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comparison rgToolFactory.py @ 19:a87a262220a4

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Adding proof of concept for optional output formats. Updated readme again
author ross lazarus ross.lazarus@gmail.com
date Tue, 05 Jun 2012 21:54:58 +1000
parents 8594478e8d2c
children 3f58115c6c5b
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18:943d4f0ee7c1 19:a87a262220a4
1 # rgToolFactory.py 1 # rgToolFactory.py
2 # derived from 2 # https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
3 # rgBaseScriptWrapper.py 3
4 # but designed to run arbitrary user supplied code 4 # this is a tool factory for simple scripts in python, R or whatever ails ye.
5 # extremely dangerous!! 5 # you paste and run your script
6 # trusted users only - private site only 6 # Only works for simple scripts that read one input from the history.
7 # a list in the xml is searched for users permitted to run this tool. 7 # Optionally can write one new history dataset,
8 # DO NOT install on a public or important site - local instance only 8 # and optionally collect any number of outputs into links on an autogenerated HTML page.
9 # generated tools are fine as they just run normally and their user cannot do anything unusually insecure 9
10 # DO NOT install on a public or important site - please.
11
12 # installed generated tools are fine if the script is safe.
13 # They just run normally and their user cannot do anything unusually insecure
14 # but please, practice safe toolshed.
15 # Read the fucking code before you install any tool
16 # especially this one
17
18 # After you get the script working on some test data, you can
19 # optionally generate a toolshed compatible gzip file
20 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
21 # safe and largely automated installation in a production Galaxy.
22
23 # If you opt for an HTML output, you get all the script outputs arranged
24 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
25 # Ugly but really inexpensive.
26 #
27 # Patches appreciated please.
10 # 28 #
11 # copyright ross lazarus (ross.lazarus@gmail.com) May 2012 29 #
30 # long route to June 2012 product
31 # Behold the awesome power of Galaxy and the toolshed with the tool factory binds to bind them
32 # derived from an integrated script model
33 # called rgBaseScriptWrapper.py
34 # Note to the unwary:
35 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
36 # There is nothing stopping a malicious user doing whatever they choose
37 # Extremely dangerous!!
38 # Totally insecure. So, trusted users only
39 #
40 # preferred model is a developer using their throw away workstation instance - ie a private site.
41 # no real risk.
42 # a list in the xml source file is searched for users permitted to run this tool.
43 # PUT some IDs in the list in the XML before you restart Galaxy to load this new tool please
44 # otherwise, the tool won't run for anybody.
45 #
46
47 #
48 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
12 # 49 #
13 # all rights reserved 50 # all rights reserved
14 # Licensed under the LGPL for your pleasure 51 # Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
15 # Derived from rgDGE.py in May 2012
16 # generalized to run required interpreter
17 # to make your own tools based on a given script and interpreter such as perl or python
18 # clone this and the corresponding xml wrapper
19 # replace the parameters/inputs/outputs and the configfile contents with your script
20 # Use the $foo syntax to place your parameter values inside the script to assign them - at run time, the script will be used as a template
21 # and returned as part of the output to the user - with the right values for all the parameters.
22 # Note that this assumes you want all the outputs arranged as a single Html file output
23 # after this generic script runner runs your script with the specified interpreter,
24 # it will collect all output files into the specified output_html, making thumbnails for all the pdfs it finds and making links for all the other files.
25 52
26 import sys 53 import sys
27 import shutil 54 import shutil
28 import subprocess 55 import subprocess
29 import os 56 import os
50 """class is a wrapper for an arbitrary script 77 """class is a wrapper for an arbitrary script
51 """ 78 """
52 79
53 def __init__(self,opts=None): 80 def __init__(self,opts=None):
54 """ 81 """
55 run the script 82 cleanup inputs, setup some outputs
56 83
57 """ 84 """
58 if opts.output_dir: # simplify for the tool tarball 85 if opts.output_dir: # simplify for the tool tarball
59 os.chdir(opts.output_dir) 86 os.chdir(opts.output_dir)
60 self.thumbformat = 'jpg' 87 self.thumbformat = 'jpg'
91 118
92 119
93 def makeXML(self): 120 def makeXML(self):
94 """ 121 """
95 Create a Galaxy xml tool wrapper for the new script as a string to write out 122 Create a Galaxy xml tool wrapper for the new script as a string to write out
96 fixme - use templating or something less fugly than this. 123 fixme - use templating or something less fugly than this example of what we produce
97 Here's an example of what we produce
98 124
99 <tool id="reverse" name="reverse" version="0.01"> 125 <tool id="reverse" name="reverse" version="0.01">
100 <description>a tabular file</description> 126 <description>a tabular file</description>
101 <command interpreter="python"> 127 <command interpreter="python">
102 reverse.py --script_path "$runMe" --interpreter "python" 128 reverse.py --script_path "$runMe" --interpreter "python"
291 <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 317 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
292 </head> 318 </head>
293 <body> 319 <body>
294 <div class="document"> 320 <div class="document">
295 """ 321 """
296 galhtmlattr = """<hr/><b><a href="http://rgenetics.org">Galaxy Tool Factory Script Wrapper</a> tool output %s run at %s</b><br/>""" 322 galhtmlattr = """<hr/><b><a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory Script Wrapper</a> tool output %s run at %s</b><br/>"""
297 galhtmlpostfix = """</div></body></html>\n""" 323 galhtmlpostfix = """</div></body></html>\n"""
298 324
299 flist = os.listdir(self.opts.output_dir) 325 flist = os.listdir(self.opts.output_dir)
300 flist = [x for x in flist if x <> 'Rplots.pdf'] 326 flist = [x for x in flist if x <> 'Rplots.pdf']
301 flist.sort() 327 flist.sort()
377 a('--make_HTML',default=None) 403 a('--make_HTML',default=None)
378 a('--help_text',default=None) 404 a('--help_text',default=None)
379 a('--tool_desc',default=None) 405 a('--tool_desc',default=None)
380 a('--new_tool',default=None) 406 a('--new_tool',default=None)
381 opts, args = op.parse_args() 407 opts, args = op.parse_args()
382 assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin' % opts.bad_user 408 assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin to add their ID to %s.xml' % (opts.bad_user,os.path.splitext(self.myname)[0])
383 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq' 409 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
384 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript' 410 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
385 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R' 411 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
386 if opts.output_dir: 412 if opts.output_dir:
387 try: 413 try: