draft2tool.py

import avro.schema
import json
import copy
from flatten import flatten
import functools
import os
from pathmapper import PathMapper, DockerPathMapper
from job import CommandLineJob
import yaml
import glob
import logging
import hashlib
import random
from process import Process, shortname, uniquename, adjustFileObjs
from errors import WorkflowException
import schema_salad.validate as validate
from aslist import aslist
import expression
import re
import urlparse
import tempfile
from builder import CONTENT_LIMIT, substitute
import shellescape
import errno

_logger = logging.getLogger("cwltool")

class ExpressionTool(Process):
    def __init__(self, toolpath_object, **kwargs):
        super(ExpressionTool, self).__init__(toolpath_object, **kwargs)

    class ExpressionJob(object):
        def run(self, **kwargs):
            try:
                self.output_callback(self.builder.do_eval(self.script), "success")
            except Exception as e:
                _logger.warn("Failed to evaluate expression:\n%s", e, exc_info=(e if kwargs.get('debug') else False))
                self.output_callback({}, "permanentFail")

    def job(self, joborder, input_basedir, output_callback, **kwargs):
        builder = self._init_job(joborder, input_basedir, **kwargs)

        j = ExpressionTool.ExpressionJob()
        j.builder = builder
        j.script = self.tool["expression"]
        j.output_callback = output_callback
        j.requirements = self.requirements
        j.hints = self.hints
        j.outdir = None
        j.tmpdir = None

        yield j

def remove_hostfs(f):
    if "hostfs" in f:
        del f["hostfs"]

def revmap_file(builder, outdir, f):
    """Remap a file back to original path. For Docker, this is outside the container.

    Uses either files in the pathmapper or remaps internal output directories
    to the external directory.
    """

    if f.get("hostfs"):
        return

    revmap_f = builder.pathmapper.reversemap(f["path"])
    if revmap_f:
        f["path"] = revmap_f[1]
        f["hostfs"] = True
        return f
    elif f["path"].startswith(builder.outdir):
        f["path"] = os.path.join(outdir, f["path"][len(builder.outdir)+1:])
        f["hostfs"] = True
        return f
    else:
        raise WorkflowException("Output file path %s must be within designated output directory (%s) or an input file pass through." % (f["path"], builder.outdir))


class CommandLineTool(Process):
    def __init__(self, toolpath_object, **kwargs):
        super(CommandLineTool, self).__init__(toolpath_object, **kwargs)

    def makeJobRunner(self):
        return CommandLineJob()

    def makePathMapper(self, reffiles, input_basedir, **kwargs):
        dockerReq, _ = self.get_requirement("DockerRequirement")
        try:
            if dockerReq and kwargs.get("use_container"):
                return DockerPathMapper(reffiles, input_basedir)
            else:
                return PathMapper(reffiles, input_basedir)
        except OSError as e:
            if e.errno == errno.ENOENT:
                raise WorkflowException("Missing input file %s" % e)

    def job(self, joborder, input_basedir, output_callback, **kwargs):
        builder = self._init_job(joborder, input_basedir, **kwargs)

        if self.tool["baseCommand"]:
            for n, b in enumerate(aslist(self.tool["baseCommand"])):
                builder.bindings.append({
                    "position": [-1000000, n],
                    "valueFrom": b
                })

        if self.tool.get("arguments"):
            for i, a in enumerate(self.tool["arguments"]):
                if isinstance(a, dict):
                    a = copy.copy(a)
                    if a.get("position"):
                        a["position"] = [a["position"], i]
                    else:
                        a["position"] = [0, i]
                    a["do_eval"] = a["valueFrom"]
                    a["valueFrom"] = None
                    builder.bindings.append(a)
                else:
                    builder.bindings.append({
                        "position": [0, i],
                        "valueFrom": a
                    })

        builder.bindings.sort(key=lambda a: a["position"])

        reffiles = set((f["path"] for f in builder.files))

        j = self.makeJobRunner()
        j.builder = builder
        j.joborder = builder.job
        j.stdin = None
        j.stdout = None
        j.successCodes = self.tool.get("successCodes")
        j.temporaryFailCodes = self.tool.get("temporaryFailCodes")
        j.permanentFailCodes = self.tool.get("permanentFailCodes")
        j.requirements = self.requirements
        j.hints = self.hints
        j.name = uniquename(kwargs.get("name", str(id(j))))

        _logger.debug("[job %s] initializing from %s%s",
                     j.name,
                     self.tool.get("id", ""),
                     " as part of %s" % kwargs["part_of"] if "part_of" in kwargs else "")
        _logger.debug("[job %s] %s", j.name, json.dumps(joborder, indent=4))


        builder.pathmapper = None

        if self.tool.get("stdin"):
            j.stdin = builder.do_eval(self.tool["stdin"])
            if isinstance(j.stdin, dict) and "ref" in j.stdin:
                j.stdin = builder.job[j.stdin["ref"][1:]]["path"]
            reffiles.add(j.stdin)

        if self.tool.get("stdout"):
            j.stdout = builder.do_eval(self.tool["stdout"])
            if os.path.isabs(j.stdout) or ".." in j.stdout:
                raise validate.ValidationException("stdout must be a relative path")

        builder.pathmapper = self.makePathMapper(reffiles, input_basedir, **kwargs)
        builder.requirements = j.requirements

        # map files to assigned path inside a container. We need to also explicitly
        # walk over input as implicit reassignment doesn't reach everything in builder.bindings
        def _check_adjust(f):
            if not f.get("containerfs"):
                f["path"] = builder.pathmapper.mapper(f["path"])[1]
                f["containerfs"] = True
            return f

        adjustFileObjs(builder.files, _check_adjust)
        adjustFileObjs(builder.bindings, _check_adjust)

        _logger.debug("[job %s] command line bindings is %s", j.name, json.dumps(builder.bindings, indent=4))
        _logger.debug("[job %s] path mappings is %s", j.name, json.dumps({p: builder.pathmapper.mapper(p) for p in builder.pathmapper.files()}, indent=4))

        dockerReq, _ = self.get_requirement("DockerRequirement")
        if dockerReq and kwargs.get("use_container"):
            out_prefix = kwargs.get("tmp_outdir_prefix")
            j.outdir = kwargs.get("outdir") or tempfile.mkdtemp(prefix=out_prefix)
            tmpdir_prefix = kwargs.get('tmpdir_prefix')
            j.tmpdir = kwargs.get("tmpdir") or tempfile.mkdtemp(prefix=tmpdir_prefix)
        else:
            j.outdir = builder.outdir
            j.tmpdir = builder.tmpdir

        createFiles, _ = self.get_requirement("CreateFileRequirement")
        j.generatefiles = {}
        if createFiles:
            for t in createFiles["fileDef"]:
                j.generatefiles[builder.do_eval(t["filename"])] = copy.deepcopy(builder.do_eval(t["fileContent"]))

        j.environment = {}
        evr, _ = self.get_requirement("EnvVarRequirement")
        if evr:
            for t in evr["envDef"]:
                j.environment[t["envName"]] = builder.do_eval(t["envValue"])

        shellcmd, _ = self.get_requirement("ShellCommandRequirement")
        if shellcmd:
            cmd = []
            for b in builder.bindings:
                arg = builder.generate_arg(b)
                if b.get("shellQuote", True):
                    arg = [shellescape.quote(a) for a in aslist(arg)]
                cmd.extend(aslist(arg))
            j.command_line = ["/bin/sh", "-c", " ".join(cmd)]
        else:
            j.command_line = flatten(map(builder.generate_arg, builder.bindings))

        j.pathmapper = builder.pathmapper
        j.collect_outputs = functools.partial(self.collect_output_ports, self.tool["outputs"], builder)
        j.output_callback = output_callback

