changeset 3:b4999701e8a8 default tip

Deleted selected files

--- a/cpy.c	Tue Feb 28 12:32:29 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,392 +0,0 @@
-#include <sys/stat.h>
-#include <sys/types.h>
-#include <unistd.h>
-#include <stdio.h>
-#include <errno.h>
-#include <stdlib.h>
-#include <pwd.h>
-#include <grp.h> // declares struct group
-#include <libgen.h> // for dirname
-#include <string.h> // for strcpy
-
-/* cpy.c  David Hoover  1/20/12
-usage:
-  cpy from.file to.file login
-
-cpy copies a file from one location to another, and then sets the ownership to a given user.  The
-program is expected to be setuid and owned by root.
-
-*/
-
-int notWriteable(char *file, char *user)
-/* Returns 1 if file not writeable by given user */
-{
-    struct stat fileStat;
-    struct passwd *own,*usr;
-    struct group *grp;
-    int i=0;
-
-    usr = getpwnam(user);
-
-/* does user exist? */
-    if (! usr)
-    {
-        fprintf(stderr,"%s: No such user\n",user);
-        exit(1);
-    }
-
-/* must be able to stat file */
-    if (stat(file, &fileStat) < 0)
-    {
-        fprintf(stderr,"%s: No such directory\n",file);
-        exit(1);
-    }
-
-/* get the owner and group information for the file */
-    own = getpwuid(fileStat.st_uid);
-    grp = getgrgid(fileStat.st_gid);
-
-/* does the file owner match the argument? */
-//    if (!strcmp(own->pw_name,user))
-    if (usr->pw_uid == fileStat.st_uid)
-    {
-//        printf("owners match!\n");
-
-/* is file writeable? */
-        if (fileStat.st_mode & S_IWUSR)
-        {
-//            printf("%s is writeable by %s\n",file,user);
-            return 0;
-        }
-        else
-        {
-//            printf("%s is not writeable by %s\n",file,user);
-        }
-    }
-    else {
-//        printf("owners don't match!\n");
-    }
-
-/* is the file group readable by the given group? */
-    if (fileStat.st_mode & S_IWGRP)
-    {
-//        printf("%s is writeable by group %s\n",file,grp->gr_name);
-
-
-/* is the user's gid the same as the file? */
-//        printf("%d\n",usr->pw_gid);
-//        printf("%d\n",fileStat.st_gid);
-        if (usr->pw_gid == fileStat.st_gid)
-        {
-//            printf("groups match!\n");
-
-/* if the path a directory is it executable? */
-            if (S_ISDIR(fileStat.st_mode))
-            {
-                if (fileStat.st_mode & S_IXGRP)
-                {
-                    return 0;
-                }
-            }
-            else {
-                return 0;
-            }
-        }
-        else
-        {
-
-/* is the user a member of the group that owns the file? */
-            while(grp->gr_mem[i] != NULL)
-            {
-                if(!strcmp(grp->gr_mem[i],user))
-                {
-//                    printf("%s is a member of the %s group\n",user,grp->gr_name);
-/* if the path a directory is it executable? */
-                    if (S_ISDIR(fileStat.st_mode))
-                    {
-                        if (fileStat.st_mode & S_IXGRP)
-                        {
-                            return 0;
-                        }
-                    }
-                    else {
-                        return 0;
-                    }
-                }
-                i++;
-            }
-    
-//            printf("%s is not a member of the %s group\n",user,grp->gr_name);
-
-        }
-    }
-    else
-    {
-//        printf("%s is not writeable by group %s\n",file,grp->gr_name);
-    }
-
-/* is the e world writeable? */
-    if (fileStat.st_mode & S_IWOTH)
-    {
-//        printf("%s is world writeable\n",file);
-        return 0;
-    }
-    else
-    {
-//        printf("%s is not world writeable\n",file);
-    }
-
-    return 1;
-}
-
-int notReadable(char *file, char *user)
-/* Returns 1 if file not readable by given user */
-{
-    struct stat fileStat;
-    struct passwd *own,*usr;
