Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/cwl/script.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1 import copy
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2 import os
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3
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4 try:
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5 import schema_salad
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6 except (ImportError, SyntaxError):
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7 # TODO: implement support for Python 2.6 and 3.X
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8 schema_salad = None
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9
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10 try:
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11 import cwltool
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12 except (ImportError, SyntaxError):
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13 cwltool = None
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14
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15 try:
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16 from cwltool.main import load_tool
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17 except (ImportError, SyntaxError):
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18 load_tool = None
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19
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20 try:
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21 from cwltool import process
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22 except (ImportError, SyntaxError):
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23 process = None
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24
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25 try:
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26 from .cwl2script import cwl2script
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27 except (ImportError, SyntaxError):
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28 cwl2script = None
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29
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30
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31 def to_script(ctx, path, job_path, **kwds):
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32 if schema_salad is None:
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33 raise Exception("This functionality requires schema_salad and Python 2.7.")
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34
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35 if cwltool is None:
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36 raise Exception("This functionality requires cwltool and Python 2.7.")
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37
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38 uri = "file://" + os.path.abspath(job_path)
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39
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40 loader = schema_salad.ref_resolver.Loader({
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41 "@base": uri,
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42 "path": {
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43 "@type": "@id"
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44 }
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45 })
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46
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47 job, _ = loader.resolve_ref(uri)
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48
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49 t = load_tool(path, False, False, cwltool.workflow.defaultMakeTool, True)
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50
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51 if type(t) == int:
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52 return t
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53
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54 process.checkRequirements(t.tool, cwl2script.supportedProcessRequirements)
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55
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56 for inp in t.tool["inputs"]:
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57 if process.shortname(inp["id"]) in job:
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58 pass
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59 elif process.shortname(inp["id"]) not in job and "default" in inp:
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60 job[process.shortname(inp["id"])] = copy.copy(inp["default"])
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61 elif process.shortname(inp["id"]) not in job and inp["type"][0] == "null":
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62 pass
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63 else:
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64 raise Exception("Missing inputs `%s`" % process.shortname(inp["id"]))
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65
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66 if not kwds.get("basedir", None):
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67 kwds["basedir"] = os.path.dirname(os.path.abspath(job_path))
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68
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69 outdir = kwds.get("outdir")
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70
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71 if t.tool["class"] == "Workflow":
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72 print(cwl2script.generateScriptForWorkflow(t, job, outdir))
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73 elif t.tool["class"] == "CommandLineTool":
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74 print(cwl2script.generateScriptForTool(t, job, outdir))
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75
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76 return 0