From 842ac4a508dd7e60123347028c823a941f34914b Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Fri, 12 Nov 2021 15:27:55 -0800
Subject: [PATCH 01/36] Add resource.projectTitle.controlled

Issue #420
---
 .../resource.projectTitle.controlled.xml      | 83 +++++++++++++++++++
 1 file changed, 83 insertions(+)
 create mode 100644 src/checks/resource.projectTitle.controlled.xml

diff --git a/src/checks/resource.projectTitle.controlled.xml b/src/checks/resource.projectTitle.controlled.xml
new file mode 100644
index 0000000..9d98838
--- /dev/null
+++ b/src/checks/resource.projectTitle.controlled.xml
@@ -0,0 +1,83 @@
+<?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>resource.projectTitle.controlled.1</id>
+   <name>Resource Project Title Controlled</name>
+   <description>Check if the project title is contained in a list of known projects.</description>
+   <type>Findable</type>
+   <level>REQUIRED</level>
+   <environment>python</environment>
+   <code><![CDATA[
+def call():
+  global output
+  global status
+  global projectTitle
+  global data
+  displayNchars = 40
+
+  import json
+  import metadig.variable as mvar
+  
+  # Read ESS-DIVE project file from remote location
+  dataFilename = "ess-dive-projects.json"
+  formatsFile = ""
+  # The checks data directory is passed via the 'mdq_params' hash
+  # The filename is known only to this check.
+  if('mdq_params' not in globals()):
+    output = "Internal error running check, mdq_params not available to check."
+    status = "ERROR"
+    return False
+  else:
+    projectFile = "{}/{}".format(mdq_params['metadigDataDir'], dataFilename)
+
+  # Retrieve the project name from the metadata
+  # A project title is not present
+  if 'projectTitle' not in globals() or projectTitle is None:
+    output = "No project name was found."
+    status = "FAILURE"
+    return False
+        
+  projectTitle = mvar.toUnicode(projectTitle)     
+  
+  # If the title in the metadata is blank, then return
+  if (mvar.isBlank(projectTitle)):
+    output = "The project name is blank."
+    status = "FAILURE"
+    return False
+  else:
+    if(len(projectTitle) > displayNchars):
+      titleShort = u"{}...".format(projectTitle[:displayNchars])
+    else:
+      titleShort = projectTitle
+  
+  # Loop through the projects in the list and see if there is 
+  # a match with the name from the metadig
+  with open(projectFile, "r") as content:
+    data = json.load(content)
+    
+  for key in data:
+    thisTitle = data[key]['projectTitle']
+    if(projectTitle == thisTitle):
+      output = "The project title was found in the project list."
+      if(len(thisTitle) > displayNchars):
+        outstr = u"{}...".format(thisTitle[:displayNchars])
+      else:
+        outstr = thisTitle
+        
+      output = "The project name \"{}\" was found.".format(outstr)
+      status = "SUCCESS"
+      return False
+      
+  output = "The project title \"{}\" was not found in the project list.".format(titleShort)
+  status = "SUCCESS"
+  return False
+      ]]></code>
+   <selector>
+      <name>projectTitle</name>
+      <xpath>/eml/dataset/project/title
+      </xpath>
+   </selector>
+   <dialect>
+      <name>Ecological Metadata Language</name>
+      <xpath>boolean(/*[local-name() = 'eml'])</xpath>
+   </dialect>
+</mdq:check>

From 3f072ad3c101d9bc3cf5aaf41c1050dbeca1984f Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Tue, 14 Dec 2021 09:34:07 -0800
Subject: [PATCH 02/36] Add resource.projectTitle.controlled

Issue #420 this check searches the official ESS/DOE project list for a match with the EML project title. If an exact match is not found, the closest fuzzy match is found, given a difference tolerance.
---
 .../resource.projectTitle.controlled.xml      | 132 +++++++++---------
 1 file changed, 68 insertions(+), 64 deletions(-)

diff --git a/src/checks/resource.projectTitle.controlled.xml b/src/checks/resource.projectTitle.controlled.xml
index 9d98838..ec40776 100644
--- a/src/checks/resource.projectTitle.controlled.xml
+++ b/src/checks/resource.projectTitle.controlled.xml
@@ -5,76 +5,80 @@
    <description>Check if the project title is contained in a list of known projects.</description>
    <type>Findable</type>
    <level>REQUIRED</level>
-   <environment>python</environment>
+   <environment>rscript</environment>
    <code><![CDATA[
-def call():
-  global output
-  global status
-  global projectTitle
-  global data
-  displayNchars = 40
-
-  import json
-  import metadig.variable as mvar
-  
-  # Read ESS-DIVE project file from remote location
-  dataFilename = "ess-dive-projects.json"
-  formatsFile = ""
-  # The checks data directory is passed via the 'mdq_params' hash
-  # The filename is known only to this check.
-  if('mdq_params' not in globals()):
-    output = "Internal error running check, mdq_params not available to check."
-    status = "ERROR"
-    return False
-  else:
-    projectFile = "{}/{}".format(mdq_params['metadigDataDir'], dataFilename)
-
-  # Retrieve the project name from the metadata
-  # A project title is not present
-  if 'projectTitle' not in globals() or projectTitle is None:
-    output = "No project name was found."
-    status = "FAILURE"
-    return False
-        
-  projectTitle = mvar.toUnicode(projectTitle)     
-  
-  # If the title in the metadata is blank, then return
-  if (mvar.isBlank(projectTitle)):
-    output = "The project name is blank."
-    status = "FAILURE"
-    return False
-  else:
-    if(len(projectTitle) > displayNchars):
-      titleShort = u"{}...".format(projectTitle[:displayNchars])
-    else:
-      titleShort = projectTitle
-  
-  # Loop through the projects in the list and see if there is 
-  # a match with the name from the metadig
-  with open(projectFile, "r") as content:
-    data = json.load(content)
+    library(jsonlite)
+    library(stringdist)
     
-  for key in data:
-    thisTitle = data[key]['projectTitle']
-    if(projectTitle == thisTitle):
-      output = "The project title was found in the project list."
-      if(len(thisTitle) > displayNchars):
-        outstr = u"{}...".format(thisTitle[:displayNchars])
-      else:
-        outstr = thisTitle
-        
-      output = "The project name \"{}\" was found.".format(outstr)
-      status = "SUCCESS"
-      return False
+    if (length(projectTitle) == 0) {
+      status <- "FAILURE"
+      message <- "No project title was found."
+    } else if (length(projectTitle) > 1) {
+      status <- "FAILURE"
+      message <- "More than one project title is present, only one is allowed."
+    } else {
+      library(stringr)
+      # Trim whitespace, split abstract on whitespace
+      projectTitle <- trimws(projectTitle)
       
-  output = "The project title \"{}\" was not found in the project list.".format(titleShort)
-  status = "SUCCESS"
-  return False
+      projectListFn <- "ess-dive-projects.json"
+      projectListPath <- sprintf("%s/%s", mdq_params[['metadigDataDir']], projectListFn)
+      projects <- read_json(projectListPath, simplifyVector = FALSE)
+      controlledProjectTitles = list()
+      # Load project titles into a simple list, for use by the string distance functions
+      for (i in 1:length(projects)) {
+          controlledProjectTitles[i] <- projects[[i]]$projectTitle
+      }
+    }  
+
+    maxDist = 100
+    diffTolerance = 0.65
+    noMatchFound <- 0
+    closestDist = maxDist
+    closestDistIndex = NA
+    smallestPercentDiff <- 10000
+    exactMatchFound <- FALSE
+    message <- list()
+    for (ictrl in 1:length(controlledProjectTitles)) {
+        dist <- stringdist(projectTitle, controlledProjectTitles[[ictrl]], method=c("lv"))
+        percentDiff <- dist/nchar(projectTitle)
+        if(percentDiff < smallestPercentDiff) {
+            smallestPercentDiff <- percentDiff
+        }
+        if(dist == 0) {
+            exactMatchFound <- TRUE
+            break
+        } else if (dist < closestDist) {
+            closestDist <- dist
+            closestDistIndex <- ictrl
+        } 
+    }
+    
+    status <- "FAILURE"
+    message <- list()
+    if (exactMatchFound) {
+        message[1] <- "The DOE project title was found in the controlled list of ESS projects."
+        message[2] <- "foo"
+        status <- "SUCCESS"
+    } else {
+        if(smallestPercentDiff < diffTolerance) {
+            # close match found
+            status <- "FAILURE"
+            message <- sprintf("The DOE project title listed is not from the controlled list of ESS projects: %s. \nThe closest match is: %s", projectTitle, controlledProjectTitles[[closestDistIndex]])
+        } else {
+            # No match found
+            message <- sprintf("The DOE project title listed is not from the controlled list of ESS projects: %s\n", projectTitle)
+            status <- "FAILURE"
+        }
+    }
+
+     mdq_result <- list(status = status,
+                        #output = list(list(value = message)))
+                        output = list(message)
       ]]></code>
    <selector>
       <name>projectTitle</name>
-      <xpath>/eml/dataset/project/title
-      </xpath>
+      <xpath>/eml/dataset/project/title</xpath>
    </selector>
    <dialect>
       <name>Ecological Metadata Language</name>

From 5a8b162726a477060c618e2c0abd2120d0d2b763 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Tue, 14 Dec 2021 09:54:24 -0800
Subject: [PATCH 03/36] Add comments, update tolerance value

Issue #420
---
 .../resource.projectTitle.controlled.xml      | 22 ++++++++++++-------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/src/checks/resource.projectTitle.controlled.xml b/src/checks/resource.projectTitle.controlled.xml
index ec40776..5cca1b4 100644
--- a/src/checks/resource.projectTitle.controlled.xml
+++ b/src/checks/resource.projectTitle.controlled.xml
@@ -10,6 +10,10 @@
     library(jsonlite)
     library(stringdist)
     
+    # This check extracts the project tilte from the metadata document and compares it
+    # to a controlled list of DOE projects for an exact match. If an exact match is not 
+    # found, the closest fuzzy match is found and displayed in the check output.
+    # Check the project title extracted from the metadata document
     if (length(projectTitle) == 0) {
       status <- "FAILURE"
       message <- "No project title was found."
@@ -21,18 +25,20 @@
       # Trim whitespace, split abstract on whitespace
       projectTitle <- trimws(projectTitle)
       
+      # Read in the controlled project title list
       projectListFn <- "ess-dive-projects.json"
       projectListPath <- sprintf("%s/%s", mdq_params[['metadigDataDir']], projectListFn)
       projects <- read_json(projectListPath, simplifyVector = FALSE)
       controlledProjectTitles = list()
-      # Load project titles into a simple list, for use by the string distance functions
+      # Load project titles into a simple list, for use with the string distance functions
       for (i in 1:length(projects)) {
           controlledProjectTitles[i] <- projects[[i]]$projectTitle
       }
     }  
 
+    # When using the fuzzy match, a candidate match cannot be more different than this percent.
+    diffTolerance = 65.0 
     maxDist = 100
-    diffTolerance = 0.65
     noMatchFound <- 0
     closestDist = maxDist
     closestDistIndex = NA
@@ -41,7 +47,7 @@
     message <- list()
     for (ictrl in 1:length(controlledProjectTitles)) {
         dist <- stringdist(projectTitle, controlledProjectTitles[[ictrl]], method=c("lv"))
-        percentDiff <- dist/nchar(projectTitle)
+        percentDiff <- (dist/nchar(projectTitle)) * 100.0
         if(percentDiff < smallestPercentDiff) {
             smallestPercentDiff <- percentDiff
         }
@@ -56,25 +62,25 @@
     
     status <- "FAILURE"
     message <- list()
+    # An exact match was found
     if (exactMatchFound) {
-        message[1] <- "The DOE project title was found in the controlled list of ESS projects."
-        message[2] <- "foo"
+        message <- "The DOE project title was found in the controlled list of ESS projects."
         status <- "SUCCESS"
     } else {
+        # An exact match was not found, print out the closest match
         if(smallestPercentDiff < diffTolerance) {
             # close match found
             status <- "FAILURE"
             message <- sprintf("The DOE project title listed is not from the controlled list of ESS projects: %s. \nThe closest match is: %s", projectTitle, controlledProjectTitles[[closestDistIndex]])
         } else {
-            # No match found
+            # No match was found within the difference tolerance
             message <- sprintf("The DOE project title listed is not from the controlled list of ESS projects: %s\n", projectTitle)
             status <- "FAILURE"
         }
     }
 
      mdq_result <- list(status = status,
-                        #output = list(list(value = message)))
-                        output = list(message)
+                        output = list(list(value = message)))
       ]]></code>
    <selector>
       <name>projectTitle</name>

From 20b70d89a7bbbcee27868cc8b4bca2f446039590 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Wed, 15 Dec 2021 17:19:04 -0800
Subject: [PATCH 04/36] Add resource.URLs.resolvable

Issue #422 This check extracts URL strings from abstract, methods, and other fields and verifies that they resolve to a web address.
---
 src/checks/resource.URLs.resolvable.xml | 102 ++++++++++++++++++++++++
 1 file changed, 102 insertions(+)
 create mode 100644 src/checks/resource.URLs.resolvable.xml

diff --git a/src/checks/resource.URLs.resolvable.xml b/src/checks/resource.URLs.resolvable.xml
new file mode 100644
index 0000000..d8783e0
--- /dev/null
+++ b/src/checks/resource.URLs.resolvable.xml
@@ -0,0 +1,102 @@
+<?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>resource.URLs.resolvable.1</id>
+   <name>Metadata Identifier Resolvable</name>
+   <description>Check that the metadata identifier exists and is resolvable.</description>
+   <type>Accessible</type>
+   <level>REQUIRED</level>
+   <environment>python</environment>
+   <code><![CDATA[
+def call():
+
+  import metadig.variable as mvar
+  import metadig.checks as checks
+  import urllib
+  import re
+  global output
+  global status
+  global textFields
+  global uniqueUrls
+  global unresolvableUrls
+
+  urls = []
+
+  # Get all URLs from these fields abstract, location description, methods, and related references
+
+  # first get all fields and concat into one string
+  # tokenize the string
+  # extract all tokens that match a url pattern, e.g. 'http*://', doi:*, https://doi.org, etc
+  # remove duplicates
+  # 
+
+  if 'textFields' not in globals() or textFields is None:
+    output = "Unable to retrieve required text fields."
+    status = "FAILURE"
+    return False
+
+  if(mvar.isBlank(textFields)):
+    output = "The required text fields are blank."
+    status = "FAILURE"
+    return False
+  
+  # Convert to unicode so that non-ascii characters don't cause decoding errors
+  textFields = mvar.toUnicode(textFields)
+  
+  # The text fields can be a textType element, so it may contain multiple subelements, i.e. <para>, etc 
+  # Since the metadig-engine is stuck at XPath 1.0, we cannot use the xpath to gather these into 
+  # a single string.
+  if(isinstance(textFields, list)):
+    textFields = ' '.join(textFields)
+    
+  # Tokenize the string and extract possible URLs
+  textTokens = textFields.split(' ')
+  for token in textTokens:
+    if(re.match("^\s*http.*:\/", token)):
+      urls.append(token)
+      # If the identifier is a 'bare' DOI (e.g. "doi:10.18739/A2027H"), then prepend with a DOI resolver link
+      # i.e. https://dx.doi.org
+    elif (re.match("^\s*doi:.*", token)):
+      urls.append("https://dx.doi.org/{}".format(token.strip()))
+      
+  uniqueUrls = list(set(urls))
+  
+  unresolvableUrls = []
+  for url in uniqueUrls:
+       resolvable, msg = checks.isResolvable(url)
+       if (not resolvable):
+         unresolvableUrls.append(url);
+         
+  output = 'unresolved: ' + ' '.join(unresolvableUrls)
+  status = "SUCCESS"
+  return True
+       
+  #if (resolvable):
+  #  if(usedD1):
+  #    output = u'{} and is resolvable using the DataONE resolve service.'.format(output)
+  #  elif(isDOI):
+  #    output = u'{} and is resolvable using a DOI resolver.'.format(output)      
+  #  else:
+  #    output = u'{} and is resolvable.'.format(output)      
+  #        
+  #  status = "SUCCESS"
+  #  return True
+  #else:
+  #  output = u"{}, but is not resolvable.".format(output)      
+  #  status = "FAILURE"
+  #  return False
+   ]]></code>
+   <selector>
+      <name>textFields</name>
+      <!--Get all URLs from these fields abstract, location description, methods, and related references. -->
+      <xpath>
+          /eml/dataset/abstract//text()[normalize-space()] |
+          /eml/dataset/abstract//ulink/@url |
+          /eml/dataset/coverage/geographicCoverage/geographicDescription/text()[normalize-space] |
+          /eml/dataset/methods/methodStep/description//text()[normalize-space()] 
+      </xpath>
+   </selector>
+   <dialect>
+      <name>Ecological Metadata Language</name>
+      <xpath>boolean(/*[local-name() = 'eml'])</xpath>
+   </dialect>
+</mdq:check>

From 27a6d0df905d3241b2bb554828a7c50691d0e7aa Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Mon, 3 Jan 2022 13:50:52 -0800
Subject: [PATCH 05/36] Improve output message

Issue #422 If unresolvable URLs are found in the checked metadata fields, output the URLs that are in error.
---
 src/checks/resource.URLs.resolvable.xml | 39 +++++++++++++------------
 1 file changed, 20 insertions(+), 19 deletions(-)

diff --git a/src/checks/resource.URLs.resolvable.xml b/src/checks/resource.URLs.resolvable.xml
index d8783e0..f1d5e0e 100644
--- a/src/checks/resource.URLs.resolvable.xml
+++ b/src/checks/resource.URLs.resolvable.xml
@@ -18,6 +18,7 @@ def call():
   global textFields
   global uniqueUrls
   global unresolvableUrls
+  maxPrint = 5
 
   urls = []
 
@@ -59,31 +60,31 @@ def call():
       urls.append("https://dx.doi.org/{}".format(token.strip()))
       
   uniqueUrls = list(set(urls))
-  
   unresolvableUrls = []
+  
+  # Check each unique URL to see if it is resolvable. The 'isResolvable' function sends an HTTP 'Head'
+  # request to the URL.
   for url in uniqueUrls:
        resolvable, msg = checks.isResolvable(url)
        if (not resolvable):
          unresolvableUrls.append(url);
          
-  output = 'unresolved: ' + ' '.join(unresolvableUrls)
-  status = "SUCCESS"
-  return True
-       
-  #if (resolvable):
-  #  if(usedD1):
-  #    output = u'{} and is resolvable using the DataONE resolve service.'.format(output)
-  #  elif(isDOI):
-  #    output = u'{} and is resolvable using a DOI resolver.'.format(output)      
-  #  else:
-  #    output = u'{} and is resolvable.'.format(output)      
-  #        
-  #  status = "SUCCESS"
-  #  return True
-  #else:
-  #  output = u"{}, but is not resolvable.".format(output)      
-  #  status = "FAILURE"
-  #  return False
+  if (len(unresolvableUrls) > 0):
+    if(len(unresolvableUrls) == 1):
+      output = u'1 unresolvable URL found: {}'.format(', '.join(unresolvableUrls[0:maxPrint]))
+    # If unresolved is more than 'maxPrint' URLs, only print first maxPrint entries
+    elif(len(unresolvableUrls) <= maxPrint):
+      output = u'{} unresolvabled URLs found: {}'.format(len(unresolvableUrls), ', '.join(unresolvableUrls))
+    else:
+      output = u'{} unresolvable URLs found, here are the first {}: {}'.format(len(unresolvableUrls), maxPrint, ', '.join(unresolvableUrls[0:maxPrint]))
+      output += u", ..."
+      
+    status = "FAILURE"
+    return False
+  else:
+    output = u"{} No unresolvable URLs were found."
+    status = "SUCCESS"
+    return True
    ]]></code>
    <selector>
       <name>textFields</name>

From 7802ba1bc7d9cc891a415cd2bbe1381e6d5b9a1e Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Tue, 4 Jan 2022 14:27:54 -0800
Subject: [PATCH 06/36] Update output when check succeeds

Issue #422
---
 src/checks/resource.URLs.resolvable.xml | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/src/checks/resource.URLs.resolvable.xml b/src/checks/resource.URLs.resolvable.xml
index f1d5e0e..dc92356 100644
--- a/src/checks/resource.URLs.resolvable.xml
+++ b/src/checks/resource.URLs.resolvable.xml
@@ -71,20 +71,29 @@ def call():
          
   if (len(unresolvableUrls) > 0):
     if(len(unresolvableUrls) == 1):
-      output = u'1 unresolvable URL found: {}'.format(', '.join(unresolvableUrls[0:maxPrint]))
+      output = u'1 URL found provided in the metadata does not resolve correctly: {}'.format(', '.join(unresolvableUrls[0:maxPrint]))
     # If unresolved is more than 'maxPrint' URLs, only print first maxPrint entries
     elif(len(unresolvableUrls) <= maxPrint):
-      output = u'{} unresolvabled URLs found: {}'.format(len(unresolvableUrls), ', '.join(unresolvableUrls))
+      output = u'{} URLS provided in the metadadta do not resolve correctly: {}'.format(len(unresolvableUrls), ', '.join(unresolvableUrls))
     else:
-      output = u'{} unresolvable URLs found, here are the first {}: {}'.format(len(unresolvableUrls), maxPrint, ', '.join(unresolvableUrls[0:maxPrint]))
+      output = u'{} URLs provided in the metadata do not resolve correctly, here are the first {}: {}'.format(len(unresolvableUrls), maxPrint, ', '.join(unresolvableUrls[0:maxPrint]))
       output += u", ..."
       
     status = "FAILURE"
     return False
   else:
-    output = u"{} No unresolvable URLs were found."
-    status = "SUCCESS"
-    return True
+    if(len(uniqueUrls) == 0):
+      output = u'No URL were found in the metadata.'
+      status = "SUCCESS"
+      return True
+    elif (len(uniqueUrls) == 1):
+      output = u'The one URL found in the metadata resolves correctly'
+      status = "SUCCESS"
+      return True
+    else:
+      output = u'All {} URLs found in the metadata resolve correctly.'.format(len(uniqueUrls))
+      status = "SUCCESS"
+      return True
    ]]></code>
    <selector>
       <name>textFields</name>

From ef485c317c016377eed3eb13374e0320f2844c70 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Tue, 4 Jan 2022 14:28:31 -0800
Subject: [PATCH 07/36] ESS-DIVE suite 1.1.0 suite definition

Issue #423
---
 src/suites/ess-dive-1.1.0.xml | 128 ++++++++++++++++++++++++++++++++++
 1 file changed, 128 insertions(+)
 create mode 100644 src/suites/ess-dive-1.1.0.xml

diff --git a/src/suites/ess-dive-1.1.0.xml b/src/suites/ess-dive-1.1.0.xml
new file mode 100644
index 0000000..42213ee
--- /dev/null
+++ b/src/suites/ess-dive-1.1.0.xml
@@ -0,0 +1,128 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<mdq:suite 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>ess-dive.data.center.suite-1.1.0</id>
+  <name>ESS-DIVE Quality Suite</name>
+  <description>This is a the ESS-DIVE Quality Suite</description>
+  <check>
+      <id>resource.projectTitle.controlled-1.0.0</id>
+      <type>Findable</type>
+      <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>metadata.URLs.resolvable-1.1.0</id>
+    <type>Findable</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>resource.funderName.controlled-1.1.0</id>
+    <type>Findable</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>resource.landingPage.present.1</id>
+    <type>Accessible</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>resource.funderName.controlled-1.0.0</id>
+    <type>Findable</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>metadata.identifier.resolvable.1</id>
+    <type>Accessible</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>entity.format.nonproprietary.1</id>
+    <type>Reusable</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>check.creator.present.1</id>
+    <type>Findable</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>check.creator.info.1</id>
+    <type>Findable</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>check.contact.1</id>
+    <type>Findable</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>contact.has.ORCID.1</id>
+    <type>Findable</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>check.contact.info.1</id>
+    <type>Findable</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>check.abstract.100.words.1</id>
+    <type>Findable</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>dataset.keywords.minimum.1</id>
+    <type>Findable</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>dataset.keywords.overlap.1</id>
+    <type>Findable</type>
+    <level>OPTIONAL</level>
+  </check>
+  <check>
+    <id>dataset.title.length2.1</id>
+    <type>Findable</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>check.identifier.is.present.1</id>
+    <type>Findable</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>check.usage.is.cc.1</id>
+    <type>Reusable</type>
+    <level>OPTIONAL</level>
+  </check>
+  <check>
+    <id>check.temporal.coverage.1</id>
+    <type>Findable</type>
+    <level>OPTIONAL</level>
+  </check>
+  <check>
+    <id>check.geographic.description.1</id>
+    <type>Findable</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>check.bounding.coordinates.1</id>
+    <type>Findable</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>check.pub.date.1</id>
+    <type>Findable</type>
+    <level>REQUIRED</level>
+  </check>
+  <check>
+    <id>check.methods.present.1</id>
+    <type>Interoperable</type>
+    <level>REQUIRED</level>
+  </check>
+  <!-- This check has been removed 2019 12 06 per LBL request
+  <check>
+    <id>dataset.keywords.controlled.1</id>
+    <type>discovery</type>
+    <level>OPTIONAL</level>
+  </check>
+  -->
+</mdq:suite>

From 3276a7595b3ce331197f7499676d2c46f693e72f Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Thu, 6 Jan 2022 14:46:26 -0800
Subject: [PATCH 08/36] Update output msgs

Issue #420 Update the output based on comments from the ESS-DIVE team
---
 src/checks/resource.projectTitle.controlled.xml | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/src/checks/resource.projectTitle.controlled.xml b/src/checks/resource.projectTitle.controlled.xml
index 5cca1b4..eff41bc 100644
--- a/src/checks/resource.projectTitle.controlled.xml
+++ b/src/checks/resource.projectTitle.controlled.xml
@@ -10,6 +10,9 @@
     library(jsonlite)
     library(stringdist)
     
+    # Currenlty fuzzy matching is disabled, but may be used in a future version of this check.
+    useFuzzyMatch <- FALSE
+    
     # This check extracts the project tilte from the metadata document and compares it
     # to a controlled list of DOE projects for an exact match. If an exact match is not 
     # found, the closest fuzzy match is found and displayed in the check output.
@@ -19,7 +22,7 @@
       message <- "No project title was found."
     } else if (length(projectTitle) > 1) {
       status <- "FAILURE"
-      message <- "More than one project title is present, only one is allowed."
+      message <- "More than one project name is present, only one is allowed."
     } else {
       library(stringr)
       # Trim whitespace, split abstract on whitespace
@@ -64,19 +67,23 @@
     message <- list()
     # An exact match was found
     if (exactMatchFound) {
-        message <- "The DOE project title was found in the controlled list of ESS projects."
+        message <- "The DOE project name was found in the controlled list of ESS projects."
         status <- "SUCCESS"
-    } else {
+    } else if (useFuzzyMatch) {
         # An exact match was not found, print out the closest match
         if(smallestPercentDiff < diffTolerance) {
             # close match found
             status <- "FAILURE"
-            message <- sprintf("The DOE project title listed is not from the controlled list of ESS projects: %s. \nThe closest match is: %s", projectTitle, controlledProjectTitles[[closestDistIndex]])
+            message <- sprintf("The DOE project name listed is not from the controlled list of ESS projects: %s. \nThe closest match is: %s", projectTitle, controlledProjectTitles[[closestDistIndex]])
         } else {
             # No match was found within the difference tolerance
-            message <- sprintf("The DOE project title listed is not from the controlled list of ESS projects: %s\n", projectTitle)
+            message <- sprintf("The DOE project name listed is not from the controlled list of ESS projects: %s\n", projectTitle)
             status <- "FAILURE"
         }
+    } else {
+        # No match was found within the difference tolerance
+        message <- sprintf("The DOE project name is not from the controlled list of ESS projects: \"%s\"\n", projectTitle)
+        status <- "FAILURE"
     }
 
      mdq_result <- list(status = status,

From 5236f7be522ac7e1266f14d530e6d9ff040281fd Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Thu, 6 Jan 2022 14:47:24 -0800
Subject: [PATCH 09/36] Update check output

Issue #422 Minor updates to check output
---
 src/checks/resource.URLs.resolvable.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/checks/resource.URLs.resolvable.xml b/src/checks/resource.URLs.resolvable.xml
index dc92356..4469376 100644
--- a/src/checks/resource.URLs.resolvable.xml
+++ b/src/checks/resource.URLs.resolvable.xml
@@ -18,7 +18,7 @@ def call():
   global textFields
   global uniqueUrls
   global unresolvableUrls
-  maxPrint = 5
+  maxPrint = 3
 
   urls = []
 
@@ -71,7 +71,7 @@ def call():
          
   if (len(unresolvableUrls) > 0):
     if(len(unresolvableUrls) == 1):
-      output = u'1 URL found provided in the metadata does not resolve correctly: {}'.format(', '.join(unresolvableUrls[0:maxPrint]))
+      output = u'1 URL provided in the metadata does not resolve correctly: {}'.format(', '.join(unresolvableUrls[0:maxPrint]))
     # If unresolved is more than 'maxPrint' URLs, only print first maxPrint entries
     elif(len(unresolvableUrls) <= maxPrint):
       output = u'{} URLS provided in the metadadta do not resolve correctly: {}'.format(len(unresolvableUrls), ', '.join(unresolvableUrls))

From d95d009262c968d163992bfeea95b8fb752aa63b Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Thu, 6 Jan 2022 14:48:57 -0800
Subject: [PATCH 10/36] Update ESS-DIVE 1.1.0 check list

Issue #423 Remove 'resource.landingPage.present' check from the ESS-DIVE 1.1.0 suite
---
 src/suites/ess-dive-1.1.0.xml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/suites/ess-dive-1.1.0.xml b/src/suites/ess-dive-1.1.0.xml
index 42213ee..bc306bf 100644
--- a/src/suites/ess-dive-1.1.0.xml
+++ b/src/suites/ess-dive-1.1.0.xml
@@ -18,11 +18,13 @@
     <type>Findable</type>
     <level>REQUIRED</level>
   </check>
+  <!--
   <check>
     <id>resource.landingPage.present.1</id>
     <type>Accessible</type>
     <level>REQUIRED</level>
   </check>
+-->
   <check>
     <id>resource.funderName.controlled-1.0.0</id>
     <type>Findable</type>

From 728700101d3bdc360601aeeb952743b355e5f036 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Thu, 20 Jan 2022 15:31:25 -0800
Subject: [PATCH 11/36] Remove fuzzy logic processing

Issue #420 Remove fuzzy logic processing; rename check file to include a version number
---
 ....xml => resource.projectTitle.controlled-1.0.0.xml} | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)
 rename src/checks/{resource.projectTitle.controlled.xml => resource.projectTitle.controlled-1.0.0.xml} (87%)

diff --git a/src/checks/resource.projectTitle.controlled.xml b/src/checks/resource.projectTitle.controlled-1.0.0.xml
similarity index 87%
rename from src/checks/resource.projectTitle.controlled.xml
rename to src/checks/resource.projectTitle.controlled-1.0.0.xml
index eff41bc..ca742c5 100644
--- a/src/checks/resource.projectTitle.controlled.xml
+++ b/src/checks/resource.projectTitle.controlled-1.0.0.xml
@@ -1,6 +1,6 @@
 <?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>resource.projectTitle.controlled.1</id>
+   <id>resource.projectTitle.controlled-1.0.0</id>
    <name>Resource Project Title Controlled</name>
    <description>Check if the project title is contained in a list of known projects.</description>
    <type>Findable</type>
@@ -13,6 +13,8 @@
     # Currenlty fuzzy matching is disabled, but may be used in a future version of this check.
     useFuzzyMatch <- FALSE
     
+    errorMessge <- "Warning: The DOE project name listed is not from the controlled list of projects. When entering project name, use the autocomplete feature to choose from the existing projects. If you can not find your project name, try entering the PI name."
+    
     # This check extracts the project tilte from the metadata document and compares it
     # to a controlled list of DOE projects for an exact match. If an exact match is not 
     # found, the closest fuzzy match is found and displayed in the check output.
@@ -74,15 +76,15 @@
         if(smallestPercentDiff < diffTolerance) {
             # close match found
             status <- "FAILURE"
-            message <- sprintf("The DOE project name listed is not from the controlled list of ESS projects: %s. \nThe closest match is: %s", projectTitle, controlledProjectTitles[[closestDistIndex]])
+            message <- sprintf("%s The closest match is: %s\n", errorMessge, controlledProjectTitles[[closestDistIndex]])
         } else {
             # No match was found within the difference tolerance
-            message <- sprintf("The DOE project name listed is not from the controlled list of ESS projects: %s\n", projectTitle)
+            message <- sprintf("%s\n", errorMessge)
             status <- "FAILURE"
         }
     } else {
         # No match was found within the difference tolerance
-        message <- sprintf("The DOE project name is not from the controlled list of ESS projects: \"%s\"\n", projectTitle)
+        message <- sprintf("%s\n", errorMessage)
         status <- "FAILURE"
     }
 

From 9f5ce480464f6a16c14604d8199bb456e7d28508 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Thu, 20 Jan 2022 15:53:11 -0800
Subject: [PATCH 12/36] Add metadata.identifier.resolvable to ESS-DIVE suite

Issue #427
---
 src/suites/ess-dive-1.1.0.xml | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/src/suites/ess-dive-1.1.0.xml b/src/suites/ess-dive-1.1.0.xml
index bc306bf..a660d73 100644
--- a/src/suites/ess-dive-1.1.0.xml
+++ b/src/suites/ess-dive-1.1.0.xml
@@ -24,12 +24,7 @@
     <type>Accessible</type>
     <level>REQUIRED</level>
   </check>
--->
-  <check>
-    <id>resource.funderName.controlled-1.0.0</id>
-    <type>Findable</type>
-    <level>REQUIRED</level>
-  </check>
+  -->
   <check>
     <id>metadata.identifier.resolvable.1</id>
     <type>Accessible</type>

From 40864afb57ecc0655c4acb71bc25f495b9d5daa8 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Fri, 21 Jan 2022 11:25:55 -0800
Subject: [PATCH 13/36] Updates to ESS-DIVE 1.1.0 suite

Issue #423 Update the ESS-DIVE 1.1.0 suite file, so that check '<level>' settings match the 1.0 suite.
---
 src/suites/ess-dive-1.1.0.xml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/suites/ess-dive-1.1.0.xml b/src/suites/ess-dive-1.1.0.xml
index a660d73..7b907ee 100644
--- a/src/suites/ess-dive-1.1.0.xml
+++ b/src/suites/ess-dive-1.1.0.xml
@@ -43,7 +43,7 @@
   <check>
     <id>check.creator.info.1</id>
     <type>Findable</type>
-    <level>REQUIRED</level>
+    <level>INFO</level>
   </check>
   <check>
     <id>check.contact.1</id>
@@ -58,7 +58,7 @@
   <check>
     <id>check.contact.info.1</id>
     <type>Findable</type>
-    <level>REQUIRED</level>
+    <level>INFO</level>
   </check>
   <check>
     <id>check.abstract.100.words.1</id>
@@ -93,17 +93,17 @@
   <check>
     <id>check.temporal.coverage.1</id>
     <type>Findable</type>
-    <level>OPTIONAL</level>
+    <level>REQUIRED</level>
   </check>
   <check>
     <id>check.geographic.description.1</id>
     <type>Findable</type>
-    <level>REQUIRED</level>
+    <level>OPTIONAL</level>
   </check>
   <check>
     <id>check.bounding.coordinates.1</id>
     <type>Findable</type>
-    <level>REQUIRED</level>
+    <level>OPTIONAL</level>
   </check>
   <check>
     <id>check.pub.date.1</id>

From e7570458b8b8b3855ecbd76f31597514b83ca619 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Fri, 21 Jan 2022 12:05:30 -0800
Subject: [PATCH 14/36] Add check.entity.present to ESS-DIVE suite

Issue #423
---
 src/suites/ess-dive-1.1.0.xml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/suites/ess-dive-1.1.0.xml b/src/suites/ess-dive-1.1.0.xml
index 7b907ee..3d11144 100644
--- a/src/suites/ess-dive-1.1.0.xml
+++ b/src/suites/ess-dive-1.1.0.xml
@@ -115,6 +115,12 @@
     <type>Interoperable</type>
     <level>REQUIRED</level>
   </check>
+  <check>
+    <id>check.entity.present.1</id>
+    <type>Interoperable</type>
+    <level>INFO</level>
+  </check>
+      
   <!-- This check has been removed 2019 12 06 per LBL request
   <check>
     <id>dataset.keywords.controlled.1</id>

From 950442733e16ed1595091bb47b7ef4ab230597d7 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Mon, 24 Jan 2022 11:22:15 -0800
Subject: [PATCH 15/36] Don't check DOI strings

Issue #422 Don't include "doi:..." as URLs - this was done for the identifier resolvability check, but isn't needed for this one. Also, made minor output message changes.
---
 src/checks/resource.URLs.resolvable.xml | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/src/checks/resource.URLs.resolvable.xml b/src/checks/resource.URLs.resolvable.xml
index 4469376..59b9bc1 100644
--- a/src/checks/resource.URLs.resolvable.xml
+++ b/src/checks/resource.URLs.resolvable.xml
@@ -1,6 +1,6 @@
 <?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>resource.URLs.resolvable.1</id>
+   <id>resource.URLs.resolvable-1.0.0</id>
    <name>Metadata Identifier Resolvable</name>
    <description>Check that the metadata identifier exists and is resolvable.</description>
    <type>Accessible</type>
@@ -52,12 +52,12 @@ def call():
   # Tokenize the string and extract possible URLs
   textTokens = textFields.split(' ')
   for token in textTokens:
-    if(re.match("^\s*http.*:\/", token)):
-      urls.append(token)
+    if(re.match("^\s*http.*:\/", token.strip())):
+      urls.append(token.strip())
+    #elif (re.match("^\s*doi:.*", token)):
       # If the identifier is a 'bare' DOI (e.g. "doi:10.18739/A2027H"), then prepend with a DOI resolver link
       # i.e. https://dx.doi.org
-    elif (re.match("^\s*doi:.*", token)):
-      urls.append("https://dx.doi.org/{}".format(token.strip()))
+      #urls.append("https://dx.doi.org/{}".format(token.strip()))
       
   uniqueUrls = list(set(urls))
   unresolvableUrls = []
@@ -68,26 +68,28 @@ def call():
        resolvable, msg = checks.isResolvable(url)
        if (not resolvable):
          unresolvableUrls.append(url);
-         
+
+  # Print errors message if unresolved URLs were found, and printing the first few unresolved.
   if (len(unresolvableUrls) > 0):
     if(len(unresolvableUrls) == 1):
-      output = u'1 URL provided in the metadata does not resolve correctly: {}'.format(', '.join(unresolvableUrls[0:maxPrint]))
+      output = u'1 of {} URLs provided in the metadata does not resolve correctly: {}'.format(len(uniqueUrls), ', '.join(unresolvableUrls[0:maxPrint]))
     # If unresolved is more than 'maxPrint' URLs, only print first maxPrint entries
     elif(len(unresolvableUrls) <= maxPrint):
-      output = u'{} URLS provided in the metadadta do not resolve correctly: {}'.format(len(unresolvableUrls), ', '.join(unresolvableUrls))
+      output = u'{} of {} URLS provided in the metadadta do not resolve correctly: {}'.format(len(unresolvableUrls), len(uniqueUrls), ', '.join(unresolvableUrls))
     else:
-      output = u'{} URLs provided in the metadata do not resolve correctly, here are the first {}: {}'.format(len(unresolvableUrls), maxPrint, ', '.join(unresolvableUrls[0:maxPrint]))
+      output = u'{} of {} URLs provided in the metadata do not resolve correctly, here are the first {}: {}'.format(len(unresolvableUrls), len(uniqueUrls), maxPrint, ', '.join(unresolvableUrls[0:maxPrint]))
       output += u", ..."
       
     status = "FAILURE"
     return False
   else:
+    # Print out success message.
     if(len(uniqueUrls) == 0):
       output = u'No URL were found in the metadata.'
       status = "SUCCESS"
       return True
     elif (len(uniqueUrls) == 1):
-      output = u'The one URL found in the metadata resolves correctly'
+      output = u'The one URL found in the metadata resolves correctly.'
       status = "SUCCESS"
       return True
     else:

From 28aeb09f9d476534e5498b9c4494e843893da12a Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Mon, 24 Jan 2022 13:30:58 -0800
Subject: [PATCH 16/36] Add ESS-DIVE award funder check

Issue #421
---
 ...ource.awardFunderName.controlled-1.0.0.xml | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 src/checks/resource.awardFunderName.controlled-1.0.0.xml

diff --git a/src/checks/resource.awardFunderName.controlled-1.0.0.xml b/src/checks/resource.awardFunderName.controlled-1.0.0.xml
new file mode 100644
index 0000000..baeb106
--- /dev/null
+++ b/src/checks/resource.awardFunderName.controlled-1.0.0.xml
@@ -0,0 +1,58 @@
+<?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>resource.awardFunderName.controlled-1.0.0</id>
+    <name>Award Funder Name Controlled</name>
+    <description>Check that an award funder name exists and is known (controlled)</description>
+    <type>Findable</type>
+    <level>OPTIONAL</level>
+    <environment>python</environment>
+    <code><![CDATA[
+def call():
+  # check: does an awardFunder exist?
+  import re
+  import java.util.ArrayList as ArrayList
+  import metadig.variable as mvar
+
+  # These global variables are read by the quality engine when
+  # the check returns
+  global output
+  global status
+  global awardFunder
+  
+  # Approved funder name, with python regex special characters escaped
+  approvedFunder = "U\.S\. DOE \> Office of Science \> Biological and Environmental Research \(BER\)"
+
+  # Item is not present
+  if 'awardFunder' not in globals() or awardFunder is None:
+    output = "An award funder was not found."
+    status = "FAILURE"
+    return False
+    
+  if(mvar.isBlank(awardFunder)):
+    output = "The award funder is blank."
+    status = "FAILURE"
+    return False
+    
+  awardFunder = re.sub(' +', ' ', awardFunder)
+  
+  # Allow additional characters before and after the approved funder, for example:
+  #  U.S. DOE > Office of Science (SC) &gt; Biological and Environmental Research (BER) (SC-23)
+  if(re.search(approvedFunder, awardFunder.strip())):
+    output = "The funding organzation \"{}\" was found in the metadata.".format(approvedFunder.replace('\\',''))
+    status = "SUCCESS"
+    return True
+  else:
+    output = "The funding organzation \"{}\" was not found in the metadata.".format(approvedFunder.replace('\\',''))
+    status = "FAILURE"
+    return False
+      ]]></code>
+    <selector>
+        <name>awardFunder</name>
+        <xpath>/eml/dataset/associatedParty[role/text()='fundingOrganization']/organizationName/text()[normalize-space()]</xpath>
+    </selector>
+    <dialect>
+        <name>Ecological Metadata Language</name>
+        <xpath>boolean(/*[local-name() = 'eml'])</xpath>
+    </dialect>
+</mdq:check>
+

From baaf81fe03fd5ac74fc466343c398e84d0fcf508 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Mon, 24 Jan 2022 15:48:24 -0800
Subject: [PATCH 17/36] Add new version of check.entity.present

Issue #126
---
 ...ity.present.check-2.0.0.xml => entity.present.check-1.0.1.xml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename src/checks/{entity.present.check-2.0.0.xml => entity.present.check-1.0.1.xml} (100%)

diff --git a/src/checks/entity.present.check-2.0.0.xml b/src/checks/entity.present.check-1.0.1.xml
similarity index 100%
rename from src/checks/entity.present.check-2.0.0.xml
rename to src/checks/entity.present.check-1.0.1.xml

From 348394d8a522b96b6c3ed96e5dd3659ed3217d3c Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Mon, 24 Jan 2022 17:18:24 -0800
Subject: [PATCH 18/36] Use versioning in filename

Issue #422
---
 ...rce.URLs.resolvable.xml => resource.URLs.resolvable-1.0.0.xml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename src/checks/{resource.URLs.resolvable.xml => resource.URLs.resolvable-1.0.0.xml} (100%)

diff --git a/src/checks/resource.URLs.resolvable.xml b/src/checks/resource.URLs.resolvable-1.0.0.xml
similarity index 100%
rename from src/checks/resource.URLs.resolvable.xml
rename to src/checks/resource.URLs.resolvable-1.0.0.xml

From ea1dfe3cd1e1f0782f7581741623af192d864231 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Mon, 24 Jan 2022 17:19:06 -0800
Subject: [PATCH 19/36] Add't versioning changes

Issue #423
---
 src/suites/ess-dive-1.1.0.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/suites/ess-dive-1.1.0.xml b/src/suites/ess-dive-1.1.0.xml
index 3d11144..1d659b1 100644
--- a/src/suites/ess-dive-1.1.0.xml
+++ b/src/suites/ess-dive-1.1.0.xml
@@ -31,7 +31,7 @@
     <level>REQUIRED</level>
   </check>
   <check>
-    <id>entity.format.nonproprietary.1</id>
+    <id>entity.format.nonproprietary-1.0.1</id>
     <type>Reusable</type>
     <level>REQUIRED</level>
   </check>

From a46235d4973c4fa665fcdd142c91d6cc72b9330e Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Wed, 26 Jan 2022 11:00:44 -0800
Subject: [PATCH 20/36] Handle multiple 'associatedParty' entries

Issue #421  updated this check to loop through all funders to look for the desired funding entity. These correspond to the EML elemnts 'associatedParty'  which are qualified with '<role>fundingOrganization</role>'.
---
 ...ource.awardFunderName.controlled-1.0.0.xml | 36 +++++++++++++------
 1 file changed, 25 insertions(+), 11 deletions(-)

diff --git a/src/checks/resource.awardFunderName.controlled-1.0.0.xml b/src/checks/resource.awardFunderName.controlled-1.0.0.xml
index baeb106..5f2a464 100644
--- a/src/checks/resource.awardFunderName.controlled-1.0.0.xml
+++ b/src/checks/resource.awardFunderName.controlled-1.0.0.xml
@@ -8,7 +8,7 @@
     <environment>python</environment>
     <code><![CDATA[
 def call():
-  # check: does an awardFunder exist?
+  # check: does the necessary awardFunder exist?
   import re
   import java.util.ArrayList as ArrayList
   import metadig.variable as mvar
@@ -17,27 +17,41 @@ def call():
   # the check returns
   global output
   global status
-  global awardFunder
+  global awardFunders
   
   # Approved funder name, with python regex special characters escaped
+  # Note that this program properly decodes both &#x3E; and &gt; as the '>' character.
   approvedFunder = "U\.S\. DOE \> Office of Science \> Biological and Environmental Research \(BER\)"
 