-    struct group *grp;
-    int i=0;
-
-    usr = getpwnam(user);
-
-/* does user exist? */
-    if (! usr)
-    {
-        fprintf(stderr,"%s: No such user\n",user);
-        exit(1);
-    }
-
-/* must be able to stat file */
-    if (stat(file, &fileStat) < 0)
-    {
-        fprintf(stderr,"%s: No such directory\n",file);
-        exit(1);
-    }
-
-/* get the owner and group information for the file */
-    own = getpwuid(fileStat.st_uid);
-    grp = getgrgid(fileStat.st_gid);
-
-/* does the file owner match the argument? */
-//    if (!strcmp(own->pw_name,user))
-    if (usr->pw_uid == fileStat.st_uid)
-    {
-//        printf("owners match!\n");
-
-/* is file readable? */
-        if (fileStat.st_mode & S_IRUSR)
-        {
-//            printf("%s is readable by %s\n",file,user);
-            return 0;
-        }
-        else
-        {
-//            printf("%s is not readable by %s\n",file,user);
-        }
-    }
-    else {
-//        printf("owners don't match!\n");
-    }
-
-/* is the file group readable by the given group? */
-    if (fileStat.st_mode & S_IRGRP)
-    {
-//        printf("%s is readable by group %s\n",file,grp->gr_name);
-
-
-/* is the user's gid the same as the file? */
-//        printf("%d\n",usr->pw_gid);
-//        printf("%d\n",fileStat.st_gid);
-        if (usr->pw_gid == fileStat.st_gid)
-        {
-//            printf("groups match!\n");
-
-/* if the path a directory is it executable? */
-            if (S_ISDIR(fileStat.st_mode))
-            {
-                if (fileStat.st_mode & S_IXGRP)
-                {
-                    return 0;
-                }
-            }
-            else {
-                return 0;
-            }
-        }
-        else
-        {
-
-/* is the user a member of the group that owns the file? */
-            while(grp->gr_mem[i] != NULL)
-            {
-                if(!strcmp(grp->gr_mem[i],user))
-                {
-//                    printf("%s is a member of the %s group\n",user,grp->gr_name);
-/* if the path a directory is it executable? */
-                    if (S_ISDIR(fileStat.st_mode))
-                    {
-                        if (fileStat.st_mode & S_IXGRP)
-                        {
-                            return 0;
-                        }
-                    }
-                    else {
-                        return 0;
-                    }
-                }
-                i++;
-            }
-    
-//            printf("%s is not a member of the %s group\n",user,grp->gr_name);
-
-        }
-    }
-    else
-    {
-//        printf("%s is not readable by group %s\n",file,grp->gr_name);
-    }
-
-/* is the e world readable? */
-    if (fileStat.st_mode & S_IROTH)
-    {
-//        printf("%s is world readable\n",file);
-        return 0;
-    }
-    else
-    {
-//        printf("%s is not world readable\n",file);
-    }
-
-    return 1;
-}
-
-int copyFile(char *src, char *dst)
-{
-//    printf("Copying %s to %s\n",src,dst);
-
-    int c;
-    FILE *fs,*ft;
-    struct stat fileStat;
-
-/* must be able to stat file */
-    if (stat(src, &fileStat) < 0)
-    {
-        fprintf(stderr,"%s: No such file\n",src);
-        exit(1);
-    }
-
-/* is path a regular file? */
-    if (S_ISDIR(fileStat.st_mode))
-    {
-        fprintf(stderr,"%s: Is a directory\n",src);
-        exit(1);
-    }
-
-    fs = fopen(src,"r");
-    if (fs==NULL) {
-        fprintf(stderr,"Can't read from file %s!\n",src);
-        exit(1);
-    }
-    ft = fopen(dst,"w");
-    if (ft==NULL) {
-        fprintf(stderr,"Can't write to file %s!\n",dst);
-        exit(1);
-    }
-
-    c = getc(fs);
-    while (c != EOF) {
-        putc(c,ft);
-        c = getc(fs);
-   }
-
-   fclose(fs);
-   fclose(ft);
-
-   return 0;
-
-}
-
-int chownToGivenUser(char *file, char *user)
-/* chown a file to the given user */
-{
-  struct passwd *usr;
-
