialect>
-   <dialect>
-      <name>Dryad Data Package and Data File Modules</name>
-      <xpath>boolean(/*[local-name() = 'DryadDataFile' or local-name() = 'DryadDataPackage'])</xpath>
-   </dialect>
    <dialect>
       <name>Ecological Metadata Language</name>
       <xpath>boolean(/*[local-name() = 'eml'])</xpath>

src/checks/entity.checksum.present.xml

@@ -19,7 +19,7 @@ def call():
  
   # Check if measurement units are present for each attribute.
   if not entitiesPresent:
-    output = "No data entities are present, so cannot check for entity checksums."
+    output = "No data entities were found so unable to check for entity checksums."
     status = "FAILURE"
     return False
     
@@ -103,6 +103,10 @@ def call():
         <xpath>./entityName</xpath>
     </subSelector>
   </selector>
+   <dialect>
+      <name>DataCite 4</name>
+      <xpath>boolean(/*[local-name() = 'resource'])</xpath>
+   </dialect>
   <dialect>
      <name>Ecological Metadata Language</name>
      <xpath>boolean(/*[local-name() = 'eml'])</xpath>

src/checks/entity.description.present.xml

@@ -20,7 +20,7 @@ def call():
   
   # Check if a entity description is present for each attribute.
   if not entityPresent:
-    output = "No entities are present so cannot check their descriptions."
+    output = "No entities were found so unable to check their descriptions."
     status = "FAILURE"
     return False
     
@@ -104,13 +104,9 @@ def call():
      </subSelector>
    </selector>
    <dialect>
-      <name>DataCite 3.1</name>
+      <name>DataCite 4</name>
       <xpath>boolean(/*[local-name() = 'resource'])</xpath>
    </dialect>
-   <dialect>
-      <name>Dryad Data Package and Data File Modules</name>
-      <xpath>boolean(/*[local-name() = 'DryadDataFile' or local-name() = 'DryadDataPackage'])</xpath>
-   </dialect>
    <dialect>
       <name>Ecological Metadata Language</name>
       <xpath>boolean(/*[local-name() = 'eml'])</xpath>

src/checks/entity.distributionURL.resolvable.xml

@@ -27,7 +27,7 @@ def call():
   
   # An entity distribution URL is not present
   if 'distributionUrl' not in globals() or distributionUrl is None:
-    output = "An entity distribution URL was not found."
+    output = "No entity distribution URL was found."
     status = "FAILURE"
     return False
          
@@ -47,7 +47,7 @@ def call():
     if(len(distributionUrl) > 1):
       output = u"The entity distribution URL '{}' was found (first of {} URLs)".format(url, len(distributionUrl))
     else:
-      output = "The entity distribution URL '{}' was found".format(url)
+      output = u"The entity distribution URL '{}' was found".format(url)
       
   # Now check if the entity identifier is a resolvable url as is. Do not attempt to use any resolver service,
   # just use the bare URL.
@@ -58,7 +58,7 @@ def call():
     status = "SUCCESS"
     return True
   else:
-    output = "{}, but is not resolvable.".format(output)      
+    output = u"{}, but is not resolvable.".format(output)      
     status = "FAILURE"
     return False
    ]]></code>
@@ -71,13 +71,9 @@ def call():
       </xpath>
    </selector>
    <dialect>
-      <name>DataCite 3.1</name>
+      <name>DataCite 4</name>
       <xpath>boolean(/*[local-name() = 'resource'])</xpath>
    </dialect>
-   <dialect>
-      <name>Dryad Data Package and Data File Modules</name>
-      <xpath>boolean(/*[local-name() = 'DryadDataFile' or local-name() = 'DryadDataPackage'])</xpath>
-   </dialect>
    <dialect>
       <name>Ecological Metadata Language</name>
       <xpath>boolean(/*[local-name() = 'eml'])</xpath>
@@ -86,8 +82,4 @@ def call():
       <name>ISO 19115 and ISO 19115-2 / ISO 19139 and ISO 19139-2</name>
       <xpath>boolean(/*[local-name() = 'MI_Metadata' or local-name() = 'MD_Metadata'])</xpath>
    </dialect>
-   <dialect>
-      <name>ISO 19115-1 / ISO 19115-3</name>
-      <xpath>boolean(/*[local-name() = 'MD_Metadata'])</xpath>
-   </dialect>
 </mdq:check>