Fixed issue #54 - Nextflow installer does not work when running behin…

…d a proxy server
nextflow-io · Jul 20, 2015 · 439b572 · 439b572
1 parent 11cde2e
commit 439b572
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Showing 8 changed files with 139 additions and 51 deletions.
diff --git a/nextflow b/nextflow
@@ -88,6 +88,23 @@ function install() {
     echo ''
 }
 
+function launch_nextflow() {
+    # the launch command line
+    local cmdline="${launcher[@]} ${args[@]}"
+
+    # start in daemon mode
+    if [[ "$bg" ]]; then
+      local pid_file="${NXF_PID_FILE:-.nextflow.pid}"
+      bash -c "exec $cmdline" &
+      disown
+      printf $! > "$pid_file"
+      exit 0
+    fi
+    # trampoline syntax -- https://github.com/puniverse/capsule/pull/71
+    exec bash -c "exec $cmdline"
+    exit 1
+}
+
 # check self-install
 if [ "$0" = "bash" ] || [ "$0" = "/bin/bash" ]; then
     if [ -d nextflow ]; then
@@ -234,7 +251,7 @@ fi
 [[ "$cmd" == "node" && ! "$NXF_MODE" ]] && NXF_MODE='gridgain'
 
 COLUMNS=${COLUMNS:-`tty -s && tput cols 2>/dev/null || true`}
-JAVA_OPTS="-noverify -Dcapsule.trampoline"
+JAVA_OPTS="-noverify -Dcapsule.trampoline -Dcapsule.java.cmd=$JAVA_CMD"
 if [[ $cmd == console ]]; then bg=1;
 else JAVA_OPTS+=" -Djava.awt.headless=true"
 fi
@@ -254,15 +271,6 @@ fi
 export JAVA_CMD
 export CAPSULE_CACHE_DIR
 
-# Start in daemon mode
-if [[ "$bg" ]]; then
-  NXF_PID_FILE=${NXF_PID_FILE:-'.nextflow.pid'}
-  `"$JAVA_CMD" $JAVA_OPTS -jar "$NXF_BIN"` "${args[@]}" &
-  disown
-  printf $! > $NXF_PID_FILE
-  exit 0
-fi
-
 # lookup the a `md5` command
 if hash md5sum 2>/dev/null; then MD5=md5sum;
 elif hash gmd5sum 2>/dev/null; then MD5=gmd5sum;
@@ -272,7 +280,8 @@ fi
 
 # when no md5 command is available fallback on default execution
 if [ ! "$MD5" ] || [ "$CAPSULE_RESET" ]; then
-    exec `"$JAVA_CMD" $JAVA_OPTS -jar "$NXF_BIN"` "${args[@]}"
+    launcher=($("$JAVA_CMD" $JAVA_OPTS -jar "$NXF_BIN"))
+    launch_nextflow
     exit 1
 fi
 
@@ -292,14 +301,14 @@ EOF
 # checked if a cached classpath file exists and it newer that the nextflow boot jar file
 LAUNCH_FILE="${NXF_LAUNCHER}/classpath-$(env_md5)"
 if [ -s "$LAUNCH_FILE" ] && [ "$LAUNCH_FILE" -nt "$NXF_BIN" ]; then
-    LAUNCHER=$(cat "$LAUNCH_FILE")
+    launcher=($(cat "$LAUNCH_FILE"))
 else
-    # otherwise run the capsule and get the result classpath in the 'LAUNCHER' and save it to a file
-    LAUNCHER=`"$JAVA_CMD" $JAVA_OPTS -jar "$NXF_BIN"`
+    # otherwise run the capsule and get the result classpath in the 'launcher' and save it to a file
+    launcher=($("$JAVA_CMD" $JAVA_OPTS -jar "$NXF_BIN"))
     [[ $? -ne 0 ]] && echo 'Unable to initialize nextflow environment' && exit $?
     mkdir -p ${NXF_LAUNCHER}
-    echo "$LAUNCHER" > "$LAUNCH_FILE"
+    echo "${launcher[@]}" > "$LAUNCH_FILE"
 fi
 
