Changeset 5930

Timestamp:

May 6, 2020, 9:43:30 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1241: Some folders for external samples are not changed to the specified group

Location:

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie

Files:

• Reggie.java (modified) (1 diff)
• grid/CufflinksJobCreator.java (modified) (1 diff)
• grid/HisatAlignJobCreator.java (modified) (1 diff)
• grid/MBafJobCreator.java (modified) (1 diff)
• grid/MipsAlignJobCreator.java (modified) (1 diff)
• grid/MipsDemuxJobCreator.java (modified) (1 diff)
• grid/RnaSeqDemuxJobCreator.java (modified) (1 diff)
• grid/ScriptUtil.java (modified) (1 diff)
• grid/StringTieJobCreator.java (modified) (1 diff)
• grid/VariantCallingJobCreator.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/Reggie.java

@@ -417 +417 @@
   
   /**
+    Get the prefix from the name. A prefix is a
+    number of letters/numbers followed by an underscore.
+    Returns null if the name has no prefix.
+    @since 4.27
+  */
+  public static String getPrefix(String name)
+  {
+    int i = name.indexOf('_');
+    return i > 0 ? name.substring(0, i) : null;
+  }
+  
+  /**
     Mark all related files for removal.
     @since 2.16

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/CufflinksJobCreator.java

@@ -502 +502 @@
       if (externalGroup != null)
       {
-        script.cmd("chgrp -R " + externalGroup + " ${CufflinksFolder} 2>> ${WD}/chgrp.out || echo [" + rawName +"] >> ${WD}/chgrp.out");
+        ScriptUtil.addChgrp(externalGroup, "${CufflinksFolder}", rawName, null, script);
       }
       script.cmd("ls -1 ${CufflinksFolder}/* >> ${WD}/files.out");

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/HisatAlignJobCreator.java

@@ -444 +444 @@
       if (externalGroup != null)
       {
-        script.cmd("chgrp -R " + externalGroup + " ${HisatFolder} 2>> ${WD}/chgrp.out || echo [" + alignedName +"] >> ${WD}/chgrp.out");
+        ScriptUtil.addChgrp(externalGroup, "${HisatFolder}", alignedName, null, script);
       }
       script.cmd("ls -1 ${HisatFolder}/* >> ${WD}/files.out");

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/MBafJobCreator.java

@@ -251 +251 @@
       if (externalGroup != null)
       {
-        script.cmd("chgrp -R " + externalGroup + " ${BamFolder}/mbaf* 2>> ${WD}/chgrp.out || echo [" + aligned.getName() +"] >> ${WD}/chgrp.out" );
+        ScriptUtil.addChgrp(externalGroup, "${BamFolder}/mbaf*", aligned.getName(), null, script);
       }
 

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/MipsAlignJobCreator.java

@@ -413 +413 @@
       if (externalGroup != null)
       {
-        script.cmd("chgrp -R " + externalGroup + " ${AlignFolder} 2>> ${WD}/chgrp.out || echo [" + alignedName +"] >> ${WD}/chgrp.out");
+        ScriptUtil.addChgrp(externalGroup, "${AlignFolder}", alignedName, null, script);
       }
       script.cmd("ls -1 ${AlignFolder}/* >> ${WD}/files.out");

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/MipsDemuxJobCreator.java

@@ -367 +367 @@
         if (externalGroup != null)
         {
-          script.cmd("chgrp -R " + externalGroup + " " + fastqFolder + " 2>> ${WD}/chgrp.out || echo [" + mergeName +"] >> ${WD}/chgrp.out");
+          ScriptUtil.addChgrp(externalGroup, fastqFolder, mergeName, archiveRoot+"/"+Reggie.getPrefix(mergeName), script);
         }
         

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/RnaSeqDemuxJobCreator.java

@@ -450 +450 @@
         if (externalGroup != null)
         {
-          script.cmd("chgrp -R " + externalGroup + " " + fastqFolder + " 2>> ${WD}/chgrp.out || echo [" + mergeName +"] >> ${WD}/chgrp.out");
+          ScriptUtil.addChgrp(externalGroup, fastqFolder, mergeName, archiveRoot+"/"+Reggie.getPrefix(mergeName), script);
         }
 

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/ScriptUtil.java

@@ -71 +71 @@
   }
 
+  /**
+    Add a 'chgrp' command to set the group of the given 'folder' and all files and subdirectories in it.
+    If a 'parentFolder' is given and is a parent folder of the 'folder' a 'chgrp' command is added
+    to parent folder up to (but not including) the parent folder. Errors are logged to ${WD}/chgrp.out.
+    'itemName' is used for logging errors only
+    @since 4.27
+  */
+  public static void addChgrp(String groupName, String folder, String itemName, String parentFolder, ScriptBuilder script)
+  {
+    // Make sure parent folder ends with '/' and folder doesn't so that the while loop breaks correctly
+    if (folder.endsWith("/")) folder = folder.substring(0, folder.length()-1);
+    if (parentFolder != null && !parentFolder.endsWith("/")) parentFolder += "/";
+
+    script.cmd("chgrp -R " + groupName + " " + folder + " 2>> ${WD}/chgrp.out || echo [" + itemName +"] >> ${WD}/chgrp.out");
+
+    while (parentFolder != null)
+    {
+      int last = folder.lastIndexOf('/');
+      if (last == -1) break;
+      folder = folder.substring(0, last); // Move up one directory: /foo/bar/x --> /foo/bar
+      // Check if we have reached the parent folder
+      if (folder.indexOf(parentFolder) == -1) break;
+      
+      script.cmd("chgrp " + groupName + " " + folder + " 2>> ${WD}/chgrp.out || echo [" + itemName +"] >> ${WD}/chgrp.out");
+    }
+  }
+  
   /**
     We only allow letters, numbers, dot, underscore and forward slash in path names.

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/StringTieJobCreator.java

@@ -297 +297 @@
       if (externalGroup != null)
       {
-        script.cmd("chgrp -R " + externalGroup + " ${StringTieFolder} 2>> ${WD}/chgrp.out || echo [" + rawName +"] >> ${WD}/chgrp.out");
+        ScriptUtil.addChgrp(externalGroup, "${StringTieFolder}", rawName, null, script);
       }
       script.cmd("ls -1 ${StringTieFolder}/* >> ${WD}/files.out");

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/VariantCallingJobCreator.java

@@ -502 +502 @@
         if (externalGroup != null)
         {
-          script.cmd("chgrp -R " + externalGroup + " ${BamFolder}/variants-* 2>> ${WD}/chgrp.out || echo [" + aligned.getName() +"] >> ${WD}/chgrp.out" );
+          ScriptUtil.addChgrp(externalGroup, "${BamFolder}/variants-*", aligned.getName(), null, script);
         }
       }
@@ -515 +515 @@
         if (externalGroup != null)
         {
-          script.cmd("chgrp -R " + externalGroup + " ${FilteredFolder}/* 2>> ${WD}/chgrp.out || echo [" + aligned.getName() +"] >> ${WD}/chgrp.out" );
+          ScriptUtil.addChgrp(externalGroup, "${FilteredFolder}", aligned.getName(), null, script);
         }
       }