This file is indexed.

/usr/bin/starch is in coop-computing-tools 4.0-1ubuntu1.

This file is owned by root:root, with mode 0o755.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
#! /usr/bin/python

# Copyright (c) 2010- The University of Notre Dame.
# This software is distributed under the GNU General Public License.
# See the file COPYING for details.

""" Starch """

from cStringIO  import StringIO
from optparse   import OptionParser
from subprocess import Popen, PIPE
from tarfile    import REGTYPE, TarInfo, open as Tar
from time       import time
from tempfile   import NamedTemporaryFile
from shutil     import copyfile, copyfileobj

from ConfigParser import ConfigParser, NoSectionError, NoOptionError

import os
import sys

# Todo

"""
1. Keep track of files added to avoid duplication (efficiency).
"""

# Global variables

STARCH_AUTODETECT = True
STARCH_VERBOSE    = False
STARCH_PLATFORM   = 'Linux'

# Shell scripts

SFX_SH='''#!/bin/sh

SFX_FILE=$0
SFX_EXIT_STATUS=0

if [ -z "$SFX_DIR" ]; then
    basename=`basename $SFX_FILE`
    SFX_DIR=`hostname`.$USER.$basename.dir

    if [ ! -z "$CONDOR_SCRATCH_DIR" ]; then
        SFX_DIR=$CONDOR_SCRATCH_DIR/$SFX_DIR
    elif [ ! -z "$_CONDOR_SCRATCH_DIR" ]; then
        SFX_DIR=$_CONDOR_SCRATCH_DIR/$SFX_DIR
    elif [ ! -z "$XGRID_AGENT_NAME" ]; then
        SFX_DIR=`pwd`/$SFX_DIR
    else
        SFX_DIR=/tmp/$SFX_DIR
    fi

    if [ ! -z "$SFX_UNIQUE" ] && [ "$SFX_UNIQUE" = 1 ]; then
        SFX_DIR=`mktemp -d -u $SFX_DIR.XXXXXX`
    fi
fi

extract() {
    if [ ! -d "$SFX_DIR" -o "$SFX_EXTRACT_FORCE" -eq 1 ]; then
        mkdir -p $SFX_DIR 2> /dev/null
        archive=`awk '/^__ARCHIVE__/ {print NR + 1; exit 0; }' $SFX_FILE`
        tail -n+$archive $SFX_FILE | tar xj -C $SFX_DIR
        SFX_EXIT_STATUS=$?
    fi
}

run() {
    $SFX_DIR/run.sh $@
    SFX_EXIT_STATUS=$?
}

if [ -z "$SFX_EXTRACT_ONLY" ]; then
    SFX_EXTRACT_ONLY=0
fi

if [ -z "$SFX_EXTRACT_FORCE" ]; then
    SFX_EXTRACT_FORCE=0
fi

if [ -z "$SFX_KEEP" ]; then
    SFX_KEEP=0
fi

if [ "$SFX_EXTRACT_ONLY" -eq 1 ]; then
    extract
    echo $SFX_DIR
    SFX_KEEP=1
else
    extract && run $@
fi

if [ "$SFX_KEEP" -ne 1 ]; then
    rm -fr $SFX_DIR
fi

exit $SFX_EXIT_STATUS

__ARCHIVE__
'''

RUN_SH = '''#!/bin/sh
SFX_DIR=`dirname $0`

if [ -d "$SFX_DIR/env" ]; then
    for f in $SFX_DIR/env/*; do
        . $f
    done
fi

if [ -d "$SFX_DIR/bin" ]; then
    export PATH=$SFX_DIR/bin:$PATH
fi

if [ -d "$SFX_DIR/lib" ]; then
    if [ x"`uname -s`" == x"Darwin" ]; then
        if [ -z "$DYLD_LIBRARY_PATH" ]; then
            export DYLD_LIBRARY_PATH=$SFX_DIR/lib
        else
            export DYLD_LIBRARY_PATH=$SFX_DIR/lib:$DYLD_LIBRARY_PATH
        fi
    else
        if [ -z "$LD_LIBRARY_PATH" ]; then
            export LD_LIBRARY_PATH=$SFX_DIR/lib
        else
            export LD_LIBRARY_PATH=$SFX_DIR/lib:$LD_LIBRARY_PATH
        fi
    fi
fi
%s
'''