-exec $LAUNCHER "${args[@]}"
-exit 1
+# finally run it
+launch_nextflow
diff --git a/src/main/groovy/nextflow/cli/Launcher.groovy b/src/main/groovy/nextflow/cli/Launcher.groovy
@@ -427,10 +427,18 @@ class Launcher implements ExitCode {
     }
 
     /**
-     * set up environment and system properties
+     * set up environment and system properties. It checks the following
+     * environment variables:
+     * <li>http_proxy</li>
+     * <li>https_proxy</li>
+     * <li>HTTP_PROXY</li>
+     * <li>HTTPS_PROXY</li>
      */
     private void setupEnvironment() {
 
+        setProxy('HTTP',System.getenv())
+        setProxy('HTTPS',System.getenv())
+
         setProxy('http',System.getenv())
         setProxy('https',System.getenv())
 
@@ -443,25 +451,25 @@ class Launcher implements ExitCode {
      * http://docs.oracle.com/javase/6/docs/technotes/guides/net/proxies.html
      * https://github.com/nextflow-io/nextflow/issues/24
      *
-     * @param qualifier Either {@code http} or {@code https}
+     * @param qualifier Either {@code http/HTTP} or {@code https/HTTPS}.
      * @param env The environment variables system map
      */
     @PackageScope
     static void setProxy(String qualifier, Map<String,String> env ) {
-        assert qualifier in ['http','https']
+        assert qualifier in ['http','https','HTTP','HTTPS']
         def str = null
-        def var = "${qualifier.toUpperCase()}_PROXY".toString()
+        def var = "${qualifier}_" + (qualifier.isLowerCase() ? 'proxy' : 'PROXY')
 
         // -- setup HTTP proxy
         try {
-            List<String> proxy = parseProxy(str = env.get(var))
+            List<String> proxy = parseProxy(str = env.get(var.toString()))
             if( proxy ) {
                 log.debug "Setting $qualifier proxy: $proxy"
-                System.setProperty("${qualifier}.proxyHost", proxy[0])
-                if( proxy[1] ) System.setProperty("${qualifier}.proxyPort", proxy[1])
+                System.setProperty("${qualifier.toLowerCase()}.proxyHost", proxy[0])
+                if( proxy[1] ) System.setProperty("${qualifier.toLowerCase()}.proxyPort", proxy[1])
             }
         }
-        catch (MalformedURLException e ) {
+        catch ( MalformedURLException e ) {
             log.warn "Not a valid $qualifier proxy: '$str' -- Check the value of variable `$var` in your environment"
         }
 

diff --git a/src/test/groovy/nextflow/cli/LauncherTest.groovy b/src/test/groovy/nextflow/cli/LauncherTest.groovy
@@ -243,17 +243,29 @@ class LauncherTest extends Specification {
         def httpsProxyPort =System.getProperty('https.proxyPort')
 
         when:
-        Launcher.setProxy('http', [HTTP_PROXY: 'alpha.com:333'])
+        Launcher.setProxy('HTTP', [HTTP_PROXY: 'alpha.com:333'])
         then:
         System.getProperty('http.proxyHost') == 'alpha.com'
         System.getProperty('http.proxyPort') == '333'
 
         when:
-        Launcher.setProxy('https', [HTTPS_PROXY: 'beta.com:5466'])
+        Launcher.setProxy('http', [http_proxy: 'gamma.com:444'])
+        then:
+        System.getProperty('http.proxyHost') == 'gamma.com'
+        System.getProperty('http.proxyPort') == '444'
+
+        when:
+        Launcher.setProxy('HTTPS', [HTTPS_PROXY: 'beta.com:5466'])
         then:
         System.getProperty('https.proxyHost') == 'beta.com'
         System.getProperty('https.proxyPort') == '5466'
 
+        when:
+        Launcher.setProxy('https', [https_proxy: 'zeta.com:6646'])
+        then:
+        System.getProperty('https.proxyHost') == 'zeta.com'
+        System.getProperty('https.proxyPort') == '6646'
+
         cleanup:
         System.setProperty('http.proxyHost', httpProxyHost ?: '')
         System.setProperty('http.proxyPort', httpProxyPort ?: '')

diff --git a/subprojects/my-capsule/build.gradle b/subprojects/my-capsule/build.gradle
@@ -22,8 +22,8 @@ apply plugin: 'application'
 
 dependencies {
     // Capsule manages the fat jar building process
-    compile 'co.paralleluniverse:capsule:1.0-rc1'
-    runtime 'co.paralleluniverse:capsule-maven:1.0-rc1'
+    compile 'co.paralleluniverse:capsule:1.0-rc2-SNAPSHOT'
+    runtime 'co.paralleluniverse:capsule-maven:1.0-rc2-SNAPSHOT'
     testCompile "junit:junit-dep:4.10"
     /* testCompile inherited from top gradle build file */
 }

diff --git a/subprojects/my-capsule/src/main/CapsuleLoader.java b/subprojects/my-capsule/src/main/CapsuleLoader.java
@@ -42,44 +42,36 @@ protected CapsuleLoader(Path jarFile) {
 
     @Override
     protected ProcessBuilder prelaunch(List<String> jvmArgs, List<String> args) {
-        ProcessBuilder pb = super.prelaunch(jvmArgs,args);
+        ProcessBuilder pb = super.prelaunch(jvmArgs, args);
 
         String drip = System.getenv().get("NXF_DRIP");
-        if( drip != null && !"".equals(drip) ) {
+        if( drip != null && !drip.isEmpty() ) {
             pb.command().set(0, drip);
             return pb;
         }
 
-        String javaCmd = System.getenv().get("JAVA_CMD");
-        if( javaCmd != null && !"".equals(javaCmd) ) {
-            // use the Java command provided by the env variable
-            pb.command().set(0, javaCmd);
-        }
-
         return pb;
     }
 
     @Override
+    @SuppressWarnings("unchecked")
     protected <T> T attribute(Map.Entry<String, T> attr) {
 
         if (ATTR_DEPENDENCIES == attr && System.getenv("NXF_GRAB") != null ) {
-            String customDeps = System.getenv("NXF_GRAB");
+            String deps = System.getenv("NXF_GRAB");
             List<String> parent = super.attribute((Map.Entry<String,List<String>>)attr);
-            return (T)extendDepsWith(System.getenv("NXF_GRAB"), parent);
+            return (T)extendDepsWith(deps, parent);
         }
 
         if (ATTR_APP_CLASS_PATH == attr && System.getenv("NXF_CLASSPATH") != null) {
             String classpath = System.getenv("NXF_CLASSPATH");
-            List<String> parent = super.attribute((Map.Entry<String, List<String>>) attr);
+            List<String> parent = super.attribute((Map.Entry<String, List<String>>)attr);
             return (T)extendClassPathWith(classpath, parent);
-
         }
 
         return super.attribute(attr);
     }
 
-
-
     static List<String> extendClassPathWith(String classpath, List<String> origin) {
         if( classpath == null || "".equals(classpath.trim()) ) {
             return origin;
@@ -90,7 +82,6 @@ static List<String> extendClassPathWith(String classpath, List<String> origin) {
             result.addAll(origin);
         }
 
-
         for( String lib : classpath.split(":") ) {
             String trimmed = lib.trim();
             if( trimmed.length()>0 )

diff --git a/subprojects/my-capsule/src/test/CapsuleLoaderTest.java b/subprojects/my-capsule/src/test/CapsuleLoaderTest.java
@@ -20,7 +20,6 @@
 
 import static org.junit.Assert.assertEquals;
 
-import java.nio.file.Paths;
 import java.util.Arrays;
 
 import org.junit.Test;
@@ -44,12 +43,10 @@ public void testExtendDeps () {
     @Test
     public void testExtendClasspath() {
         assertEquals( CapsuleLoader.extendClassPathWith(null, null), null );
-
-        assertEquals( CapsuleLoader.extendClassPathWith("x", null), Arrays.asList(Paths.get("x")));
-        assertEquals( CapsuleLoader.extendClassPathWith("x:y ", null), Arrays.asList(Paths.get("x"), Paths.get("y")));
-        assertEquals( CapsuleLoader.extendClassPathWith("x :: y ", null), Arrays.asList(Paths.get("x"), Paths.get("y")));
-
-        assertEquals( CapsuleLoader.extendClassPathWith("x:y:z", Arrays.asList(Paths.get("lib1.jar"), Paths.get("lib2.jar"))), Arrays.asList( Paths.get("lib1.jar"), Paths.get("lib2.jar"), Paths.get("x"), Paths.get("y"), Paths.get("z")));
+        assertEquals( CapsuleLoader.extendClassPathWith("x", null), Arrays.asList("x"));
+        assertEquals( CapsuleLoader.extendClassPathWith("x:y ", null), Arrays.asList("x","y"));
+        assertEquals( CapsuleLoader.extendClassPathWith("x :: y ", null), Arrays.asList("x","y"));
+        assertEquals( CapsuleLoader.extendClassPathWith("x:y:z", Arrays.asList("lib1.jar","lib2.jar")), Arrays.asList( "lib1.jar","lib2.jar","x","y","z"));
 
     }
 

diff --git a/subprojects/nxf-commons/src/main/nextflow/extension/Bolts.groovy b/subprojects/nxf-commons/src/main/nextflow/extension/Bolts.groovy
@@ -211,6 +211,49 @@ class Bolts {
         StringUtils.uncapitalize(self)
     }
 
+    /**
+     * Check if a alphabetic characters in a string are lowercase. Non alphabetic characters are ingored
+     * @param self The string to check
+     * @return {@true} if the string contains no uppercase characters, {@code false} otherwise
+     */
+    static boolean isLowerCase(String self) {
+        if( self ) for( int i=0; i<self.size(); i++ ) {
+            if( Character.isUpperCase(self.charAt(i)))
+                return false
+        }
+        return true
+    }
+
+    /**
+     * Check if a alphabetic characters in a string are uppercase. Non alphabetic characters are ignored
+     * @param self The string to check
+     * @return {@true} if the string contains no lowercase characters, {@code false} otherwise
+     */
+    static boolean isUpperCase(String self) {
+        if( self ) for( int i=0; i<self.size(); i++ ) {
+            if( Character.isLowerCase(self.charAt(i)))
+                return false
+        }
+        return true
+    }
+
+    /**
+     * Check if ALL characters in a string are lowercase.
+     * @param self The string to check
+     * @return {@true} when all characters are uppercase, {@code false} otherwise
+     */
+    static boolean isAllLowerCase(String self) {
+        StringUtils.isAllLowerCase(self)
+    }
+
+    /**
+     * Check if ALL characters in a string are uppercase.
+     * @param self The string to check
+     * @return {@true} when all characters are uppercase, {@code false} otherwise
+     */
+    static boolean isAllUpperCase(String self) {
+        StringUtils.isAllUpperCase(self)
+    }
 
     static private Pattern getPattern( obj ) {
 

diff --git a/subprojects/nxf-commons/src/test/nextflow/extension/BoltsTest.groovy b/subprojects/nxf-commons/src/test/nextflow/extension/BoltsTest.groovy
@@ -178,4 +178,32 @@ class BoltsTest extends Specification {
         salut.findBestMatchesFor('helo') == ['hello','halo']
     }
 
+    def 'should check lower case strings' () {
+        expect:
+        'abc'.isLowerCase()
+        !'AAA'.isLowerCase()
+        '1a11a1a'.isLowerCase()
+    }
+
+    def 'should check upper case strings' () {
+        expect:
+        'ABCD'.isUpperCase()
+        !'aaaa'.isUpperCase()
+        '1A11A1A'.isUpperCase()
+    }
+
+    def 'should check all lower case strings' () {
+        expect:
+        'abc'.isAllLowerCase()
+        !'AAA'.isAllLowerCase()
+        !'1a11a1a'.isAllLowerCase()
+    }
+
+    def 'should check all upper case strings' () {
+        expect:
+        'ABCD'.isAllUpperCase()
+        !'aaaa'.isAllUpperCase()
+        !'1A11A1A'.isAllUpperCase()
+    }
+
 }