-  usr = getpwnam(user);
-
-//  printf("UID = %d\n",usr->pw_uid);
-//  printf("GID = %d\n",usr->pw_gid);
-
-//  printf("chown %s %d,%d\n",file,usr->pw_uid,usr->pw_gid);
-  if (chown(file,usr->pw_uid,usr->pw_gid))
-  {
-      fprintf(stderr,"Can't chown %s\n",file);
-      exit(1);
-  }
-  return 0;
-}
-
-int explodePath(char *file, char *user)
-/* Returns 1 if file not readable by given user */
-{
-    char **path;
-    char *dir;
-    char newfile[10000];
-    int i;
-
-    strcpy(newfile,file);
-    if (!notReadable(newfile,user))
-    {
-      dir = dirname(newfile);
-      if (strcmp(dir,"/"))
-        explodePath(dir,user);
-    }
-    else
-    {
-        fprintf(stderr,"%s: Permission denied.\n",file);
-        exit(1);
-    }
-
-    return 0;
-}
-
-main(int argc, char **argv)
-{
-    char *dir;
-    char newfile[10000];
-    struct stat fileStat;
-
-/* must have two arguments */
-    if (argc != 4)
-    {
-        fprintf(stderr,"usage: cpy source dest user\n");
-        exit(1);
-    }
-
-/* is filepath writeable by given user? */
-    strcpy(newfile,argv[2]);
-    dir = dirname(newfile);
-    if (!notWriteable(dir,argv[3]))
-    { 
- 
-/* is filepath readable by given user? */
-      explodePath(dir,argv[3]);
-
-/* dest file must not exist yet */
-    if (!(stat(argv[2], &fileStat) < 0))
-    {
-        fprintf(stderr,"%s: File already exists.\n",argv[2]);
-        exit(1);
-    }
-
-/* copy the file and change the owner */
-      copyFile(argv[1],argv[2]);
-      chownToGivenUser(argv[2],argv[3]);
-    }
-    else 
-    {
-      fprintf(stderr,"%s: Permission denied.\n",argv[2]);
-      exit(1);
-    }
-
-    exit(0);
-}

--- a/export_local_file.sh	Tue Feb 28 12:32:29 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-###
-### The shell script: export_local_file.sh
-###
-### The script basically copies a Galaxy dataset (param 1, dataset_NNNNN.dat) 
-### to the destination file (param 2, {/data,/home}/filename
-###
-#!/bin/sh
-
-INPUT="$1"
-DEST="$2"
-EMAIL="$3"
-OUTPUT="$4"
-USER=`echo $EMAIL | sed -e 's#@.*##'`
-
-if [ -z "$DEST" ]; then
-	echo "Usage: $0 [INPUT] [DEST]" >&2
-	exit 1
-fi
-
-# Filter any unwanted directories
-
-if [[ `echo $DEST | grep -c ^/data/` -lt 1 ]] && [[ `echo $DEST | grep -c ^/home/` -lt 1 ]] ; then
-  echo "Error: \"$DEST\" is not allowed" >&2
-  exit 1
-fi
-
-# Do the deed
-
-cpy $INPUT $DEST "$USER"
-dataset=`basename $INPUT`
-if [ $? != 0  ]; then
-  echo "Error: $USER failed to copy dataset $dataset to \"$DEST\"" >&2 
-  exit 1
-fi
-
-echo "Dataset $dataset successfully exported to \"$DEST\"" >> $OUTPUT
-
-exit 0
-
-###
-###
-###
-

--- a/export_local_file.xml	Tue Feb 28 12:32:29 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-<?xml version="1.0"?>
-<tool id="export_local_file" name="Export dataset">
-  <description>to a local filesytem</description>
-  <command interpreter="sh">export_local_file.sh $input '$filepath' $userEmail $output</command>
-  <inputs>   
-    <param name="input" type="data" label="Dataset"/>
-    <param name="filepath" type="text" size="100" label="Absolute file path" />
-  </inputs>
-  <outputs>
-    <data format="txt" name="output" label="local export: $filepath" />
-  </outputs>
-  <help>
-
-.. class:: infomark
-
-**Copying files**
-
-This tool will allow you to export a single file from Galaxy to a local filesystem.
-You must have permission to write the file to the given directory, and the file must not yet exist.  This tool will
-not overwrite a pre-existing file.
-
-.. class:: warningmark
-
-**Important Notes**
-
-- The file path must be a file, not a directory
-- You must give the fullpath to the file (/home/user/myfile.txt, not ./myfile.txt)
-- You must have permission to write the file in the given directory
-
------
-
-**Example**
-
-- /home/user/bamfiles/abc123.bam
-- /data/anotheruser/data/good_data/very_good_data.txt
-
-  </help>
-</tool>