# Create SFX

def create_sfx(sfx_path, executables, libraries, data, environments, command):
    """ Create self-extracting executable

    Directory structure:
        bin         Executables
        lib         Libraries
        env         Environment Scripts (static)
        run.sh      Script that contains command
    """

    tmp_file = NamedTemporaryFile()
    tmp_file.close()

    arc_path = tmp_file.name
    archive  = Tar(arc_path, 'w:bz2')

    debug('adding executables...')
    executables = find_executables(executables)
    for exe_path, real_path in executables:
        exe_name = os.path.basename(exe_path)
        exe_info = archive.gettarinfo(real_path, os.path.join('bin', exe_name))
        exe_info.mode = 0755

        debug('    adding executable: %s (%s)' % (exe_name, real_path))
        archive.addfile(exe_info, open(real_path))

    debug('adding libraries...')
    libraries = find_libraries(libraries, executables)
    for lib_path, real_path in libraries:
        lib_name = os.path.basename(lib_path)
        lib_info = archive.gettarinfo(real_path, os.path.join('lib', lib_name))

        debug('    adding library: %s (%s)' % (lib_name, real_path))
        archive.addfile(lib_info, open(real_path))

    debug('adding data...')
    for data_path, real_path in map(lambda s: s.split(':'), data):
        add_data_to_archive(archive, os.path.normpath(data_path), os.path.normpath(real_path))

    debug('adding environment scripts...')
    for env_path, real_path in find_files(environments, 'PWD'):
        env_name = os.path.basename(env_path)
        env_info = archive.gettarinfo(real_path, os.path.join('env', env_name))

        debug('    adding environment script: %s (%s)' % (env_name, real_path))
        archive.addfile(env_info, open(real_path))

    run_info = TarInfo('run.sh')
    run_info_data  = RUN_SH % command
    run_info.mode  = 0755
    run_info.mtime = time()
    run_info.size  = len(run_info_data)

    debug('adding run.sh...')
    archive.addfile(run_info, StringIO(run_info_data))
    archive.close()

    if os.path.exists(sfx_path):
        os.unlink(sfx_path)

    debug('creating sfx...')
    sfx_file = open(sfx_path, 'a+')
    copyfileobj(StringIO(SFX_SH), sfx_file)
    copyfileobj(open(arc_path, 'r'), sfx_file)
    sfx_file.close()

    debug('cleaning up...')
    os.chmod(sfx_path, 0755)
    os.unlink(arc_path)

def add_data_to_archive(archive, data_path, real_path):
    if os.path.isdir(real_path):
        for root, dirs, files in os.walk(real_path):
            for n in files + dirs:
                dp = os.path.join(root.replace(real_path, data_path), n)
                rp = os.path.join(root, n)
                add_data_to_archive(archive, dp, rp)
    else:
        data_info = archive.gettarinfo(os.path.realpath(real_path), data_path)
        debug('    adding data: %s (%s)' % (data_path, real_path))
        archive.addfile(data_info, open(real_path))

# Print utilities

def debug(s):
    if STARCH_VERBOSE:
        print '[D]', s

def warn(s):
    print >>sys.stderr, '[W]', s

def error(s):
    print >>sys.stderr, '[E]', s
    sys.exit(1)

# Find file utilities

def find_files(files, env_var, default_paths = None):
    if default_paths:
        paths = default_paths
    else:
        paths = [os.curdir]

    if env_var in os.environ:
        paths.extend(os.environ[env_var].split(':'))

    for file in files:
        is_found = False
        for path in paths:
            file_path = os.path.join(path, file)
            if os.path.exists(file_path):
                is_found = True
                yield file_path, os.path.realpath(file_path)
                break
        if not is_found:
            error('could not find file: %s' % file)
    raise StopIteration


def find_executables(executables):
    exes = []
    for ep, rp in find_files(executables, 'PATH'):
        exes.append((ep, rp))
    return exes


def find_libraries(libraries, executables):
    libs = []