-  # Item is not present
-  if 'awardFunder' not in globals() or awardFunder is None:
+  # No award funders are present
+  if 'awardFunders' not in globals() or awardFunders is None:
     output = "An award funder was not found."
     status = "FAILURE"
     return False
     
-  if(mvar.isBlank(awardFunder)):
+  if(mvar.isBlank(awardFunders)):
     output = "The award funder is blank."
     status = "FAILURE"
     return False
     
-  awardFunder = re.sub(' +', ' ', awardFunder)
+  # Convert all values to unicode
+  awardFunders = mvar.toUnicode(awardFunders)
+  # If only a single value is returned (type "unicode" vs type "list"), then convert to a list
+  # for easier processing
+  if(isinstance(awardFunders, unicode)):
+    awardFunders = [awardFunders]
+    
+  found = False
+  for i in range(0, len(awardFunders)):
+    thisFunder = re.sub(' +', ' ', awardFunders[i])
   
-  # Allow additional characters before and after the approved funder, for example:
-  #  U.S. DOE > Office of Science (SC) &gt; Biological and Environmental Research (BER) (SC-23)
-  if(re.search(approvedFunder, awardFunder.strip())):
+    # Allow additional characters before and after the approved funder, for example:
+    #  U.S. DOE > Office of Science (SC) &gt; Biological and Environmental Research (BER) (SC-23)
+    if(re.search(approvedFunder, thisFunder.strip())):
+      found = True
+      break
+      
+  if(found):
     output = "The funding organzation \"{}\" was found in the metadata.".format(approvedFunder.replace('\\',''))
     status = "SUCCESS"
     return True
@@ -45,9 +59,9 @@ def call():
     output = "The funding organzation \"{}\" was not found in the metadata.".format(approvedFunder.replace('\\',''))
     status = "FAILURE"
     return False
-      ]]></code>
+    ]]></code>
     <selector>
-        <name>awardFunder</name>
+        <name>awardFunders</name>
         <xpath>/eml/dataset/associatedParty[role/text()='fundingOrganization']/organizationName/text()[normalize-space()]</xpath>
     </selector>
     <dialect>

From e1a155f665ac610eb2b21aaaed12946b097e1302 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Mon, 31 Jan 2022 15:31:19 -0800
Subject: [PATCH 21/36] Add entity.type.nonproprietary

Issue #436 ESS-DIVE has decided to use this check instead of entity.format.nonproprietary.
---
 src/checks/entity.type.nonpropriety.xml | 103 ++++++++++++++++++++++++
 1 file changed, 103 insertions(+)
 create mode 100644 src/checks/entity.type.nonpropriety.xml

diff --git a/src/checks/entity.type.nonpropriety.xml b/src/checks/entity.type.nonpropriety.xml
new file mode 100644
index 0000000..7a2465e
--- /dev/null
+++ b/src/checks/entity.type.nonpropriety.xml
@@ -0,0 +1,103 @@
+<?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>entity.type.nonproprietary-1.0.0</id>
+   <name>Non proprietary entity format</name>
+   <description>Check that all entities use non-propietary formats.</description>
+   <type>Reusable</type>
+   <level>REQUIRED</level>
+   <environment>python</environment>
+   <code><![CDATA[
+def call():
+  global output
+  global status
+  global mdq_params
+  global entityTypes
+  global entityNames
+  
+  # Check the data formats for all data entities.
+  # The check fails if the specified data format matches a format marked as proprietary.
+  # This check uses a reformatted copy of the DataONE format list, that is usually kept in the file 
+  # /opt/local/metadig/DataONEformats.csv. This file is manually edited to mark specific formats as proprietary. This file is obtained using the DataONE 'formats'
+  # service, i.e 'https://cn.dataone.org/cn/v2/formats'.
+  
+  import metadig.variable as mvar
+  import csv
+  maxPrint = 5
+  
+  def isProprietary(formats, thisFormat):
+    for row in formats:
+      if (row[4].lower().strip() in ("yes", "y", "true", "t", "1")):
+        if(row[2].lower().strip() == thisFormat.lower().strip()):
+          return True
+        if(row[3].lower().strip() == thisFormat.lower().strip()):
+          return True
+        
+    return False
+  
+  # Are any entity formats present?
+  if ('entityTypes' not in globals() or entityTypes is None):
+    output = "No data entities (files) were found so unable to check for proprietary formats."
+    status = "FAILURE"
+    return False
+    
+  dataFilename = "DataONEformats.csv"
+  formatsFile = ""
+  # The checks data directory is passed via the 'mdq_params' hash
+  # The filename is known only to this check.
+  if('mdq_params' not in globals()):
+    output = "Internal error running check, mdq_params not available to check."
+    status = "ERROR"
+    return False
+  else:
+    formatsFile = "{}/{}".format(mdq_params['metadigDataDir'], dataFilename)
+  
+  # Create list with the DataONE formats
+  formats = []
+  with open(formatsFile, 'rb') as csvfile:
+      fmtreader = csv.reader(csvfile, delimiter=',', quotechar='"')
+      for row in fmtreader:
+        formats.append(row)
+
+  entityTypes = mvar.toUnicode(entityTypes)
+  
+  # If only a single value is returned (vs type "list"), then convert to a list
+  # for easier processing
+  if(isinstance(entityTypes, unicode)):
+    entityTypes = [entityTypes]
+  
+  proprietaryFound = []
+        
+  # Check each entity format and see if it is in the 'proprietary' list, which
+  # is based on all formats from DataONE that have been manually determined t  o be
+  # proprietary
+  for i in range(0, len(entityTypes)):
+    # Check if the entity format is a single string or arrayList
+    thisFormat = entityTypes[i]
+    if(isProprietary(formats, thisFormat)):
+      proprietaryFound.append(thisFormat)
+      
+  if(len(proprietaryFound) > 0):
+    fmts = list(set([f.encode('UTF8') for f in proprietaryFound]))
+    output = u"It is recommended that non-proprietary file formats be used where possible. These {} proprietary data formats (out of {} total formats) were found: {}".format(len(fmts), len(entityTypes), ', '.join(fmts[0:maxPrint]))
+    if(len(fmts) > maxPrint):
+      output += u", ..."
+    status = "FAILURE"
+    return False
+  else:
+    output = "No proprietary data formats found (out of {} total formats.".format(len(entityTypes))
+    status = "SUCCESS"
+    return True
+      ]]></code>
+    <selector>
+      <name>entityTypes</name>
+      <xpath>/eml/dataset/otherEntity/entityType</xpath>
+    </selector>
+    <selector>
+      <name>entityNames</name>
+      <xpath>/eml/dataset/otherEntity/entityNames</xpath>
+   </selector>
+   <dialect>
+      <name>Ecological Metadata Language</name>
+      <xpath>boolean(/*[local-name() = 'eml'])</xpath>
+   </dialect>
+</mdq:check>

From 037ff8c7a535ec0ea969141dfb5ec887edad54ac Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Wed, 2 Feb 2022 15:45:44 -0800
Subject: [PATCH 22/36] Correct grammatical error

Issue #436
---
 src/checks/entity.type.nonpropriety.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/checks/entity.type.nonpropriety.xml b/src/checks/entity.type.nonpropriety.xml
index 7a2465e..fac66a0 100644
--- a/src/checks/entity.type.nonpropriety.xml
+++ b/src/checks/entity.type.nonpropriety.xml
@@ -84,7 +84,7 @@ def call():
     status = "FAILURE"
     return False
   else:
-    output = "No proprietary data formats found (out of {} total formats.".format(len(entityTypes))
+    output = "No proprietary data formats found (out of {} total formats).".format(len(entityTypes))
     status = "SUCCESS"
     return True
       ]]></code>

From 4d762cbd59d0c858028f25a9689903ff04c50b61 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Wed, 2 Feb 2022 15:46:50 -0800
Subject: [PATCH 23/36] Disable fuzzy string matching

Issue #420
---
 ...resource.projectTitle.controlled-1.0.0.xml | 54 ++++++++++---------
 1 file changed, 29 insertions(+), 25 deletions(-)

diff --git a/src/checks/resource.projectTitle.controlled-1.0.0.xml b/src/checks/resource.projectTitle.controlled-1.0.0.xml
index ca742c5..3c11b9d 100644
--- a/src/checks/resource.projectTitle.controlled-1.0.0.xml
+++ b/src/checks/resource.projectTitle.controlled-1.0.0.xml
@@ -8,12 +8,13 @@
    <environment>rscript</environment>
    <code><![CDATA[
     library(jsonlite)
-    library(stringdist)
+    #library(stringdist)
     
     # Currenlty fuzzy matching is disabled, but may be used in a future version of this check.
-    useFuzzyMatch <- FALSE
+    # The ESS-DIVE project title list is located at https://data.ess-dive.lbl.gov/js/themes/ess-dive/data/projects.json
+    #useFuzzyMatch <- FALSE
     
-    errorMessge <- "Warning: The DOE project name listed is not from the controlled list of projects. When entering project name, use the autocomplete feature to choose from the existing projects. If you can not find your project name, try entering the PI name."
+    errorMessage <- "Warning: The DOE project name listed is not from the controlled list of projects. When entering the project name, use the autocomplete feature to choose from the existing projects. If you can not find your project name, try entering the PI name."
     
     # This check extracts the project tilte from the metadata document and compares it
     # to a controlled list of DOE projects for an exact match. If an exact match is not 
@@ -51,18 +52,21 @@
     exactMatchFound <- FALSE
     message <- list()
     for (ictrl in 1:length(controlledProjectTitles)) {
-        dist <- stringdist(projectTitle, controlledProjectTitles[[ictrl]], method=c("lv"))
-        percentDiff <- (dist/nchar(projectTitle)) * 100.0
-        if(percentDiff < smallestPercentDiff) {
-            smallestPercentDiff <- percentDiff
-        }
-        if(dist == 0) {
+        if(tolower(projectTitle) == tolower(controlledProjectTitles[[ictrl]])) {
             exactMatchFound <- TRUE
-            break
-        } else if (dist < closestDist) {
-            closestDist <- dist
-            closestDistIndex <- ictrl
-        } 
+        }
+    #    dist <- stringdist(projectTitle, controlledProjectTitles[[ictrl]], method=c("lv"))
+    #    percentDiff <- (dist/nchar(projectTitle)) * 100.0
+    #    if(percentDiff < smallestPercentDiff) {
+    #        smallestPercentDiff <- percentDiff
+    #    }
+    #    if(dist == 0) {
+    #        exactMatchFound <- TRUE
+    #        break
+    #    } else if (dist < closestDist) {
+    #        closestDist <- dist
+    #        closestDistIndex <- ictrl
+    #    } 
     }
     
     status <- "FAILURE"
@@ -71,17 +75,17 @@
     if (exactMatchFound) {
         message <- "The DOE project name was found in the controlled list of ESS projects."
         status <- "SUCCESS"
-    } else if (useFuzzyMatch) {
-        # An exact match was not found, print out the closest match
-        if(smallestPercentDiff < diffTolerance) {
-            # close match found
-            status <- "FAILURE"
-            message <- sprintf("%s The closest match is: %s\n", errorMessge, controlledProjectTitles[[closestDistIndex]])
-        } else {
-            # No match was found within the difference tolerance
-            message <- sprintf("%s\n", errorMessge)
-            status <- "FAILURE"
-        }
+    #} else if (useFuzzyMatch) {
+    #    # An exact match was not found, print out the closest match
+    #    if(smallestPercentDiff < diffTolerance) {
+    #        # close match found
+    #        status <- "FAILURE"
+    #        message <- sprintf("%s The closest match is: %s\n", errorMessge, controlledProjectTitles[[closestDistIndex]])
+    #    } else {
+    #        # No match was found within the difference tolerance
+    #        message <- sprintf("%s\n", errorMessge)
+    #        status <- "FAILURE"
+    #    }
     } else {
         # No match was found within the difference tolerance
         message <- sprintf("%s\n", errorMessage)

