Merge branch 'dev-0.2.0'

.gitignore

@@ -37,3 +37,6 @@ rsconnect/
 
 # Intellij project directory
 .idea/
+
+# Ant distribution directory
+dist/**

README.md

@@ -1,7 +1,7 @@
 ## metadig-checks: MetaDIG suites and checks for data and metadata improvement and guidance.
 
 
-- **Author**: Matthew B. Jones, Peter Slaughter ([NCEAS](http://www.nceas.ucsb.edu), Ted Habermann, Sean Gordon
+- **Author**: Matthew B. Jones, Peter Slaughter ([NCEAS](http://www.nceas.ucsb.edu)), Ted Habermann, Sean Gordon
 - **License**: [Apache 2](http://opensource.org/licenses/Apache-2.0)
 - [**Submit Bugs and feature requests**](https://github.com/NCEAS/metadig-checks/issues)
 

bin/stageFiles.py

@@ -0,0 +1,73 @@
+#!/Library/Frameworks/Python.framework/Versions/3.6/bin/python3
+
+import xml.etree.ElementTree as ET
+import os
+import re
+import argparse
+
+from shutil import copyfile
+
+# Locate files starting at path, with filenames that match a regex
+def findfiles(path, regex):
+    #print("regex: {}".format(regex))
+    regObj = re.compile(regex)
+    res = []
+    for root, dirs, fnames in os.walk(path):
+        for fname in fnames:
+            #print("fname: {}".format(fname))
+            if regObj.match(fname):
+                res.append(os.path.join(root, fname))
+                #print("root: {}, fname: {}".format(root, fname))
+    return res
+
+if __name__ == '__main__':
+
+    parser = argparse.ArgumentParser(description='stage MetaDIG checks and suites.')
+    parser.add_argument('src', metavar='N', type=str, nargs='+',
+                        help='source directory')
+    parser.add_argument('dst', metavar='N', type=str, nargs='+',
+                        help='destination directory')
+    parser.add_argument('suites', metavar='N', type=str, nargs='+',
+                        help='suites to stage')
+
+    args = parser.parse_args()
+    src = args.src[0]
+    dst = args.dst[0]
+    suites = args.suites[0].split(",")
+    cwd = os.getcwd()
+
+    print("source: {}".format(src))
+    print("destination: {}".format(dst))
+    print("suites: {}".format(suites))
+
+    for suite in suites:
+        # Parse the next suite XML to and find all the checks listed
+        print("processing suite: {}".format(suite))
+        copyfile("src/suites/{}".format(suite), "{}/suites/{}".format(dst, suite))
+
+        tree = ET.parse('src/suites/{}'.format(suite))
+        root = tree.getroot()
+
+        # Loop through all '<check' elements in this suite XML file
+        for check in root.findall('check'):
+            # Get the <id> element from the check
+            id = check.find('id').text
+            print("id: {}".format(id))
+
+        #print findfiles('src/checks', "<id>\s*{}\s*</id>".format(id))
+        #print findfiles('./src/checks', "<id>\s*{}\s*</id>".format(id))
+
+            # Find all check files available
+            checkFiles = findfiles('{}/checks'.format(src), "^.*xml$")
+            #print checkFiles
+            # for this id, search each check file to find the check file with this id
+            for file in checkFiles:
+                #print("file {}".format(file))
+                with open(file) as thisFile:
+                    if id in thisFile.read():
+                        print('found check id {} in file {}'.format(id, file))
+                        srcfile = "{}/{}".format(cwd, file)
+                        fname = os.path.basename(file)
+                        dstfile = "{}/{}/checks/{}".format(cwd, dst, fname)
+                        print("cp {} {}".format(srcfile, dstfile))
+                        copyfile(srcfile, dstfile)

build.properties

@@ -0,0 +1,15 @@
+# Ant build properties files for the metadig-checks build
+
+# MetaDIG checks version
+metadig-checks.version=0.2.0
+
+build=build
+dist=dist
+src=src
+bin=bin
+data=data
+# The script that reads suite XML files and copies all needed checks to dist
+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

build.xml

@@ -0,0 +1,59 @@
+<project name="MetaDIG-checks" default="dist" basedir=".">
+  <!-- This build file provides tasks to create distributions for the 
+       MetaDIG Quality Engine. 
+       Set properties in the file 'build.properties' to control the operation
+       of the tasks
+  -->
+  <property file="build.properties" />
+  <description>
+    MetaDIG Quality Engine Suites and Checks
+  </description>
+  <target name="init">
+    <!-- Create the time stamp -->
+    <tstamp/>   
+  </target>
+  <target name="dist" depends="init"
+        description="generate the MetaDIG Checks distribution">
+    <!-- Create the distribution directory -->
+    <mkdir dir="${dist}"/>
+    <mkdir dir="${dist}/checks"/>
+    <mkdir dir="${dist}/data"/>
+    <mkdir dir="${dist}/suites"/>
+
+    <copy todir="${dist}/data">
+      <fileset dir="${data}">
+      </fileset>
+    </copy>
+
+    <exec executable="${bin}/${stagescript}" spawn="false" output="stage.log">  
+        <arg value="src"/>
+        <arg value="dist"/>
+        <arg value="${suites}"/>
+    </exec>
+
+    <tar destfile="${dist}/metadig-checks-${metadig-checks.version}.tar">
+      <tarfileset dir="${dist}/checks"
+                  prefix="checks"
+                  preserveLeadingSlashes="false">
+        <include name="*.xml"/>
+      </tarfileset>
+      <tarfileset dir="${dist}/suites"
+                  prefix="suites"
+                  preserveLeadingSlashes="false">
+        <include name="*.xml"/>
+      </tarfileset>
+      <tarfileset dir="${dist}/data"
+                  prefix="data"
+                  preserveLeadingSlashes="false">
+        <include name="*.*"/>
+      </tarfileset>
+    </tar>
+  </target>
+
+  <target name="clean"
+        description="clean up">
+    <!-- Delete the ${build} and ${dist} directory trees -->
+    <delete dir="${build}"/>
+    <delete dir="${dist}"/>
+  </target>
+</project>