|
38
|
1 #!/usr/bin/env python
|
|
30
|
2 # rgToolFactory.py
|
|
|
3 # see https://github.com/fubar2/toolfactory
|
|
|
4 #
|
|
|
5 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
|
|
|
6 #
|
|
|
7 # all rights reserved
|
|
|
8 # Licensed under the LGPL
|
|
|
9 # suggestions for improvement and bug fixes welcome at https://github.com/fubar2/toolfactory
|
|
|
10 #
|
|
|
11 # July 2020: BCC was fun and I feel like rip van winkle after 5 years.
|
|
|
12 # Decided to
|
|
|
13 # 1. Fix the toolfactory so it works - done for simplest case
|
|
|
14 # 2. Fix planemo so the toolfactory function works
|
|
|
15 # 3. Rewrite bits using galaxyxml functions where that makes sense - done
|
|
|
16 #
|
|
|
17 # removed all the old complications including making the new tool use this same script
|
|
|
18 # galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml
|
|
|
19 # No support for automatic HTML file creation from arbitrary outputs
|
|
|
20 # TODO: add option to run that code as a post execution hook
|
|
|
21 # TODO: add additional history input parameters - currently only one
|
|
|
22
|
|
36
|
23
|
|
|
24 import argparse
|
|
|
25 import logging
|
|
|
26 import os
|
|
|
27 import re
|
|
|
28 import shutil
|
|
30
|
29 import subprocess
|
|
36
|
30 import sys
|
|
|
31 import tarfile
|
|
|
32 import tempfile
|
|
30
|
33 import time
|
|
36
|
34
|
|
30
|
35 import galaxyxml.tool as gxt
|
|
|
36 import galaxyxml.tool.parameters as gxtp
|
|
38
|
37
|
|
36
|
38 import lxml
|
|
30
|
39
|
|
36
|
40 myversion = "V2.1 July 2020"
|
|
30
|
41 verbose = True
|
|
|
42 debug = True
|
|
36
|
43 toolFactoryURL = "https://github.com/fubar2/toolfactory"
|
|
|
44 ourdelim = "~~~"
|
|
30
|
45
|
|
38
|
46 # --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label
|
|
|
47 # ~~~$input_help"
|
|
30
|
48 IPATHPOS = 0
|
|
|
49 ICLPOS = 1
|
|
|
50 IFMTPOS = 2
|
|
|
51 ILABPOS = 3
|
|
|
52 IHELPOS = 4
|
|
|
53 IOCLPOS = 5
|
|
38
|
54
|
|
30
|
55 # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL
|
|
|
56 ONAMEPOS = 0
|
|
|
57 OFMTPOS = 1
|
|
|
58 OCLPOS = 2
|
|
|
59 OOCLPOS = 3
|
|
|
60
|
|
38
|
61 # --additional_parameters="$i.param_name~~~$i.param_value~~~
|
|
|
62 # $i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL~~~i$.param_CLoverride"
|
|
30
|
63 ANAMEPOS = 0
|
|
|
64 AVALPOS = 1
|
|
|
65 ALABPOS = 2
|
|
|
66 AHELPPOS = 3
|
|
|
67 ATYPEPOS = 4
|
|
|
68 ACLPOS = 5
|
|
38
|
69 AOVERPOS = 6
|
|
|
70 AOCLPOS = 7
|
|
30
|
71
|
|
36
|
72
|
|
38
|
73 foo = len(lxml.__version__)
|
|
|
74 # fug you, flake8. Say my name!
|
|
|
75
|
|
30
|
76 def timenow():
|
|
|
77 """return current time as a string
|
|
|
78 """
|
|
36
|
79 return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
|
|
30
|
80
|
|
|
81
|
|
|
82 def quote_non_numeric(s):
|
|
|
83 """return a prequoted string for non-numerics
|
|
|
84 useful for perl and Rscript parameter passing?
|
|
|
85 """
|
|
|
86 try:
|
|
|
87 _ = float(s)
|
|
|
88 return s
|
|
|
89 except ValueError:
|
|
|
90 return '"%s"' % s
|
|
|
91
|
|
|
92
|
|
36
|
93 html_escape_table = {"&": "&", ">": ">", "<": "<", "$": r"\$"}
|
|
30
|
94
|
|
|
95
|
|
|
96 def html_escape(text):
|
|
|
97 """Produce entities within text."""