From db3ba465624d168de0b308008a43539d9455dc51 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Wed, 2 Feb 2022 15:47:37 -0800
Subject: [PATCH 24/36] Add related references

Issue #422
---
 src/checks/resource.URLs.resolvable-1.0.0.xml | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/checks/resource.URLs.resolvable-1.0.0.xml b/src/checks/resource.URLs.resolvable-1.0.0.xml
index 59b9bc1..f9b43ec 100644
--- a/src/checks/resource.URLs.resolvable-1.0.0.xml
+++ b/src/checks/resource.URLs.resolvable-1.0.0.xml
@@ -52,7 +52,12 @@ def call():
   # Tokenize the string and extract possible URLs
   textTokens = textFields.split(' ')
   for token in textTokens:
-    if(re.match("^\s*http.*:\/", token.strip())):
+    token = token.strip()
+    token = token.strip('.')
+    token = token.strip(';')
+    token = token.strip('(')
+    token = token.strip(')')
+    if(re.match(".*http.*:\/\/", token.strip())):
       urls.append(token.strip())
     #elif (re.match("^\s*doi:.*", token)):
       # If the identifier is a 'bare' DOI (e.g. "doi:10.18739/A2027H"), then prepend with a DOI resolver link
@@ -85,7 +90,7 @@ def call():
   else:
     # Print out success message.
     if(len(uniqueUrls) == 0):
-      output = u'No URL were found in the metadata.'
+      output = u'No URLs were found in the metadata.'
       status = "SUCCESS"
       return True
     elif (len(uniqueUrls) == 1):
@@ -104,7 +109,8 @@ def call():
           /eml/dataset/abstract//text()[normalize-space()] |
           /eml/dataset/abstract//ulink/@url |
           /eml/dataset/coverage/geographicCoverage/geographicDescription/text()[normalize-space] |
-          /eml/dataset/methods/methodStep/description//text()[normalize-space()] 
+          /eml/dataset/methods/methodStep/description//text()[normalize-space()] |
+          /eml/dataset/additionalInfo//text()[normalize-space()]
       </xpath>
    </selector>
    <dialect>

From 15f22981452e8d1a78f17efc8e7d8317502a568b Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Wed, 2 Feb 2022 15:48:28 -0800
Subject: [PATCH 25/36] Update check version numbers, update some names

Issue #423
---
 src/suites/ess-dive-1.1.0.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/suites/ess-dive-1.1.0.xml b/src/suites/ess-dive-1.1.0.xml
index 1d659b1..ae7dcae 100644
--- a/src/suites/ess-dive-1.1.0.xml
+++ b/src/suites/ess-dive-1.1.0.xml
@@ -9,16 +9,16 @@
       <level>REQUIRED</level>
   </check>
   <check>
-    <id>metadata.URLs.resolvable-1.1.0</id>
+    <id>resource.URLs.resolvable-1.0.0</id>
     <type>Findable</type>
     <level>REQUIRED</level>
   </check>
   <check>
-    <id>resource.funderName.controlled-1.1.0</id>
+    <id>resource.awardFunderName.controlled-1.0.0</id>
     <type>Findable</type>
     <level>REQUIRED</level>
   </check>
-  <!--
+  <!-- Not included in 1.1.0 suite
   <check>
     <id>resource.landingPage.present.1</id>
     <type>Accessible</type>
@@ -31,7 +31,7 @@
     <level>REQUIRED</level>
   </check>
   <check>
-    <id>entity.format.nonproprietary-1.0.1</id>
+    <id>entity.type.nonproprietary-1.0.0</id>
     <type>Reusable</type>
     <level>REQUIRED</level>
   </check>

From f1ac27e8ce280fb221503d224de0ac20279483ee Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Mon, 14 Feb 2022 10:18:58 -0800
Subject: [PATCH 26/36] Handle DataONE private documents

Issue #60
---
 .../metadata.identifier.resolvable-1.1.0.xml  | 101 ++++++++++++++++++
 src/checks/metadata.identifier.resolvable.xml |   2 +-
 2 files changed, 102 insertions(+), 1 deletion(-)
 create mode 100644 src/checks/metadata.identifier.resolvable-1.1.0.xml

diff --git a/src/checks/metadata.identifier.resolvable-1.1.0.xml b/src/checks/metadata.identifier.resolvable-1.1.0.xml
new file mode 100644
index 0000000..fea176a
--- /dev/null
+++ b/src/checks/metadata.identifier.resolvable-1.1.0.xml
@@ -0,0 +1,101 @@
+<?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>metadata.identifier.resolvable.1</id>
+   <name>Metadata Identifier Resolvable</name>
+   <description>Check that the metadata identifier exists and is resolvable.</description>
+   <type>Accessible</type>
+   <level>REQUIRED</level>
+   <environment>python</environment>
+   <code><![CDATA[
+def call():
+  global output
+  global status
+
+  import metadig.variable as mvar
+  import metadig.checks as checks
+  import urllib
+  import re
+  global metadataIdentifier
+
+  d1_resolve_service="https://cn.dataone.org/cn/v2/resolve/"
+
+  # check if a metadata identifier is present
+  if 'metadataIdentifier' not in globals() or metadataIdentifier is None:
+    output = "A metadata identifier was not found."
+    status = "FAILURE"
+    return False
+    
+  metadataIdentifier = mvar.toUnicode(metadataIdentifier)
+  
+  # This should only be a single value, but if not (a list is returned) just get the first 
+  # one
+  if(isinstance(metadataIdentifier, list)):
+    metadataIdentifier = metadataIdentifier[0]
+
+  if (mvar.isBlank(metadataIdentifier)):
+    output = "The metadata identifier is blank."
+    status = "FAILURE"
+    return False
+  else:
+    output = u"The metadata identifier '{}' was found ".format(metadataIdentifier)
+    id = metadataIdentifier
+    
+  # Now check if the metadata identifier is a resolvable url. If it doesn't look like a URL, then 
+  # see if DataONE knows about it.
+  usedD1 = False
+  isDOI = False
+  if(re.match("^\s*http.*:\/", id)):
+    resolvable, msg = checks.isResolvable(id)
+  elif(re.match('doi:', id)):
+    isDOI = True
+    # If the identifier is a 'bare' DOI (e.g. "doi:10.18739/A2027H"), then prepend with a DOI resolver link
+    # i.e. https://dx.doi.org
+    resolvable, msg = checks.isResolvable("https://dx.doi.org/{}".format(id.strip()))
+  else:
+    usedD1 = True
+    url = "{}{}".format(d1_resolve_service,urllib.quote(id))
+    resolvable, msg = checks.isResolvable(url)
+        
+  if (resolvable):
+    if(usedD1):
+      output = u'{} and is resolvable using the DataONE resolve service.'.format(output)
+    elif(isDOI):
+      output = u'{} and is resolvable using a DOI resolver.'.format(output)      
+    else:
+      output = u'{} and is resolvable.'.format(output)      
+          
+    status = "SUCCESS"
+    return True
+  else:
+    # If the URL is unresolvable because it is private, and it is a DataONE identifier, then this
+    # special case will pass. Print an appropriate messge explaining this.
+    isPrivate = re.search("unauthorized", str.lower())
+    if(isPrivate && useD1):
+      output = u'{} and is resolvable using the DataONE resolve service, but is not publicly readable'.format(output)
+      status = "SUCCESS"
+    else:  
+      output = u"{}, but is not resolvable.".format(output)      
+      status = "FAILURE"
+      return False
+   ]]></code>
+   <selector>
+      <name>metadataIdentifier</name>
+      <xpath>
+             /resource/identifier |
+             /*/fileIdentifier/*/text()[normalize-space()] |
+             /eml/@packageId
+      </xpath>
+   </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>
diff --git a/src/checks/metadata.identifier.resolvable.xml b/src/checks/metadata.identifier.resolvable.xml
index 1adb3fd..d0ca377 100644
--- a/src/checks/metadata.identifier.resolvable.xml
+++ b/src/checks/metadata.identifier.resolvable.xml
@@ -37,7 +37,7 @@ def call():
     status = "FAILURE"
     return False
   else:
-    output = u"The metadata identifier '{}' was found)".format(metadataIdentifier)
+    output = u"The metadata identifier '{}' was found ".format(metadataIdentifier)
     id = metadataIdentifier
     
   # Now check if the metadata identifier is a resolvable url. If it doesn't look like a URL, then 

From a8deeee72a7017f9cba69badfba46048a9f2212e Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Mon, 14 Feb 2022 10:23:56 -0800
Subject: [PATCH 27/36] Improve parsing for URLS

Issue #422 When parsing the designated EML elements for URLs, make sure to strip off any punctuation that is not part of the URL before attempting to see if it resolves (i.e. '(', ')', ';', '.', ',')
---
 src/checks/resource.URLs.resolvable-1.0.0.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/checks/resource.URLs.resolvable-1.0.0.xml b/src/checks/resource.URLs.resolvable-1.0.0.xml
index f9b43ec..583ad46 100644
--- a/src/checks/resource.URLs.resolvable-1.0.0.xml
+++ b/src/checks/resource.URLs.resolvable-1.0.0.xml
@@ -54,6 +54,7 @@ def call():
   for token in textTokens:
     token = token.strip()
     token = token.strip('.')
+    token = token.strip(',')
     token = token.strip(';')
     token = token.strip('(')
     token = token.strip(')')

From a11501c77016a99e3bbf3533e00de40d40f46d04 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Mon, 14 Feb 2022 10:51:48 -0800
Subject: [PATCH 28/36] Include check version in filename

Issue #436
---
 ...y.type.nonpropriety.xml => entity.type.nonpropriety-1.0.0.xml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename src/checks/{entity.type.nonpropriety.xml => entity.type.nonpropriety-1.0.0.xml} (100%)

diff --git a/src/checks/entity.type.nonpropriety.xml b/src/checks/entity.type.nonpropriety-1.0.0.xml
similarity index 100%
rename from src/checks/entity.type.nonpropriety.xml
rename to src/checks/entity.type.nonpropriety-1.0.0.xml

From f8b8508516716030114b73acbe3d76d1c78f6d02 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Mon, 14 Feb 2022 11:06:15 -0800
Subject: [PATCH 29/36] Improve search for funder string

Issue #421
---
 src/checks/resource.awardFunderName.controlled-1.0.0.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/checks/resource.awardFunderName.controlled-1.0.0.xml b/src/checks/resource.awardFunderName.controlled-1.0.0.xml
index 5f2a464..aaa781c 100644
--- a/src/checks/resource.awardFunderName.controlled-1.0.0.xml
+++ b/src/checks/resource.awardFunderName.controlled-1.0.0.xml
@@ -20,8 +20,8 @@ def call():
   global awardFunders
   
   # Approved funder name, with python regex special characters escaped
-  # Note that this program properly decodes both &#x3E; and &gt; as the '>' character.
-  approvedFunder = "U\.S\. DOE \> Office of Science \> Biological and Environmental Research \(BER\)"
+  approvedFunder = "U.S. DOE > Office of Science > Biological and Environmental Research (BER)"
+  approvedFunderRegex = "U.S. DOE .* Office of Science .* Biological and Environmental Research \(BER\)"
 
   # No award funders are present
   if 'awardFunders' not in globals() or awardFunders is None:
@@ -44,10 +44,10 @@ def call():
   found = False
   for i in range(0, len(awardFunders)):
     thisFunder = re.sub(' +', ' ', awardFunders[i])
-  
+    
     # Allow additional characters before and after the approved funder, for example:
     #  U.S. DOE > Office of Science (SC) &gt; Biological and Environmental Research (BER) (SC-23)
-    if(re.search(approvedFunder, thisFunder.strip())):
+    if(re.match(approvedFunderRegex, thisFunder.strip())):
       found = True
       break
       

From 1690b61451fe65c712921be082c656c238a3aca1 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Mon, 14 Feb 2022 11:09:28 -0800
Subject: [PATCH 30/36] Minor change to output message

Issue #420
---
 src/checks/resource.projectTitle.controlled-1.0.0.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/checks/resource.projectTitle.controlled-1.0.0.xml b/src/checks/resource.projectTitle.controlled-1.0.0.xml
index 3c11b9d..99fe9d6 100644
--- a/src/checks/resource.projectTitle.controlled-1.0.0.xml
+++ b/src/checks/resource.projectTitle.controlled-1.0.0.xml
@@ -14,7 +14,7 @@
     # The ESS-DIVE project title list is located at https://data.ess-dive.lbl.gov/js/themes/ess-dive/data/projects.json
     #useFuzzyMatch <- FALSE
     
-    errorMessage <- "Warning: The DOE project name listed is not from the controlled list of projects. When entering the project name, use the autocomplete feature to choose from the existing projects. If you can not find your project name, try entering the PI name."
+    errorMessage <- "The DOE project name listed is not from the controlled list of projects. When entering the project name, use the autocomplete feature to choose from the existing projects. If you can not find your project name, try entering the PI name."
     
     # This check extracts the project tilte from the metadata document and compares it
     # to a controlled list of DOE projects for an exact match. If an exact match is not 

From 344e53858e68a968dcfced333148009ce1ed449b Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Mon, 14 Feb 2022 11:11:55 -0800
Subject: [PATCH 31/36] Improve output message

---
 src/checks/identifierIsPresent.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/checks/identifierIsPresent.xml b/src/checks/identifierIsPresent.xml
index 44dd857..dee889b 100644
--- a/src/checks/identifierIsPresent.xml
+++ b/src/checks/identifierIsPresent.xml
@@ -9,10 +9,10 @@
   <code><![CDATA[
 if (length(identifier) > 0) {
 mdq_result <- list(status = "SUCCESS",
-                   output = list(list(value = "An identifier is present.")))
+                   output = list(list(value = "An identifier associated with this metadata document is present.")))
 } else {
 mdq_result <- list(status = "FAILURE",
-                   output = list(list(value = "An identifier is not present.")))
+                   output = list(list(value = "An identifier associated with this metadata document is not present.")))
 }
     ]]>
   </code>

From 1badfab511f0f33c1837b0b34a038e3b8432f44e Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Mon, 14 Feb 2022 11:15:02 -0800
Subject: [PATCH 32/36] Changed some ESS-DIVE suite checks to 'OPTIONAL'

Issue #423 Changed these checks to optional:
- resource.projectTitle.controlled
- resource.awardFunderName.controlled
- metadata.identifier.resolvable
- entity.type.nonproprietary
---
 src/suites/ess-dive-1.1.0.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/suites/ess-dive-1.1.0.xml b/src/suites/ess-dive-1.1.0.xml
index ae7dcae..8b18f7f 100644
--- a/src/suites/ess-dive-1.1.0.xml
+++ b/src/suites/ess-dive-1.1.0.xml
@@ -6,7 +6,7 @@
   <check>
       <id>resource.projectTitle.controlled-1.0.0</id>
       <type>Findable</type>
-      <level>REQUIRED</level>
+      <level>OPTIONAL</level>
   </check>
   <check>
     <id>resource.URLs.resolvable-1.0.0</id>
@@ -16,7 +16,7 @@
   <check>
     <id>resource.awardFunderName.controlled-1.0.0</id>
     <type>Findable</type>
-    <level>REQUIRED</level>
+    <level>OPTIONAL</level>
   </check>
   <!-- Not included in 1.1.0 suite
   <check>
@@ -28,12 +28,12 @@
   <check>
     <id>metadata.identifier.resolvable.1</id>
     <type>Accessible</type>
-    <level>REQUIRED</level>
+    <level>OPTIONAL</level>
   </check>
   <check>
     <id>entity.type.nonproprietary-1.0.0</id>
     <type>Reusable</type>
-    <level>REQUIRED</level>
+    <level>OPTIONAL</level>
   </check>
   <check>
     <id>check.creator.present.1</id>

From 054639bf7e9963042d8c39f53d68dd228b21fcfb Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Tue, 15 Feb 2022 10:22:00 -0800
Subject: [PATCH 33/36] Add check/msg for Excel files

Issue #436
---
 src/checks/entity.type.nonpropriety-1.0.0.xml | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/src/checks/entity.type.nonpropriety-1.0.0.xml b/src/checks/entity.type.nonpropriety-1.0.0.xml
index fac66a0..10f51fe 100644
--- a/src/checks/entity.type.nonpropriety-1.0.0.xml
+++ b/src/checks/entity.type.nonpropriety-1.0.0.xml
@@ -20,9 +20,15 @@ def call():
   # /opt/local/metadig/DataONEformats.csv. This file is manually edited to mark specific formats as proprietary. This file is obtained using the DataONE 'formats'
   # service, i.e 'https://cn.dataone.org/cn/v2/formats'.
   
+  # An additional step is made in this check - if any entities with a Microsoft Excel mediaType are found, then an informational message is printed as a tip to 
+  # ensure that CSV files are included that correspond to the Excel file. As it is not possible to know if the dataset author has exported tabs from the
+  # Excel file into more reusable CSV format, this tip is printed.
+  
   import metadig.variable as mvar
   import csv
   maxPrint = 5
+  excelMediaTypes = ("application/vnd.ms-excel", "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet")
+  excelFileFound = False
   
   def isProprietary(formats, thisFormat):
     for row in formats:
@@ -72,19 +78,29 @@ def call():
   # proprietary
   for i in range(0, len(entityTypes)):
     # Check if the entity format is a single string or arrayList
-    thisFormat = entityTypes[i]
+    thisFormat = entityTypes[i].strip()
     if(isProprietary(formats, thisFormat)):
       proprietaryFound.append(thisFormat)
+    # Check if an Excel file was encountered
+    if(thisFormat.lower().strip() in excelMediaTypes):
+      excelFileFound = True
       
   if(len(proprietaryFound) > 0):
     fmts = list(set([f.encode('UTF8') for f in proprietaryFound]))
     output = u"It is recommended that non-proprietary file formats be used where possible. These {} proprietary data formats (out of {} total formats) were found: {}".format(len(fmts), len(entityTypes), ', '.join(fmts[0:maxPrint]))
     if(len(fmts) > maxPrint):
       output += u", ..."
+    else:
+      output += u"."
+      
+    if(excelFileFound):
+      output += u" TIP: If you have not already, upload a csv version for any excel file(s) included."
     status = "FAILURE"
     return False
   else:
     output = "No proprietary data formats found (out of {} total formats).".format(len(entityTypes))
+    if(excelFileFound):
+      output += u" TIP: If you have not already, upload a csv version for any excel file(s) included."
     status = "SUCCESS"
     return True
       ]]></code>

From 57bd3d22c329c591d89a3886f09154698ab2247e Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Tue, 15 Feb 2022 10:43:55 -0800
Subject: [PATCH 34/36] Update  a check version number

Issue #423
---
 src/checks/metadata.identifier.resolvable-1.1.0.xml | 2 +-
 src/suites/ess-dive-1.1.0.xml                       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/checks/metadata.identifier.resolvable-1.1.0.xml b/src/checks/metadata.identifier.resolvable-1.1.0.xml
index fea176a..9d7a444 100644
--- a/src/checks/metadata.identifier.resolvable-1.1.0.xml
+++ b/src/checks/metadata.identifier.resolvable-1.1.0.xml
@@ -1,6 +1,6 @@
 <?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>metadata.identifier.resolvable.1</id>
+   <id>metadata.identifier.resolvable-1.1.0</id>
    <name>Metadata Identifier Resolvable</name>
    <description>Check that the metadata identifier exists and is resolvable.</description>
    <type>Accessible</type>
diff --git a/src/suites/ess-dive-1.1.0.xml b/src/suites/ess-dive-1.1.0.xml
index 8b18f7f..407f160 100644
--- a/src/suites/ess-dive-1.1.0.xml
+++ b/src/suites/ess-dive-1.1.0.xml
@@ -26,7 +26,7 @@
   </check>
   -->
   <check>
-    <id>metadata.identifier.resolvable.1</id>
+    <id>metadata.identifier.resolvable-1.1.0</id>
     <type>Accessible</type>
     <level>OPTIONAL</level>
   </check>

From bdbe3409236148f470777ccec3c3f18a3ce50ef2 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Tue, 15 Feb 2022 10:50:37 -0800
Subject: [PATCH 35/36] Add data file for project name check

Issue #420
---
 data/ess-dive-projects.json | 3532 +++++++++++++++++++++++++++++++++++
 1 file changed, 3532 insertions(+)
 create mode 100644 data/ess-dive-projects.json

