8000 cover more field for import_cwl and add appropriate unit tests · illusional/python-cwlgen@cd5198f · GitHub
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cover more field for import_cwl and add appropriate unit tests
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4 files changed

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-4
10000 lines changed

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‎.gitignore

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@@ -0,0 +1,2 @@
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test/__pycache__
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cwlgen/__pycache__

‎cwlgen/import_cwl.py

Lines changed: 263 additions & 4 deletions
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@@ -18,7 +18,8 @@
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logging.basicConfig(level=logging.INFO)
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logger = logging.getLogger(__name__)
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# Class(es) ------------------------------
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# Class(es) ------------------------------
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class CWLToolParser(object):
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"""
@@ -28,7 +29,7 @@ class CWLToolParser(object):
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def _init_tool(self, cwl_dict):
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"""
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Init tool from existing CWL tool.
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:param cwl_dict: Full content of CWL file
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:type cwl_dict: DICT
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"""
@@ -161,7 +162,7 @@ def _load_outputs(self, tool, outputs_el):
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def import_cwl(self, cwl_path):
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"""
163164
Load content of cwl into the :class:`cwlgen.CommandLineTool` object.
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:param cwl_path: Path of the CWL tool to be loaded.
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:type cwl_path: STRING
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:return: CWL tool content in cwlgen model.
@@ -172,7 +173,7 @@ def import_cwl(self, cwl_path):
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tool = self._init_tool(cwl_dict)
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for key, element in cwl_dict.items():
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try:
175-
getattr(self, '_load_{}'.format(key))(tool, element)
176+
getattr(self, '_load_{}'.format(key))(tool, element)
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except AttributeError:
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logger.warning(key + " content is not processed (yet).")
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return tool
@@ -183,6 +184,95 @@ class InputsParser(object):
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Class to parse content of inputs from an existing CWL Tool.
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"""
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def _load_label(self, input_obj, label_el):
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"""
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Load the content of type into the input object.
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:param input_obj: input obj
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:type input_obj: : :class:`cwlgen.CommandInputParameter`
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:param label_el: Content of label
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:type label_el: STRING
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"""
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input_obj.label = label_el
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def _load_secondaryFiles(self, input_obj, secfile_el):
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"""
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Load the content of secondaryFiles into the input object.
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:param input_obj: input obj
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:type input_obj: : :class:`cwlgen.CommandInputParameter`
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:param secfile_el: Content of secondaryFile
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:type secfile_el: STRING
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"""
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input_obj.secondary_file = secfile_el
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def _load_format(self, input_obj, format_el):
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"""
 6D4E
211+
Load the content of format into the input object.
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:param input_obj: input obj
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:type input_obj: : :class:`cwlgen.CommandInputParameter`
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:param format_el: Content of format
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:type format_el: STRING
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"""
218+
input_obj.format = format_el
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220+
def _load_streamable(self, input_obj, stream_el):
221+
"""
222+
Load the content of streamable into the input object.
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:param input_obj: input obj
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:type input_obj: : :class:`cwlgen.CommandInputParameter`
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:param stream_el: Content of streamable
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:type type_el: BOOLEAN
228+
"""
229+
input_obj.streamable = stream_el
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231+
def _load_doc(self, input_obj, doc_el):
232+
"""
233+
Load the content of doc into the input object.
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:param input_obj: input obj
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:type input_obj: : :class:`cwlgen.CommandInputParameter`
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:param doc_el: Content of doc
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:type doc_el: STRING
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"""
240+
input_obj.doc = doc_el
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242+
def _load_inputBinding(self, input_obj, inpb_el):
243+
"""
244+
Load the content of inputBinding into the input object.
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:param input_obj: input obj
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:type input_obj: : :class:`cwlgen.CommandInputParameter`
248+
:param inpb_el: Content of inputBinding
249+
:type inpb_el: DICT
250+
"""
251+
ibparser = InputBindingParser()
252+
ibparser.load_inbinding(input_obj, inpb_el)
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254+
def _load_default(self, input_obj, def_el):
255+
"""
256+
Load the content of default into the input object.
257+
258+
:param input_obj: input obj
259+
:type input_obj: : :class:`cwlgen.CommandInputParameter`
260+
:param default_el: Content of default
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:type default_el: STRING
262+
"""
263+
input_obj.default = def_el
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265+
def _load_type(self, input_obj, type_el):
266+
"""
267+
Load the content of type into the input object.
268+
269+
:param input_obj: input obj
270+
:type input_obj: : :class:`cwlgen.CommandInputParameter`
271+
:param type_el: Content of type
272+
:type type_el: STRING
273+
"""
274+
input_obj.type = type_el
275+
186276
def load_inputs(self, inputs, inputs_el):
187277
"""
188278
Load the content of inputs into the inputs list.
@@ -203,11 +293,180 @@ def load_inputs(self, inputs, inputs_el):
203293
inputs.append(input_obj)
204294

205295

296+
class InputBindingParser(object):
297+
"""
298+
Class to parse content of inputBinding of input from existing CWL Tool.
299+
"""
300+
301+
def _load_loadContents(self, inbinding_obj, loadcontents_el):
302+
"""
303+
Load the content of loadContents into the input object.
304+
305+
:param inbinding_obj: input_binding object
306+
:loadContents inbinding_obj: : :class:`cwlgen.CommandLineBinding`
307+
:param loadcontents_el: Content of loadContents
308+
:loadContents loadcontents_el: BOOLEAN
309+
"""
310+
inbinding_obj.load_contents = loadcontents_el
311+
312+
def _load_position(self, inbinding_obj, position_el):
313+
"""
314+
Load the content of position into the input object.
315+
316+
:param inbinding_obj: input_binding object
317+
:loadContents inbinding_obj: : :class:`cwlgen.CommandLineBinding`
318+
:param position_el: Content of loadContents
319+
:loadContents position_el: INT
320+
"""
321+
inbinding_obj.position = position_el
322+
323+
def _load_prefix(self, inbinding_obj, prefix_el):
324+
"""
325+
Load the content of prefix into the input object.
326+
327+
:param inbinding_obj: input_binding object
328+
:loadContents inbinding_obj: : :class:`cwlgen.CommandLineBinding`
329+
:param prefix_el: Content of loadContents
330+
:loadContents prefix_el: STRING
331+
"""
332+
inbinding_obj.prefix = prefix_el
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334+
def _load_separate(self, inbinding_obj, separate_el):
335+
"""
336+
Load the content of separate into the input object.
337+
338+
:param inbinding_obj: input_binding object
339+
:loadContents inbinding_obj: : :class:`cwlgen.CommandLineBinding`
340+
:param separate_el: Content of loadContents
341+
:loadContents separate_el: BOOLEAN
342+
"""
343+
inbinding_obj.separate = separate_el
344+
345+
def _load_itemSeparator(self, inbinding_obj, itemsep_el):
346+
"""
347+
Load the content of itemSeparator into the input object.
348+
349+
:param inbinding_obj: input_binding object
350+
:loadContents inbinding_obj: : :class:`cwlgen.CommandLineBinding`
351+
:param itemsep_el: Content of loadContents
352+
:loadContents itemsep_el: STRING
353+
"""
354+
inbinding_obj.item_separator = itemsep_el
355+
356+
def _load_valueFrom(self, inbinding_obj, valuefrom_el):
357+
"""
358+
Load the content of valueFrom into the input object.
359+
360+
:param inbinding_obj: input_binding object
361+
:loadContents inbinding_obj: : :class:`cwlgen.CommandLineBinding`
362+
:param valuefrom_el: Content of loadContents
363+
:loadContents valuefrom_el: STRING
364+
"""
365+
inbinding_obj.value_from = valuefrom_el
366+
367+
def _load_shellQuote(self, inbinding_obj, shellquote_el):
368+
"""
369+
Load the content of shellQuote into the input object.
370+
371+
:param inbinding_obj: input_binding object
372+
:loadContents inbinding_obj: : :class:`cwlgen.CommandLineBinding`
373+
:param shellquote_el: Content of loadContents
374+
:loadContents shellquote_el: BOOLEAN
375+
"""
376+
inbinding_obj.shell_quote = shellquote_el
377+
378+
def load_inbinding(self, input_obj, inbinding_el):
379+
"""
380+
Load the content of inputBinding into the input object.
381+
382+
:param input_obj: input object
383+
:type input_obj: :class:`cwlgen.CommandInputParameter`
384+
:param inbinding_el: Content of inputs
385+
:type inbinding_el: DICT
386+
"""
387+
inbinding_obj = cwlgen.CommandLineBinding()
388+
for key, value in inbinding_el.items():
389+
try:
390+
getattr(self, '_load_{}'.format(key))(inbinding_obj, value)
391+
except AttributeError:
392+
logger.warning(key + " content for inputBinding is not processed (yet).")
393+
input_obj.input_binding = inbinding_obj
394+
395+
206396
class OutputsParser(object):
207397
"""
208398
Class to parse content of outputs from an existing CWL Tool.
209399
"""
210400

401+
def _load_label(self, output_obj, label_el):
402+
"""
403+
Load the content of type into the output object.
404+
405+
:param output_obj: output obj
406+
:type output_obj: : :class:`cwlgen.CommandInputParameter`
407+
:param label_el: Content of label
408+
:type label_el: STRING
409+
"""
410+
output_obj.label = label_el
411+
412+
def _load_secondaryFiles(self, output_obj, secfile_el):
413+
"""
414+
Load the content of secondaryFiles into the output object.
415+
416+
:param output_obj: output obj
417+
:type output_obj: : :class:`cwlgen.CommandInputParameter`
418+
:param secfile_el: Content of secondaryFile
419+
:type secfile_el: STRING
420+
"""
421+
output_obj.secondary_file = secfile_el
422+
423+
def _load_format(self, output_obj, format_el):
424+
"""
425+
Load the content of format into the output object.
426+
427+
:param output_obj: output obj
428+
:type output_obj: : :class:`cwlgen.CommandInputParameter`
429+
:param format_el: Content of format
430+
:type format_el: STRING
431+
"""
432+
output_obj.format = format_el
433+
434+
def _load_streamable(self, output_obj, stream_el):
435+
"""
436+
Load the content of streamable into the output object.
437+
438+
:param output_obj: output obj
439+
:type output_obj: : :class:`cwlgen.CommandInputParameter`
440+
:param stream_el: Content of streamable
441+
:type type_el: BOOLEAN
442+
"""
443+
output_obj.streamable = stream_el
444+
445+
def _load_doc(self, output_obj, doc_el):
446+
"""
447+
Load the content of doc into the output object.
448+
449+
:param output_obj: output obj
450+
:type output_obj: : :class:`cwlgen.CommandInputParameter`
451+
:param doc_el: Content of doc
452+
:type doc_el: STRING
453+
"""
454+
output_obj.doc = doc_el
455+
456+
def _load_outputBinding(self, output_obj, inpb_el):
457+
pass
458+
459+
def _load_type(self, output_obj, type_el):
460+
"""
461+
Load the content of type into the output object.
462+
463+
:param output_obj: output obj
464+
:type output_obj: : :class:`cwlgen.CommandInputParameter`
465+
:param type_el: Content of type
466+
:type type_el: STRING
467+
"""
468+
output_obj.type = type_el
469+
211470
def load_outputs(self, outputs, outputs_el):
212471
"""
213472
Load the content of outputs into the outputs list.

‎test/import_cwl.cwl

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Original file line numberDiff line numberDiff line change
@@ -9,3 +9,28 @@ doc: "super_doc"
99
stdin: "in"
1010
stderr: "err"
1111
stdout: "out"
12+
inputs:
13+
INPUT1:
14+
label: label_in
15+
secondaryFiles: 'sec_file_in'
16+
format: format_1930
17+
streamable: True
18+
default: 'def_in'
19+
doc: 'documentation_in'
20+
inputBinding:
21+
loadContents: True
22+
position: 0
23+
prefix: --input
24+
separate: True
25+
itemSeparator: ';'
26+
valueFrom: here
27+
shellQuote: True
28+
type: File
29+
outputs:
30+
OUTPUT1:
31+
label: label_out
32+
secondaryFiles: 'sec_file_out'
33+
format: format_1930
34+
streamable: True
35+
doc: 'documentation_out'
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type: File

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