--- a/env/lib/python3.7/site-packages/planemo/cwl/cwl2script/cwl2script.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,200 +0,0 @@
-import argparse
-import cwltool.main
-import sys
-import os
-import schema_salad
-import logging
-from cwltool.process import checkRequirements, shortname, adjustFiles
-import shellescape
-import re
-import copy
-import json
-
-needs_shell_quoting = re.compile(r"""(^$|[\s|&;()<>\'"$@])""").search
-glob_metacharacters = re.compile(r"""[\[\]\*?]""").search
-
-def maybe_quote(arg):
-    return shellescape.quote(arg) if needs_shell_quoting(arg) else arg
-
-def generateScriptForTool(tool, job, outdir):
-    for j in tool.job(job, "", None, outdir=outdir):
-        return ("""mkdir -p %s  # output directory
-mkdir -p %s  # temporary directory
-%s%s%s
-rm -r %s     # clean up temporary directory
-""" % (maybe_quote(j.outdir), maybe_quote(j.tmpdir),
-                                        " ".join([maybe_quote(arg) for arg in (j.command_line)]),
-                           ' < %s' % maybe_quote(j.stdin) if j.stdin else '',
-                                         ' > %s' % maybe_quote(os.path.join(j.outdir, j.stdout)) if j.stdout else '',
-       maybe_quote(j.tmpdir)),
-                j.outdir, j.tmpdir)
-
-
-def generateScriptForWorkflow(cwlwf, cwljob, outdir):
-    promises = {}
-    jobs = {}
-    script = ["#!/bin/sh",
-              "",
-              "# Workflow generated from %s using cwl2script" % (cwlwf.tool["id"]),
-              ""
-              "set -x",
-              ""
-          ]
-
-    outdirs = []
-
-    for inp in cwlwf.tool["inputs"]:
-        promises[inp["id"]] = (cwlwf, cwljob[shortname(inp["id"])])
-
-    alloutputs_fufilled = False
-    while not alloutputs_fufilled:
-        # Iteratively go over the workflow steps, adding jobs to the script as their
-        # dependencies are fufilled by upstream workflow inputs or
-        # step outputs.  Loop exits when the workflow outputs
-        # are satisfied.
-
-        alloutputs_fufilled = True
-
-        progress = False
-        for step in cwlwf.steps:
-            if step.tool["id"] not in jobs:
-                stepinputs_fufilled = True
-                for inp in step.tool["inputs"]:
-                    if "source" in inp and inp["source"] not in promises:
-                        stepinputs_fufilled = False
-                if stepinputs_fufilled:
-                    jobobj = {}
-
-                    # TODO: Handle multiple inbound links
-                    # TODO: Handle scatter/gather
-                    # (both are discussed in section 5.1.2 in CWL spec draft-2)
-
-                    script.append("# Run step %s" % step.tool["id"])
-
-                    for inp in step.tool["inputs"]:
-                        if "source" in inp:
-                            jobobj[shortname(inp["id"])] = promises[inp["source"]][1]
-                            script.append("# depends on step %s" % promises[inp["source"]][0].tool["id"])
-                        elif "default" in inp:
-                            d = copy.copy(inp["default"])
-                            jobobj[shortname(inp["id"])] = d
-
-                    (wfjob, joboutdir, jobtmpdir) = generateScriptForTool(step.embedded_tool, jobobj, None)
-                    outdirs.append(joboutdir)
-
-                    jobs[step.tool["id"]] = True
-
-                    script.append(wfjob)
-
-                    for out in step.tool["outputs"]:
-                        for toolout in step.embedded_tool.tool["outputs"]:
-                            if shortname(toolout["id"]) == shortname(out["id"]):
-                                if toolout["type"] != "File":
-                                    raise Exception("Only supports file outputs")
-                                if glob_metacharacters(toolout["outputBinding"]["glob"]):
-                                    raise Exception("Only support glob with concrete filename.")
-                                promises[out["id"]] = (step, {"class":"File", "path": os.path.join(joboutdir, toolout["outputBinding"]["glob"])})
-                    progress = True
-
-        for out in cwlwf.tool["outputs"]:
-            if "source" in out:
-                if out["source"] not in promises:
-                    alloutputs_fufilled = False
-
-        if not alloutputs_fufilled and not progress:
-            raise Exception("Not making progress")
-
-    outobj = {}
-    script.append("# Move output files to the current directory")
-
-    for out in cwlwf.tool["outputs"]:
-        f = promises[out["source"]][1]
-        script.append("mv %s ." % (maybe_quote(f["path"])))
-        f["path"] = os.path.basename(f["path"])
-
-        if f.get("secondaryFiles"):
-            script.append("mv %s ." % (' '.join([maybe_quote(sf["path"]) for sf in f["secondaryFiles"]])))
-            for sf in f["secondaryFiles"]:
-                sf["path"] = os.path.basename(sf["path"])
-
-        outobj[shortname(out["id"])] = f
-
-    script.append("")
-    script.append("# Clean up staging output directories")
-    script.append("rm -r %s" % (' '.join([maybe_quote(od) for od in outdirs])))
-    script.append("")
-
-    script.append("# Generate final output object")
-    script.append("echo '%s'" % json.dumps(outobj, indent=4))
-
-    return "\n".join(script)
-
-
-
-supportedProcessRequirements = ["SchemaDefRequirement"]
-
-def main(args=None):
-    parser = argparse.ArgumentParser()
-    parser.add_argument("cwltool", type=str)
-    parser.add_argument("cwljob", type=str)
-
-    parser.add_argument("--conformance-test", action="store_true")
-    parser.add_argument("--no-container", action="store_true")
-    parser.add_argument("--basedir", type=str)
-    parser.add_argument("--outdir", type=str, default=os.getcwd())
-
-    options = parser.parse_args(args)
-
-    uri = "file://" + os.path.abspath(options.cwljob)
-
-    if options.conformance_test:
-        loader = schema_salad.ref_resolver.Loader({})
-    else:
-        loader = schema_salad.ref_resolver.Loader({
-            "@base": uri,
-            "path": {
-                "@type": "@id"
-            }
-        })
-
-    job, _ = loader.resolve_ref(uri)
-
-    t = cwltool.main.load_tool(options.cwltool, False, False, cwltool.workflow.defaultMakeTool, True)
-
-    if type(t) == int:
-        return t
-
-    try:
-        checkRequirements(t.tool, supportedProcessRequirements)
-    except Exception as e:
-        logging.error(e)
-        return 33
-
-    for inp in t.tool["inputs"]:
-        if shortname(inp["id"]) in job:
-            pass
-        elif shortname(inp["id"]) not in job and "default" in inp:
-            job[shortname(inp["id"])] = copy.copy(inp["default"])
-        elif shortname(inp["id"]) not in job and inp["type"][0] == "null":
-            pass
-        else:
-            raise Exception("Missing inputs `%s`" % shortname(inp["id"]))
-
-    if options.conformance_test:
-        sys.stdout.write(json.dumps(cwltool.main.single_job_executor(t, job, options.basedir, options, conformance_test=True), indent=4))
-        return 0
-
-    if not options.basedir:
-        options.basedir = os.path.dirname(os.path.abspath(options.cwljob))
-
-    outdir = options.outdir
-
-    if t.tool["class"] == "Workflow":
-        print generateScriptForWorkflow(t, job, outdir)
-    elif t.tool["class"] == "CommandLineTool":
-        print generateScriptForTool(t, job, outdir)
-
-    return 0
-
-if __name__=="__main__":
-    sys.exit(main(sys.argv[1:]))