|
|
|
98 return "".join(html_escape_table.get(c, c) for c in text)
|
|
|
99
|
|
|
100
|
|
|
101 def html_unescape(text):
|
|
|
102 """Revert entities within text. Multiple character targets so use replace"""
|
|
36
|
103 t = text.replace("&", "&")
|
|
|
104 t = t.replace(">", ">")
|
|
|
105 t = t.replace("<", "<")
|
|
|
106 t = t.replace("\\$", "$")
|
|
30
|
107 return t
|
|
|
108
|
|
|
109
|
|
|
110 def parse_citations(citations_text):
|
|
|
111 """
|
|
|
112 """
|
|
|
113 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
|
|
|
114 citation_tuples = []
|
|
|
115 for citation in citations:
|
|
|
116 if citation.startswith("doi"):
|
|
38
|
117 citation_tuples.append(("doi", citation[len("doi") :].strip()))
|
|
30
|
118 else:
|
|
38
|
119 citation_tuples.append(
|
|
|
120 ("bibtex", citation[len("bibtex") :].strip())
|
|
|
121 )
|
|
30
|
122 return citation_tuples
|
|
|
123
|
|
|
124
|
|
|
125 class ScriptRunner:
|
|
|
126 """Wrapper for an arbitrary script
|
|
|
127 uses galaxyxml
|
|
|
128
|
|
|
129 """
|
|
36
|
130
|
|
30
|
131 def __init__(self, args=None):
|
|
|
132 """
|
|
|
133 prepare command line cl for running the tool here
|
|
|
134 and prepare elements needed for galaxyxml tool generation
|
|
|
135 """
|
|
|
136
|
|
|
137 self.infiles = [x.split(ourdelim) for x in args.input_files]
|
|
|
138 self.outfiles = [x.split(ourdelim) for x in args.output_files]
|
|
|
139 self.addpar = [x.split(ourdelim) for x in args.additional_parameters]
|
|
|
140 self.args = args
|
|
|
141 self.cleanuppar()
|
|
|
142 self.lastclredirect = None
|
|
|
143 self.lastxclredirect = None
|
|
|
144 self.cl = []
|
|
|
145 self.xmlcl = []
|
|
36
|
146 self.is_positional = self.args.parampass == "positional"
|
|
30
|
147 aCL = self.cl.append
|
|
36
|
148 assert args.parampass in [
|
|
|
149 "0",
|
|
|
150 "argparse",
|
|
|
151 "positional",
|
|
|
152 ], 'Parameter passing in args.parampass must be "0","positional" or "argparse"'
|
|
|
153 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
|
|
30
|
154 self.tool_id = self.tool_name
|
|
36
|
155 if self.args.interpreter_name:
|
|
|
156 exe = "$runMe"
|
|
|
157 else:
|
|
|
158 exe = self.args.exe_package
|
|
|
159 assert (
|
|
|
160 exe is not None
|
|
|
161 ), "No interpeter or executable passed in - nothing to run so cannot build"
|
|
|
162 self.tool = gxt.Tool(
|
|
|
163 self.args.tool_name,
|
|
|
164 self.tool_id,
|
|
|
165 self.args.tool_version,
|
|
|
166 self.args.tool_desc,
|
|
|
167 exe,
|
|
|
168 )
|
|
|
169 self.tinputs = gxtp.Inputs()
|
|
|
170 self.toutputs = gxtp.Outputs()
|
|
|
171 self.testparam = []
|
|
|
172 if (
|
|
|
173 self.args.runmode == "Executable" or self.args.runmode == "system"
|
|
|
174 ): # binary - no need
|
|
30
|
175 aCL(self.args.exe_package) # this little CL will just run
|
|
36
|
176 else:
|
|
|
177 self.prepScript()
|
|
30
|
178 self.elog = "%s_error_log.txt" % self.tool_name
|
|
|
179 self.tlog = "%s_runner_log.txt" % self.tool_name
|
|
|
180
|
|
36
|
181 if self.args.parampass == "0":
|
|
30
|
182 self.clsimple()
|
|
|
183 else:
|
|
|
184 clsuffix = []
|
|
|
185 xclsuffix = []
|
|
|
186 for i, p in enumerate(self.infiles):
|
|
38
|
187 if p[IOCLPOS] == "STDIN":
|
|
|
188 appendme = [
|
|
|
189 p[IOCLPOS],
|
|
|
190 p[ICLPOS],
|
|
|
191 p[IPATHPOS],
|
|
|
192 "< %s" % p[IPATHPOS],
|
|
|
193 ]
|
|
|
194 xappendme = [
|
|
|
195 p[IOCLPOS],
|
|
|
196 p[ICLPOS],
|
|
|
197 p[IPATHPOS],
|
|
|
198 "< $%s" % p[ICLPOS],
|
|
|
199 ]
|
|
|
200 else:
|
|
|
201 appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""]
|
|
|
202 xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""]
|
|
30
|
203 clsuffix.append(appendme)
|
|
38
|
204 xclsuffix.append(xappendme)
|
|
36
|
205 # print('##infile i=%d, appendme=%s' % (i,appendme))
|
|
30
|
206 for i, p in enumerate(self.outfiles):
|
|
|
207 if p[OOCLPOS] == "STDOUT":
|
|
36
|
208 self.lastclredirect = [">", p[ONAMEPOS]]
|
|
|
209 self.lastxclredirect = [">", "$%s" % p[OCLPOS]]
|
|
30
|
210 else:
|
|
38
|
211 clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""])
|
|
|
212 xclsuffix.append(
|
|
|
213 [p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""]
|
|
|
214 )
|
|
36
|
215 for p in self.addpar:
|
|
38
|
216 clsuffix.append(
|
|
|
217 [p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]]
|
|
|
218 )
|
|
|
219 xclsuffix.append(
|
|
|
220 [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]]
|
|
|
221 )
|
|
30
|
222 clsuffix.sort()
|
|
|
223 xclsuffix.sort()
|
|
|
224 self.xclsuffix = xclsuffix
|
|
|
225 self.clsuffix = clsuffix
|
|
36
|
226 if self.args.parampass == "positional":
|
|
30
|
227 self.clpositional()
|
|
|
228 else:
|
|
|
229 self.clargparse()
|
|
36
|
230
|
|
|
231 def prepScript(self):
|
|
|
232 aCL = self.cl.append
|
|
|
233 rx = open(self.args.script_path, "r").readlines()
|
|
|
234 rx = [x.rstrip() for x in rx]
|
|
|
235 rxcheck = [x.strip() for x in rx if x.strip() > ""]
|
|
|
236 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
|
|
|
237 self.script = "\n".join(rx)
|
|
|
238 fhandle, self.sfile = tempfile.mkstemp(
|
|
38
|
239 prefix=self.tool_name, suffix="_%s" % (self.args.interpreter_name)
|
|
36
|
240 )
|
|
|
241 tscript = open(self.sfile, "w")
|
|
|
242 tscript.write(self.script)
|
|
|
243 tscript.close()
|
|
38
|
244 self.indentedScript = " %s" % "\n".join(
|
|
|
245 [" %s" % html_escape(x) for x in rx]
|
|
|
246 )
|
|
|
247 self.escapedScript = "%s" % "\n".join(
|
|
|
248 [" %s" % html_escape(x) for x in rx]
|
|
|
249 )
|
|
36
|
250 art = "%s.%s" % (self.tool_name, self.args.interpreter_name)
|
|
|
251 artifact = open(art, "wb")
|
|
|
252 artifact.write(bytes(self.script, "utf8"))
|
|
|
253 artifact.close()
|
|
|
254 aCL(self.args.interpreter_name)
|
|
|
255 aCL(self.sfile)
|
|
|
256
|
|
30
|
257 def cleanuppar(self):
|
|
|
258 """ positional parameters are complicated by their numeric ordinal"""
|
|
36
|
259 for i, p in enumerate(self.infiles):
|
|
|
260 if self.args.parampass == "positional":
|
|
|
261 assert p[ICLPOS].isdigit(), (
|
|
|
262 "Positional parameters must be ordinal integers - got %s for %s"
|
|
|
263 % (p[ICLPOS], p[ILABPOS])
|
|
|
264 )
|
|
30
|
265 p.append(p[ICLPOS])
|
|
|
266 if p[ICLPOS].isdigit() or self.args.parampass == "0":
|
|
36
|
267 scl = "input%d" % (i + 1)
|
|
30
|
268 p[ICLPOS] = scl
|
|
|
269 self.infiles[i] = p
|
|
36
|
270 for i, p in enumerate(
|
|
|
271 self.outfiles
|
|
|
272 ): # trying to automagically gather using extensions
|
|
|
273 if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT":
|
|
|
274 assert p[OCLPOS].isdigit(), (
|
|
|
275 "Positional parameters must be ordinal integers - got %s for %s"
|
|
|
276 % (p[OCLPOS], p[ONAMEPOS])
|
|
|
277 )
|
|
30
|
278 p.append(p[OCLPOS])
|
|
|
279 if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT":
|
|
|
280 scl = p[ONAMEPOS]
|
|
|
281 p[OCLPOS] = scl
|
|
|
282 self.outfiles[i] = p
|
|
36
|
283 for i, p in enumerate(self.addpar):
|
|
|
284 if self.args.parampass == "positional":
|
|
|
285 assert p[ACLPOS].isdigit(), (
|
|
|
286 "Positional parameters must be ordinal integers - got %s for %s"
|
|
|
287 % (p[ACLPOS], p[ANAMEPOS])
|
|
|
288 )
|
|
30
|
289 p.append(p[ACLPOS])
|
|
|
290 if p[ACLPOS].isdigit():
|
|
36
|
291 scl = "input%s" % p[ACLPOS]
|
|
30
|
292 p[ACLPOS] = scl
|
|
|
293 self.addpar[i] = p
|
|
36
|
294
|
|
30
|
295 def clsimple(self):
|
|
|
296 """ no parameters - uses < and > for i/o
|
|
|
297 """
|
|
|
298 aCL = self.cl.append
|
|
36
|
299 aCL("<")
|
|
30
|
300 aCL(self.infiles[0][IPATHPOS])
|
|
36
|
301 aCL(">")
|
|
30
|
302 aCL(self.outfiles[0][OCLPOS])
|
|
|
303 aXCL = self.xmlcl.append
|
|
36
|
304 aXCL("<")
|
|
|
305 aXCL("$%s" % self.infiles[0][ICLPOS])
|
|
|
306 aXCL(">")
|
|
|
307 aXCL("$%s" % self.outfiles[0][ONAMEPOS])
|
|
30
|
308
|
|
|
309 def clpositional(self):
|
|
|
310 # inputs in order then params
|
|
|
311 aCL = self.cl.append
|
|
38
|
312 for (o_v, k, v, koverride) in self.clsuffix:
|
|
30
|
313 if " " in v:
|
|
|
314 aCL("%s" % v)
|
|
|
315 else:
|
|
|
316 aCL(v)
|
|
|
317 aXCL = self.xmlcl.append
|
|
38
|
318 for (o_v, k, v, koverride) in self.xclsuffix:
|
|
30
|
319 aXCL(v)
|
|
|
320 if self.lastxclredirect:
|
|
|
321 aXCL(self.lastxclredirect[0])
|
|
|
322 aXCL(self.lastxclredirect[1])
|
|
|
323
|
|
|
324 def clargparse(self):
|
|
|
325 """ argparse style
|
|
|
326 """
|
|
|
327 aCL = self.cl.append
|
|
|
328 aXCL = self.xmlcl.append
|
|
|
329 # inputs then params in argparse named form
|
|
38
|
330 for (o_v, k, v, koverride) in self.xclsuffix:
|
|
|
331 if koverride > "":
|
|
|
332 k = koverride
|
|
|
333 elif len(k.strip()) == 1:
|
|
36
|
334 k = "-%s" % k
|
|
34
|
335 else:
|
|
36
|
336 k = "--%s" % k
|
|
30
|
337 aXCL(k)
|
|
|
338 aXCL(v)
|
|
38
|
339 for (o_v, k, v, koverride) in self.clsuffix:
|
|
|
340 if koverride > "":
|
|
|
341 k = koverride
|
|
|
342 elif len(k.strip()) == 1:
|
|
36
|
343 k = "-%s" % k
|
|
30
|
344 else:
|
|
36
|
345 k = "--%s" % k
|
|
30
|
346 aCL(k)
|
|
|
347 aCL(v)
|
|
|
348
|
|
36
|
349 def getNdash(self, newname):
|
|
|
350 if self.is_positional:
|
|
|
351 ndash = 0
|
|
|
352 else:
|
|
|
353 ndash = 2
|
|
|
354 if len(newname) < 2:
|
|
|
355 ndash = 1
|
|
|
356 return ndash
|
|
30
|
357
|
|
36
|
358 def doXMLparam(self):
|
|
|
359 """flake8 made me do this..."""
|
|
|
360 for p in self.outfiles:
|
|
|
361 newname, newfmt, newcl, oldcl = p
|
|
|
362 ndash = self.getNdash(newcl)
|
|
|
363 aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash)
|
|
|
364 aparm.positional = self.is_positional
|
|
|
365 if self.is_positional:
|
|
|
366 if oldcl == "STDOUT":
|
|
|
367 aparm.positional = 9999999
|
|
|
368 aparm.command_line_override = "> $%s" % newcl
|
|
|
369 else:
|
|
|
370 aparm.positional = int(oldcl)
|
|
|
371 aparm.command_line_override = "$%s" % newcl
|
|
|
372 self.toutputs.append(aparm)
|
|
38
|
373 tp = gxtp.TestOutput(
|
|
|
374 name=newcl, value="%s_sample" % newcl, format=newfmt
|
|
|
375 )
|
|
36
|
376 self.testparam.append(tp)
|
|
|
377 for p in self.infiles:
|
|
|
378 newname = p[ICLPOS]
|
|
|
379 newfmt = p[IFMTPOS]
|
|
|
380 ndash = self.getNdash(newname)
|
|
|
381 if not len(p[ILABPOS]) > 0:
|
|
|
382 alab = p[ICLPOS]
|
|
|
383 else:
|
|
|
384 alab = p[ILABPOS]
|
|
|
385 aninput = gxtp.DataParam(
|
|
|
386 newname,
|
|
|
387 optional=False,
|
|
|
388 label=alab,
|
|
|
389 help=p[IHELPOS],
|
|
|
390 format=newfmt,
|
|
|
391 multiple=False,
|
|
|
392 num_dashes=ndash,
|
|
|
393 )
|
|
|
394 aninput.positional = self.is_positional
|
|
|
395 self.tinputs.append(aninput)
|
|
|
396 tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
|
|
|
397 self.testparam.append(tparm)
|
|
|
398 for p in self.addpar:
|
|
38
|
399 newname, newval, newlabel, newhelp, newtype, newcl, override, oldcl = p
|
|
36
|
400 if not len(newlabel) > 0:
|
|
|
401 newlabel = newname
|
|
|
402 ndash = self.getNdash(newname)
|
|
|
403 if newtype == "text":
|
|
|
404 aparm = gxtp.TextParam(
|
|
|
405 newname,
|
|
|
406 label=newlabel,
|
|
|
407 help=newhelp,
|
|
|
408 value=newval,
|
|
|
409 num_dashes=ndash,
|
|
|
410 )
|
|
|
411 elif newtype == "integer":
|
|
|
412 aparm = gxtp.IntegerParam(
|
|
|
413 newname,
|
|
|
414 label=newname,
|
|
|
415 help=newhelp,
|
|
|
416 value=newval,
|
|
|
417 num_dashes=ndash,
|
|
|
418 )
|
|
|
419 elif newtype == "float":
|
|
|
420 aparm = gxtp.FloatParam(
|
|
|
421 newname,
|
|
|
422 label=newname,
|
|
|
423 help=newhelp,
|
|
|
424 value=newval,
|
|
|
425 num_dashes=ndash,
|
|
|
426 )
|
|
|
427 else:
|
|
|
428 raise ValueError(
|
|
|
429 'Unrecognised parameter type "%s" for\
|
|
|
430 additional parameter %s in makeXML'
|
|
|
431 % (newtype, newname)
|
|
|
432 )
|
|
|
433 aparm.positional = self.is_positional
|
|
|
434 if self.is_positional:
|
|
|
435 aninput.positional = int(oldcl)
|
|
|
436 self.tinputs.append(aparm)
|
|
|
437 self.tparm = gxtp.TestParam(newname, value=newval)
|
|
|
438 self.testparam.append(tparm)
|
|
|
439
|
|
|
440 def doNoXMLparam(self):
|
|
|
441 alab = self.infiles[0][ILABPOS]
|
|
|
442 if len(alab) == 0:
|
|
|
443 alab = self.infiles[0][ICLPOS]
|
|
|
444 max1s = (
|
|
|
445 "Maximum one input if parampass is 0 - more than one input files supplied - %s"
|
|
|
446 % str(self.infiles)
|
|
|
447 )
|
|
|
448 assert len(self.infiles) == 1, max1s
|
|
|
449 newname = self.infiles[0][ICLPOS]
|
|
|
450 aninput = gxtp.DataParam(
|
|
|
451 newname,
|
|
|
452 optional=False,
|
|
|
453 label=alab,
|
|
|
454 help=self.infiles[0][IHELPOS],
|
|
|
455 format=self.infiles[0][IFMTPOS],
|
|
|
456 multiple=False,
|
|
|
457 num_dashes=0,
|
|
|
458 )
|
|
|
459 aninput.command_line_override = "< $%s" % newname
|
|
|
460 aninput.positional = self.is_positional
|
|
|
461 self.tinputs.append(aninput)
|
|
|
462 tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
|
|
|
463 self.testparam.append(tp)
|
|
|
464 newname = self.outfiles[0][OCLPOS]
|
|
|
465 newfmt = self.outfiles[0][OFMTPOS]
|
|
|
466 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
|
|
|
467 anout.command_line_override = "> $%s" % newname
|
|
|
468 anout.positional = self.is_positional
|
|
|
469 self.toutputs.append(anout)
|
|
38
|
470 tp = gxtp.TestOutput(
|
|
|
471 name=newname, value="%s_sample" % newname, format=newfmt
|
|
|
472 )
|
|
36
|
473 self.testparam.append(tp)
|
|
30
|
474
|
|
|
475 def makeXML(self):
|
|
|
476 """
|
|
|
477 Create a Galaxy xml tool wrapper for the new script
|
|
|
478 Uses galaxyhtml
|
|
|
479 Hmmm. How to get the command line into correct order...
|
|
|
480 """
|
|
36
|
481 self.tool.command_line_override = self.xmlcl
|
|
30
|
482 if self.args.interpreter_name:
|
|
38
|
483 self.tool.interpreter = self.args.interpreter_name
|
|
30
|
484 if self.args.help_text:
|
|
36
|
485 helptext = open(self.args.help_text, "r").readlines()
|
|
30
|
486 helptext = [html_escape(x) for x in helptext]
|
|
36
|
487 self.tool.help = "".join([x for x in helptext])
|
|
30
|
488 else:
|
|
36
|
489 self.tool.help = (
|
|
|
490 "Please ask the tool author (%s) for help \
|
|
|
491 as none was supplied at tool generation\n"
|
|
|
492 % (self.args.user_email)
|
|
|
493 )
|
|
|
494 self.tool.version_command = None # do not want
|
|
30
|
495 requirements = gxtp.Requirements()
|
|
36
|
496
|
|
30
|
497 if self.args.interpreter_name:
|
|
36
|
498 if self.args.interpreter_name == "python":
|
|
|
499 requirements.append(
|
|
38
|
500 gxtp.Requirement(
|
|
|
501 "package", "python", self.args.interpreter_version
|
|
|
502 )
|
|
36
|
503 )
|
|
|
504 elif self.args.interpreter_name not in ["bash", "sh"]:
|
|
|
505 requirements.append(
|
|
|
506 gxtp.Requirement(
|
|
|
507 "package",
|
|
|
508 self.args.interpreter_name,
|
|
|
509 self.args.interpreter_version,
|
|
|
510 )
|
|
|
511 )
|
|
30
|
512 else:
|
|
|
513 if self.args.exe_package and self.args.parampass != "system":
|
|
36
|
514 requirements.append(
|
|
|
515 gxtp.Requirement(
|
|
38
|
516 "package",
|
|
|
517 self.args.exe_package,
|
|
|
518 self.args.exe_package_version,
|
|
36
|
519 )
|
|
|
520 )
|
|
|
521 self.tool.requirements = requirements
|
|
|
522 if self.args.parampass == "0":
|
|
38
|
523 self.doNoXMLparam()
|
|
30
|
524 else:
|
|
38
|
525 self.doXMLparam()
|
|
36
|
526 self.tool.outputs = self.toutputs
|
|
|
527 self.tool.inputs = self.tinputs
|
|
|
528 if self.args.runmode not in ["Executable", "system"]:
|
|
30
|
529 configfiles = gxtp.Configfiles()
|
|
|
530 configfiles.append(gxtp.Configfile(name="runMe", text=self.script))
|
|
36
|
531 self.tool.configfiles = configfiles
|
|
30
|
532 tests = gxtp.Tests()
|
|
|
533 test_a = gxtp.Test()
|
|
36
|
534 for tp in self.testparam:
|
|
30
|
535 test_a.append(tp)
|
|
|
536 tests.append(test_a)
|
|
36
|
537 self.tool.tests = tests
|
|
|
538 self.tool.add_comment(
|
|
|
539 "Created by %s at %s using the Galaxy Tool Factory."
|
|
|
540 % (self.args.user_email, timenow())
|
|
|
541 )
|
|
|
542 self.tool.add_comment("Source in git at: %s" % (toolFactoryURL))
|
|
|
543 self.tool.add_comment(
|
|
|
544 "Cite: Creating re-usable tools from scripts doi: 10.1093/bioinformatics/bts573"
|
|
|
545 )
|
|
|
546 exml = self.tool.export()
|
|
38
|
547 xf = open('%s.xml' % self.tool_name, "w")
|
|
30
|
548 xf.write(exml)
|
|
36
|
549 xf.write("\n")
|
|
30
|
550 xf.close()
|
|
|
551 # ready for the tarball
|
|
|
552
|
|
|
553 def makeTooltar(self):
|
|
|
554 """
|
|
|
555 a tool is a gz tarball with eg
|
|
|
556 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
|
|
|
557 NOTE names for test inputs and outputs are munged here so must
|
|
|
558 correspond to actual input and output names used on the generated cl
|
|
|
559 """
|
|
|
560 retval = self.run()
|
|
|
561 if retval:
|
|
38
|
562 sys.stderr.write(
|
|
|
563 "## Run failed. Cannot build yet. Please fix and retry"
|
|
|
564 )
|
|
30
|
565 sys.exit(1)
|
|
36
|
566 tdir = "tfout"
|
|
30
|
567 if not os.path.exists(tdir):
|
|
|
568 os.mkdir(tdir)
|
|
|
569 self.makeXML()
|
|
36
|
570 testdir = os.path.join(tdir, "test-data")
|
|
30
|
571 if not os.path.exists(testdir):
|
|
|
572 os.mkdir(testdir) # make tests directory
|
|
|
573 for p in self.infiles:
|
|
|
574 pth = p[IPATHPOS]
|
|
36
|
575 dest = os.path.join(testdir, "%s_sample" % p[ICLPOS])
|
|
30
|
576 shutil.copyfile(pth, dest)
|
|
|
577 for p in self.outfiles:
|
|
|
578 pth = p[OCLPOS]
|
|
36
|
579 if p[OOCLPOS] == "STDOUT" or self.args.parampass == "0":
|
|
30
|
580 pth = p[ONAMEPOS]
|
|
36
|
581 dest = os.path.join(testdir, "%s_sample" % p[ONAMEPOS])
|
|
30
|
582 shutil.copyfile(pth, dest)
|
|
|
583 dest = os.path.join(tdir, p[ONAMEPOS])
|
|
36
|
584 shutil.copyfile(pth, dest)
|
|
30
|
585 else:
|
|
|
586 pth = p[OCLPOS]
|
|
36
|
587 dest = os.path.join(testdir, "%s_sample" % p[OCLPOS])
|
|
30
|
588 shutil.copyfile(pth, dest)
|
|
|
589 dest = os.path.join(tdir, p[OCLPOS])
|
|
36
|
590 shutil.copyfile(pth, dest)
|
|
30
|
591
|
|
|
592 if os.path.exists(self.tlog) and os.stat(self.tlog).st_size > 0:
|
|
38
|
593 shutil.copyfile(self.tlog, os.path.join(testdir, "test1_log_outfiletxt"))
|
|
36
|
594 if self.args.runmode not in ["Executable", "system"]:
|
|
|
595 stname = os.path.join(tdir, "%s" % (self.sfile))
|
|
30
|
596 if not os.path.exists(stname):
|
|
|
597 shutil.copyfile(self.sfile, stname)
|
|
38
|
598 xreal = '%s.xml' % self.tool_name
|
|
|
599 xout = os.path.join(tdir,xreal)
|
|
|
600 shutil.copyfile(xreal, xout)
|
|
36
|
601 tarpath = "toolfactory_%s.tgz" % self.tool_name
|
|
|
602 tf = tarfile.open(tarpath, "w:gz")
|
|
|
603 tf.add(name=tdir, arcname=self.tool_name)
|
|
30
|
604 tf.close()
|
|
|
605 shutil.copyfile(tarpath, self.args.new_tool)
|
|
38
|
606 shutil.copyfile(xreal,"tool_xml.txt")
|
|
|
607 repdir = "TF_run_report_tempdir"
|
|
|
608 if not os.path.exists(repdir):
|
|
|
609 os.mkdir(repdir)
|
|
|
610 repoutnames = [x[OCLPOS] for x in self.outfiles]
|
|
|
611 with os.scandir('.') as outs:
|
|
|
612 for entry in outs:
|
|
|
613 if entry.name.endswith('.tgz') or not entry.is_file():
|
|
|
614 continue
|
|
|
615 if entry.name in repoutnames:
|
|
|
616 shutil.copyfile(entry.name,os.path.join(repdir,entry.name))
|
|
|
617 elif entry.name == "%s.xml" % self.tool_name:
|
|
|
618 shutil.copyfile(entry.name,os.path.join(repdir,"new_tool_xml"))
|
|
30
|
619 return retval
|
|
|
620
|
|
|
621 def run(self):
|
|
|
622 """
|
|
|
623 Some devteam tools have this defensive stderr read so I'm keeping with the faith
|
|
|
624 Feel free to update.
|
|
|
625 """
|
|
36
|
626 s = "run cl=%s" % str(self.cl)
|
|
|
627
|
|
30
|
628 logging.debug(s)
|
|
36
|
629 scl = " ".join(self.cl)
|
|
30
|
630 err = None
|
|
36
|
631 if self.args.parampass != "0":
|
|
|
632 ste = open(self.elog, "wb")
|
|
30
|
633 if self.lastclredirect:
|
|
38
|
634 sto = open(
|
|
|
635 self.lastclredirect[1], "wb"
|
|
|
636 ) # is name of an output file
|
|
30
|
637 else:
|
|
36
|
638 sto = open(self.tlog, "wb")
|
|
30
|
639 sto.write(
|
|
36
|
640 bytes(
|
|
38
|
641 "## Executing Toolfactory generated command line = %s\n"
|
|
|
642 % scl,
|
|
36
|
643 "utf8",
|
|
|
644 )
|
|
|
645 )
|
|
30
|
646 sto.flush()
|
|
36
|
647 p = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste)
|
|
30
|
648 sto.close()
|
|
|
649 ste.close()
|
|
36
|
650 tmp_stderr = open(self.elog, "rb")
|
|
|
651 err = ""
|
|
30
|
652 buffsize = 1048576
|
|
|
653 try:
|
|
|
654 while True:
|
|
|
655 err += str(tmp_stderr.read(buffsize))
|
|
|
656 if not err or len(err) % buffsize != 0:
|
|
|
657 break
|
|
|
658 except OverflowError:
|
|
|
659 pass
|
|
|
660 tmp_stderr.close()
|
|
|
661 retval = p.returncode
|
|
|
662 else: # work around special case of simple scripts that take stdin and write to stdout
|
|
36
|
663 sti = open(self.infiles[0][IPATHPOS], "rb")
|
|
|
664 sto = open(self.outfiles[0][ONAMEPOS], "wb")
|
|
30
|
665 # must use shell to redirect
|
|
|
666 p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti)
|
|
|
667 retval = p.returncode
|
|
|
668 sto.close()
|
|
|
669 sti.close()
|
|
|
670 if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:
|
|
|
671 os.unlink(self.tlog)
|
|
|
672 if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0:
|
|
|
673 os.unlink(self.elog)
|
|
|
674 if p.returncode != 0 and err: # problem
|
|
|
675 sys.stderr.write(err)
|
|
36
|
676 logging.debug("run done")
|
|
30
|
677 return retval
|
|
|
678
|
|
|
679
|
|
|
680 def main():
|
|
|
681 """
|
|
|
682 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
|
|
|
683 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
|
|
|
684 </command>
|
|
|
685 """
|
|
|
686 parser = argparse.ArgumentParser()
|
|
|
687 a = parser.add_argument
|
|
36
|
688 a("--script_path", default="")
|
|
|
689 a("--tool_name", default=None)
|
|
|
690 a("--interpreter_name", default=None)
|
|
|
691 a("--interpreter_version", default=None)
|
|
|
692 a("--exe_package", default=None)
|
|
|
693 a("--exe_package_version", default=None)
|
|
|
694 a("--input_files", default=[], action="append")
|
|
|
695 a("--output_files", default=[], action="append")
|
|
|
696 a("--user_email", default="Unknown")
|
|
|
697 a("--bad_user", default=None)
|
|
|
698 a("--make_Tool", default=None)
|
|
|
699 a("--help_text", default=None)
|
|
|
700 a("--tool_desc", default=None)
|
|
|
701 a("--tool_version", default=None)
|
|
|
702 a("--citations", default=None)
|
|
|
703 a("--additional_parameters", action="append", default=[])
|
|
|
704 a("--edit_additional_parameters", action="store_true", default=False)
|
|
|
705 a("--parampass", default="positional")
|
|
|
706 a("--tfout", default="./tfout")
|
|
|
707 a("--new_tool", default="new_tool")
|
|
|
708 a("--runmode", default=None)
|
|
30
|
709 args = parser.parse_args()
|
|
36
|
710 assert not args.bad_user, (
|
|
|
711 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file'
|
|
|
712 % (args.bad_user, args.bad_user)
|
|
|
713 )
|
|
38
|
714 assert (
|
|
|
715 args.tool_name
|
|
|
716 ), "## Tool Factory expects a tool name - eg --tool_name=DESeq"
|
|
36
|
717 assert (
|
|
|
718 args.interpreter_name or args.exe_package
|
|
|
719 ), "## Tool Factory wrapper expects an interpreter or an executable package"
|
|
|
720 assert args.exe_package or (
|
|
|
721 len(args.script_path) > 0 and os.path.isfile(args.script_path)
|
|
|
722 ), "## Tool Factory wrapper expects a script path - eg --script_path=foo.R if no executable"
|
|
38
|
723 args.input_files = [
|
|
|
724 x.replace('"', "").replace("'", "") for x in args.input_files
|
|
|
725 ]
|
|
30
|
726 # remove quotes we need to deal with spaces in CL params
|
|
|
727 for i, x in enumerate(args.additional_parameters):
|
|
38
|
728 args.additional_parameters[i] = args.additional_parameters[i].replace(
|
|
|
729 '"', ""
|
|
|
730 )
|
|
30
|
731 r = ScriptRunner(args)
|
|
|
732 if args.make_Tool:
|
|
|
733 retcode = r.makeTooltar()
|
|
|
734 else:
|
|
|
735 retcode = r.run()
|
|
|
736 if retcode:
|
|
|
737 sys.exit(retcode) # indicate failure to job runner
|
|
|
738
|
|
|
739
|
|
|
740 if __name__ == "__main__":
|
|
|
741 main()
|