    for lp, rp in find_files(libraries, 'LD_LIBRARY_PATH', ['/lib', '/lib64', '/usr/lib', '/usr/lib64']):
        libs.append((lp, rp))

    if STARCH_AUTODETECT:
        for exe_path, real_path in executables:
            if STARCH_PLATFORM == 'Darwin':
                libs.extend(autodetect_libraries_darwin(exe_path))
            else:
                libs.extend(autodetect_libraries_linux(exe_path))

    return libs


def autodetect_libraries_linux(executable):
    libs = []

    try:
        p = Popen(['ldd', executable], stdout = PIPE)
        for line in p.communicate()[0].split('\n'):
            try:
                lib_path = line.split('=>')[-1].strip().split()[0]
                if os.path.exists(lib_path):
                    libs.append((lib_path, os.path.realpath(lib_path)))
            except Exception, e:
                pass
    except Exception, e:
        error('could not execute ldd on %s: %s' % (executable, str(e)))

    return libs


def autodetect_libraries_darwin(executable):
    libs = []

    try:
        p = Popen(['otool', '-L', executable], stdout = PIPE)
        for line in p.communicate()[0].split('\n'):
            try:
                lib_path = line.split('(')[0].strip()
                if os.path.exists(lib_path):
                    libs.append((lib_path, os.path.realpath(lib_path)))
            except Exception, e:
                pass
    except Exception, e:
        error('could not execute otool on %s: %s' % (executable, str(e)))

    return libs


# Configuration Parser

class StarchConfigParser(ConfigParser):
    def get(self, section, name, default = None):
        try:
            return ConfigParser.get(self, section, name)
        except (NoSectionError, NoOptionError), e:
            return default

# Parse commandline options

def parse_command_line_options():
    global STARCH_VERBOSE
    global STARCH_AUTODETECT
    global STARCH_PLATFORM

    parser = OptionParser('%prog [options] <sfx_path>')

    parser.add_option('-A', dest = 'autodetect', action = 'store_false',
        help = 'Do not automatically detect library dependencies (default: enabled).', default=True)
    parser.add_option('-C', dest = 'config', action = 'store',
        help = 'Use configuration file.', metavar = 'cfg', default = None)
    parser.add_option('-c', dest = 'command', action = 'store',
        help = 'Specify command to execute.', metavar = 'cmd', default = '')
    parser.add_option('-d', dest = 'data', action = 'append',
        help = 'Add data (new path:old path).', metavar = 'npath:opath', default = [])
    parser.add_option('-e', dest = 'environments', action = 'append',
        help = 'Add environment script.', metavar = 'env', default = [])
    parser.add_option('-l', dest = 'libraries', action = 'append',
        help = 'Add library.', metavar = 'lib', default = [])
    parser.add_option('-x', dest = 'executables', action = 'append',
        help = 'Add executable.', metavar = 'exe', default = [])
    parser.add_option('-v', dest = 'verbose', action = 'store_true',
        help = 'Display verbose messages.', default = False)

    (options, args) = parser.parse_args()

    if len(args) != 1:
        parser.print_help()
        sys.exit(1)

    STARCH_VERBOSE    = options.verbose
    STARCH_AUTODETECT = options.autodetect
    STARCH_PLATFORM   = os.uname()[0]

    if options.config:
        if not os.path.exists(options.config):
            error('config file \'%s\' does not exist' % options.config)

        config = StarchConfigParser()
        config.read(options.config)

        options.executables.extend(config.get('starch', 'executables', '').split())
        options.libraries.extend(config.get('starch', 'libraries', '').split())
        options.data.extend(config.get('starch', 'data', '').split())
        options.environments.extend(config.get('starch', 'environments', '').split())
        if not options.command:
            options.command = config.get('starch', 'command', '')
    
    if not options.executables:
        error('no executables specified')

    if not options.command:
        options.command = os.path.basename(options.executables[0]) + ' $@'
        warn('no command specified, so using: %s' % options.command)
    
    debug('command ... ' + options.command)

    return args[0], options.executables, options.libraries, \
                    options.data, options.environments, options.command

# Main execution

if __name__ == '__main__':
    create_sfx(*parse_command_line_options())

# vim: set sts=4 sw=4 ts=8 expandtab ft=python: