[GH-29] Read credentials from ENV or secrets.

Enable the plugin to read credentials from the environment variable:
* MMC_ADDRESS: address of the op center
* MMC_USERNAME: login username
* MMC_PASSWORD: login password

Hide the password in the log.

Add samples in the README to illustrate how to input the credentials
with NextFlow secrets.

README.md

@@ -122,6 +122,41 @@ float {
   * `commonExtra` allows the user to specify other submit parameters.  This parameter
     will be appended to every float submit command.
 
+### Configure with environment variables
+
+The plugin allows the user to set credentials with environment variables.
+If the credentials are not available in the configuration file, it will try
+reading these environment variables.
+
+* `MMC_ADDRESS` for operation center address.  Separate multiple addresses with `,`.
+* `MMC_USERNAME` for login username
+* `MMC_PASSWORD` for login password
+
+
+### Configure with NextFlow secrets
+
+User can use NextFlow secrets to input the credentials.  Here is an example:
+
+```bash
+nextflow secrets set MMC_USERNAME "..."
+nextflow secrets set MMC_PASSWORD "..."
+```
+
+In the configuration file, you can reference the secrets like this:
+
+```groovy
+float {
+    username = secrets.MMC_USERNAME
+    password = secrets.MMC_PASSWORD
+}
+```
+
+If the secret is not available, NextFlow reports error like this:
+
+```
+Unknown config secret 'MMC_USERNAME'
+```
+
 ## Task Sample
 
 For each process, users could supply their requirements for the CPU, memory and image.

plugins/nf-float/src/main/com/memverge/nextflow/FloatConf.groovy

@@ -25,6 +25,11 @@ import org.apache.commons.lang.StringUtils
  */
 @CompileStatic
 class FloatConf {
+    static String MMC_ADDRESS = "MMC_ADDRESS"
+    static String MMC_USERNAME = "MMC_USERNAME"
+    static String MMC_PASSWORD = "MMC_PASSWORD"
+    static String ADDR_SEP = ","
+
     /** credentials for op center */
     String username
     String password
@@ -67,14 +72,27 @@ class FloatConf {
             return
         }
         username = node.username
+        if (StringUtils.length(username) == 0) {
+            username = System.getenv(MMC_USERNAME)
+        }
         password = node.password
+        if (StringUtils.length(password) == 0) {
+            password = System.getenv(MMC_PASSWORD)
+        }
         if (node.address instanceof Collection) {
             addresses = (node.address as Collection).collect {
                 it.toString()
             }
         } else {
-            addresses = node.address.toString()
-                    .split(",")
+            String address = node.address
+            if (StringUtils.length(address) == 0) {
+                address = System.getenv(MMC_ADDRESS)
+                if (address == null) {
+                    address = ""
+                }
+            }
+            addresses = address.toString()
+                    .split(ADDR_SEP)
                     .toList()
                     .stream()
                     .filter { it.size() > 0 }
@@ -117,6 +135,7 @@ class FloatConf {
     }
 
     List<String> getCliPrefix(String address = "") {
+        validate()
         if (StringUtils.length(address) == 0) {
             address = addresses[0]
         }

plugins/nf-float/src/main/com/memverge/nextflow/FloatGridExecutor.groovy

@@ -162,6 +162,11 @@ class FloatGridExecutor extends AbstractGridExecutor {
         return floatConf.getCliPrefix(address)
     }
 
+    private String toCmdString(List<String> floatCmd) {
+        def ret = floatCmd.join(" ")
+        return ret.replace("-p ${floatConf.password}", "-p ***")
+    }
+
     @Override
     List<String> getSubmitCommandLine(TaskRun task, Path scriptFile) {
         validateTaskConf(task.config)
@@ -180,7 +185,7 @@ class FloatGridExecutor extends AbstractGridExecutor {
         cmd << '--name'
         cmd << floatJobs.getJobName(task.id)
         cmd.addAll(getExtra(task))
-        log.info "[float] submit job: ${cmd.join(' ')}"
+        log.info "[float] submit job: ${toCmdString(cmd)}"
         return cmd
     }
 
@@ -212,7 +217,7 @@ class FloatGridExecutor extends AbstractGridExecutor {
             if (ret != 0) {
                 def m = """\
                 Unable to kill pending jobs
-                - cmd executed: ${cmd.join(' ')}
+                - cmd executed: ${toCmdString(cmd)}}
                 - exit status : $ret
                 - output      :
                 """.stripIndent()
@@ -243,7 +248,7 @@ class FloatGridExecutor extends AbstractGridExecutor {
             cmd << 'scancel'
             cmd << '-j'
             cmd << id
-            log.info "[float] cancel job: ${cmd.join(' ')}"
+            log.info "[float] cancel job: ${toCmdString(cmd)}"
             ret.add(cmd)
         }
         return ret
@@ -260,7 +265,7 @@ class FloatGridExecutor extends AbstractGridExecutor {
         def cmd = getCmdPrefix0()
         cmd << 'scancel'
         cmd << '-j'
-        log.info "[float] cancel job: ${cmd.join(' ')}"
+        log.info "[float] cancel job: ${toCmdString(cmd)}"
         return cmd
     }
 
@@ -298,7 +303,7 @@ class FloatGridExecutor extends AbstractGridExecutor {
         cmd << 'squeue'
         cmd << '--format'
         cmd << 'json'
-        log.info "[float] query job status: ${cmd.join(' ')}"
+        log.info "[float] query job status: ${toCmdString(cmd)}"
         return cmd
     }