diff --git a/data/ess-dive-projects.json b/data/ess-dive-projects.json
new file mode 100644
index 0000000..b9a9b76
--- /dev/null
+++ b/data/ess-dive-projects.json
@@ -0,0 +1,3532 @@
+{
+  "Soil Carbon Biogeochemistry": {
+    "projectTitle": "Soil Carbon Biogeochemistry",
+    "piLastName": "Bailey",
+    "piFirstName": "Vanessa",
+    "piInstitution": "Pacific Northwest National Laboratory",
+    "piEmail": "Vanessa.Bailey@pnnl.gov",
+    "sponsorProgram": "TES",
+    "type": "Lab Awards",
+    "shortName": null
+  },
+  "Connecting AmeriFlux to the Globe, Extending the Partnership with the Global Flux Network, FLUXNET": {
+    "projectTitle": "Connecting AmeriFlux to the Globe, Extending the Partnership with the Global Flux Network, FLUXNET",
+    "piLastName": "Baldocchi",
+    "piFirstName": "Dennis",
+    "piInstitution": "Universiy of California, Berkeley",
+    "piEmail": "baldocchi@berkeley.edu",
+    "sponsorProgram": "TES",
+    "type": "University Awards",
+    "shortName": null
+  },
+  "Collaborative Research on Ecophysiological Controls on Amazonian Precipitation Seasonality and Variability": {
+    "projectTitle": "Collaborative Research on Ecophysiological Controls on Amazonian Precipitation Seasonality and Variability",
+    "piLastName": "Berry\nGentine\nLee\nLintner",
+    "piFirstName": "Joseph\nPierre\nJung-Eun\nBenjamin",
+    "piInstitution": "Carnegie Institution of Washington\nColumbia University\nBrown University\nRutgers University",
+    "piEmail": "joeberry@stanford.edu\npg2328@columbia.edu\njungelee.kim@gmail.com\nlintner@envsci.rutgers.edu",
+    "sponsorProgram": "TES",
+    "type": "University Awards",
+    "shortName": null
+  },
+  "Multi-scale Carbon Cycle Observations and Ecosystem Process Modeling at Niwot Rid": {
+    "projectTitle": "Multi-scale Carbon Cycle Observations and Ecosystem Process Modeling at Niwot Rid",
+    "piLastName": "Bowling\nBowling",
+    "piFirstName": "David\nDavid",
+    "piInstitution": "University of Utah\nUniversity of Utah, Salt Lake City, UT",
+    "piEmail": "david.bowling@utah.edu\ndavid.bowling@utah.edu",
+    "sponsorProgram": "TES",
+    "type": "University Awards",
+    "shortName": null
+  },
+  "Scaling from Flux Towers to Ecosystem Models: Regional Constraints on Carbon Cycle Processes from Atmospheric Carbonyl Sulfide": {
+    "projectTitle": "Scaling from Flux Towers to Ecosystem Models: Regional Constraints on Carbon Cycle Processes from Atmospheric Carbonyl Sulfide",
+    "piLastName": "Campbell\nCampbell",
+    "piFirstName": "Elliott\nJohn",
+    "piInstitution": "University of California, Merced\nThe Regents of the University of California, Merced, CA",
+    "piEmail": "ecampbell3@ucmerced.edu\necampbell3@ucmerced.edu",
+    "sponsorProgram": "TES",
+    "type": "University Awards",
+    "shortName": null
+  },
+  "Effects of Warming on Tropical Forest Carbon Cycling: Investigating Temperature Regulation of Key Tropical Tree and Soil Processes": {
+    "projectTitle": "Effects of Warming on Tropical Forest Carbon Cycling: Investigating Temperature Regulation of Key Tropical Tree and Soil Processes",
+    "piLastName": "Cavaleri\nReed",
+    "piFirstName": "Molly\nSasha",
+    "piInstitution": "Michigan Technological University\nUS Geological Survey",
+    "piEmail": "macavale@mtu.edu\nscreed@usgs.gov",
+    "sponsorProgram": "TES",
+    "type": "University Awards",
+    "shortName": null
+  },
+  "Next-Generation Ecosystem Experiments (NGEE) Tropics": {
+    "projectTitle": "Next-Generation Ecosystem Experiments (NGEE) Tropics",
+    "piLastName": "Chambers",
+    "piFirstName": "Jeffrey",
+    "piInstitution": "Lawrence Berkeley National Laboratory",
+    "piEmail": "jchambers@lbl.gov",
+    "sponsorProgram": "TES",
+    "type": "Lab Awards",
+    "shortName": "NGEE Tropics"
+  },
+  "Incorporating Rhizosphere Interactions and Soil Physical Properties into a Soil Carbon Degradation Model through Experimenting Across Ecotypes": {
+    "projectTitle": "Incorporating Rhizosphere Interactions and Soil Physical Properties into a Soil Carbon Degradation Model through Experimenting Across Ecotypes",
+    "piLastName": "Classen",
+    "piFirstName": "Aimee",
+    "piInstitution": "University of Tennessee",
+    "piEmail": "Aimee.Classen@uvm.edu",
+    "sponsorProgram": "TES",
+    "type": "University Awards",
+    "shortName": null
+  },
+  "Consequences of Plant Nutrient Uptake for Soil Carbon Stabilization": {
+    "projectTitle": "Consequences of Plant Nutrient Uptake for Soil Carbon Stabilization",
+    "piLastName": "Cusack",
+    "piFirstName": "Daniela",
+    "piInstitution": "University of California, Los Angles",
+    "piEmail": "dcusack@geog.ucla.edu",
+    "sponsorProgram": "TES",
+    "type": "Early Career",
+    "shortName": null
+  },
+  "Resolving Conflicting Physical and Biochemical Feedbacks to Climate in Response to Long-Term Warming": {
+    "projectTitle": "Resolving Conflicting Physical and Biochemical Feedbacks to Climate in Response to Long-Term Warming",
+    "piLastName": "DeAngelis",
+    "piFirstName": "Kristen",
+    "piInstitution": "University of Massachusetts Amherst",
+    "piEmail": "deangelis@microbio.umass.edu",
+    "sponsorProgram": "TES",
+    "type": "University Awards",
+    "shortName": null
+  },
+  "Confronting Models with Regional CO2 Observations": {
+    "projectTitle": "Confronting Models with Regional CO2 Observations",
+    "piLastName": "Ehleringer",
+    "piFirstName": "James",
+    "piInstitution": "University of Utah",
+    "piEmail": "jim.ehleringer@utah.edu",
+    "sponsorProgram": "TES",
+    "type": "University Awards",
+    "shortName": null
+  },
+  "Linking Topographic Variation in Belowground C Processes with Hydrological Processes to Improve Earth System Models": {
+    "projectTitle": "Linking Topographic Variation in Belowground C Processes with Hydrological Processes to Improve Earth System Models",
+    "piLastName": "Eissenstat",
+    "piFirstName": "David",
+    "piInstitution": "Pennsylvania State University",
+    "piEmail": "dme9@psu.edu",
+    "sponsorProgram": "TES",
+    "type": "University Awards",
+    "shortName": null
+  },
+  "Modeling the Effects of Warming and Elevated CO2 on Decomposition in a Northern Minnesota Black Spruce Peatland": {
+    "projectTitle": "Modeling the Effects of Warming and Elevated CO2 on Decomposition in a Northern Minnesota Black Spruce Peatland",
+    "piLastName": "Finzi",
+    "piFirstName": "Adrien",
+    "piInstitution": "Boston University",
+    "piEmail": "afinzi@bu.edu",
+    "sponsorProgram": "TES",
+    "type": "University Awards",
+    "shortName": null
+  },
+  "Nutrient Cycle Impacts on Forest Ecosystem Carbon Cycling: Improved Prediction of Climate Feedbacks from Coupled C-Nutrient Dynamics from Ecosystem to Regional Scales": {
+    "projectTitle": "Nutrient Cycle Impacts on Forest Ecosystem Carbon Cycling: Improved Prediction of Climate Feedbacks from Coupled C-Nutrient Dynamics from Ecosystem to Regional Scales",
+    "piLastName": "Fisher",
+    "piFirstName": "Joshua",
+    "piInstitution": "University of California- Los Angeles",
+    "piEmail": "jfisher@jifresse.ucla.edu",
+    "sponsorProgram": "TES",
+    "type": "University Awards",
+    "shortName": null
+  },
+  "The Carbon-Nutrient Economy of the Rhizosphere: Improving Biogeochemical Prediction and Scaling Feedbacks From Ecosystem to Regional Scales": {
+    "projectTitle": "The Carbon-Nutrient Economy of the Rhizosphere: Improving Biogeochemical Prediction and Scaling Feedbacks From Ecosystem to Regional Scales",
+    "piLastName": "Fisher",
+    "piFirstName": "Joshua",
+    "piInstitution": "University of California-Los Angeles",
+    "piEmail": "jfisher@jifresse.ucla.edu",
+    "sponsorProgram": "TES",
+    "type": "University Awards",
+    "shortName": null
+  },
+  "Arctic Shrub Expansion, Plant Functional Trait Variation, and Effects on Belowground Carbon Cycling": {
+    "projectTitle": "Arctic Shrub Expansion, Plant Functional Trait Variation, and Effects on Belowground Carbon Cycling",
+    "piLastName": "Fraterrigo",
+    "piFirstName": "Jennifer",
+    "piInstitution": "University of Illinois",
+    "piEmail": "jmf@illinois.edu",
+    "sponsorProgram": "TES",
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+  "Phenolic Compounds and Black Carbon Feedback Controls on Peat Decomposition and Carbon Accumulation in Southeastern Peatlands under Regimes of Seasonal Drought, Drainage and Frequent Fire: A New Model for Management of Carbon Sequestration": {
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+    "piInstitution": "Duke University",
+    "piEmail": "curtr@duke.edu",
+    "sponsorProgram": "TES",
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+  "Regional Vulnerability of Permafrost Carbon to Climate Change: A Multifactor Experiment and Model Network": {
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+    "piFirstName": "Ted",
+    "piInstitution": "Northern Arizona University",
+    "piEmail": "Ted.Schuur@nau.edu",
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+    "shortName": "TES-SFA"
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+  "Understanding Litter Input Controls on Soil Organic Matter Turnover and Formation are Essential for Improving Carbon-Climate Feedback Predictions for Arctic, Tundra Ecosystems": {
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+    "piEmail": "matthew.wallenstein@colostate.edu",
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+  "Use of Stable Mercury Isotopes to Assess Mercury and Methylmercury Transformation and Transport across Critical Interfaces from the Molecular to the Watershed Scale": {
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+    "sponsorProgram": "TES",
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+    "type": "Grant",
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+    "type": "Interagency Agreement",
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+  "Evaluating the Contribution of Climate Forcing and Forest Dynamics to Accelerating Carbon Sequestration by Forest Ecosystems in the Northeastern U.S.": {
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+    "sponsorProgram": "TES",
+    "type": "Grant",
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+  "Using a Regional Cluster of AmeriFlux Sites in Central California to Advance Our Knowledge on Decadal-Scale Ecosystem-Atmosphere Carbon Dioxide Exchange": {
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+    "sponsorProgram": "TES",
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+    "sponsorProgram": "TES",
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+    "piFirstName": "Russell",
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+    "sponsorProgram": "TES",
+    "type": "Grant",
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+    "sponsorProgram": "TES",
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+  "Ecosystem-Atmosphere Exchange Over a Mixed Deciduous Forest in the Midwest: How Does the Carbon Budget Respond to Short-and Long-Term Climate Variability?": {
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+    "piInstitution": "The Trustees of Indiana University, Bloomington, IN",
+    "piEmail": "frahman@thetrustees.org",
+    "sponsorProgram": "TES",
+    "type": "Grant",
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+    "sponsorProgram": "TES",
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+  "EFFECTS OF DISTURBANCE ON CARBON SEQUESTRATION IN THE NEW JERSEY PINE BARRENS": {
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+    "piInstitution": "Rutgers - State University of New Jersey, Newark, Newark, NJ",
+    "piEmail": "karinavr@newark.rutgers.edu",
+    "sponsorProgram": "TES",
+    "type": "Grant",
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+  },
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+  "Advanced Global Atmospheric Gases Experiment (AGAGE)": {
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+  },
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+    "piEmail": "cvaradarajan@lbl.gov",
+    "sponsorProgram": "ECRP",
+    "type": null,
+    "shortName": "iNAIADS"
+  }
+}

From b7435cd9d0cb692475171811d7537e157902a131 Mon Sep 17 00:00:00 2001
From: gothub <slaughter@nceas.ucsb.edu>
Date: Thu, 24 Feb 2022 11:29:09 -0800
Subject: [PATCH 36/36] Minor changes for ESS-DIVE 1.1.0 suite

Issue #423
---
 build.properties                                    |  5 +++--
 src/checks/metadata.identifier.resolvable-1.1.0.xml |  4 ++--
 src/checks/resource.URLs.resolvable-1.0.0.xml       | 12 +++++++++---
 3 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/build.properties b/build.properties
index 2225d7f..f083003 100644
--- a/build.properties
+++ b/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
diff --git a/src/checks/metadata.identifier.resolvable-1.1.0.xml b/src/checks/metadata.identifier.resolvable-1.1.0.xml
index 9d7a444..602bcea 100644
--- a/src/checks/metadata.identifier.resolvable-1.1.0.xml
+++ b/src/checks/metadata.identifier.resolvable-1.1.0.xml
@@ -69,8 +69,8 @@ def call():
   else:
     # If the URL is unresolvable because it is private, and it is a DataONE identifier, then this
     # special case will pass. Print an appropriate messge explaining this.
-    isPrivate = re.search("unauthorized", str.lower())
-    if(isPrivate && useD1):
+    isPrivate = re.search("unauthorized", msg.lower())
+    if(isPrivate and usedD1):
       output = u'{} and is resolvable using the DataONE resolve service, but is not publicly readable'.format(output)
       status = "SUCCESS"
     else:  
diff --git a/src/checks/resource.URLs.resolvable-1.0.0.xml b/src/checks/resource.URLs.resolvable-1.0.0.xml
index 583ad46..127c19c 100644
--- a/src/checks/resource.URLs.resolvable-1.0.0.xml
+++ b/src/checks/resource.URLs.resolvable-1.0.0.xml
@@ -48,14 +48,20 @@ def call():
   # a single string.
   if(isinstance(textFields, list)):
     textFields = ' '.join(textFields)
-    
+
+  # If the text spans multiple lines, convert line breaks to spaces
+  textFields = textFields.replace('\n', ' ')
+  textFields = textFields.replace('\r', ' ')
+  # Convert separater characters to spaces to assist parsing
+  textFields = textFields.replace(",", " ")
+  textFields = textFields.replace(";", " ")
+  
   # Tokenize the string and extract possible URLs
   textTokens = textFields.split(' ')
+  
   for token in textTokens:
     token = token.strip()
     token = token.strip('.')
-    token = token.strip(',')
-    token = token.strip(';')
     token = token.strip('(')
     token = token.strip(')')
     if(re.match(".*http.*:\/\/", token.strip())):