        yield j

    def collect_output_ports(self, ports, builder, outdir):
        try:
            ret = {}
            custom_output = os.path.join(outdir, "cwl.output.json")
            if builder.fs_access.exists(custom_output):
                with builder.fs_access.open(custom_output, "r") as f:
                    ret = yaml.load(f)
                _logger.debug("Raw output from %s: %s", custom_output, json.dumps(ret, indent=4))
                adjustFileObjs(ret, remove_hostfs)
                adjustFileObjs(ret, functools.partial(revmap_file, builder, outdir))
                adjustFileObjs(ret, remove_hostfs)
                validate.validate_ex(self.names.get_name("outputs_record_schema", ""), ret)
                return ret

            for port in ports:
                fragment = shortname(port["id"])
                ret[fragment] = self.collect_output(port, builder, outdir)
            if ret:
                adjustFileObjs(ret, remove_hostfs)
            validate.validate_ex(self.names.get_name("outputs_record_schema", ""), ret)
            return ret if ret is not None else {}
        except validate.ValidationException as e:
            raise WorkflowException("Error validating output record, " + str(e) + "\n in " + json.dumps(ret, indent=4))

    def collect_output(self, schema, builder, outdir):
        r = None
        if "outputBinding" in schema:
            binding = schema["outputBinding"]
            globpatterns = []

            revmap = functools.partial(revmap_file, builder, outdir)

            if "glob" in binding:
                r = []
                for gb in aslist(binding["glob"]):
                    gb = builder.do_eval(gb)
                    if gb:
                        globpatterns.extend(aslist(gb))

                for gb in globpatterns:
                    if gb.startswith("/"):
                        raise WorkflowError("glob patterns must not start with '/'")
                    try:
                        r.extend([{"path": g, "class": "File", "hostfs": True}
                                  for g in builder.fs_access.glob(os.path.join(outdir, gb))])
                    except (OSError, IOError) as e:
                        _logger.warn(str(e))

                for files in r:
                    checksum = hashlib.sha1()
                    with builder.fs_access.open(files["path"], "rb") as f:
                        contents = f.read(CONTENT_LIMIT)
                        if binding.get("loadContents"):
                            files["contents"] = contents
                        filesize = 0
                        while contents != "":
                            checksum.update(contents)
                            filesize += len(contents)
                            contents = f.read(1024*1024)
                    files["checksum"] = "sha1$%s" % checksum.hexdigest()
                    files["size"] = filesize
                    if "format" in schema:
                        files["format"] = builder.do_eval(schema["format"], context=files)

            optional = False
            singlefile = False
            if isinstance(schema["type"], list):
                if "null" in schema["type"]:
                    optional = True
                if "File" in schema["type"]:
                    singlefile = True
            elif schema["type"] == "File":
                singlefile = True

            if "outputEval" in binding:
                r = builder.do_eval(binding["outputEval"], context=r)
                if singlefile:
                    # Handle single file outputs not wrapped in a list
                    if r is not None and not isinstance(r, (list, tuple)):
                        r = [r]
                    if optional and r is None:
                        pass
                    elif (r is None or len(r) != 1 or not isinstance(r[0], dict) or "path" not in r[0]):
                        raise WorkflowException("Expression must return a file object for %s." % schema["id"])

            if singlefile:
                if not r and not optional:
                    raise WorkflowException("Did not find output file with glob pattern: '{}'".format(globpatterns))
                elif not r and optional:
                    pass
                elif isinstance(r, list):
                    if len(r) > 1:
                        raise WorkflowException("Multiple matches for output item that is a single file.")
                    else:
                        r = r[0]

            # Ensure files point to local references outside of the run environment
            adjustFileObjs(r, revmap)

            if "secondaryFiles" in schema:
                for primary in aslist(r):
                    if isinstance(primary, dict):
                        primary["secondaryFiles"] = []
                        for sf in aslist(schema["secondaryFiles"]):
                            if isinstance(sf, dict) or "$(" in sf or "${" in sf:
                                sfpath = builder.do_eval(sf, context=r)
                                if isinstance(sfpath, basestring):
                                    sfpath = revmap({"path": sfpath, "class": "File"})
                            else:
                                sfpath = {"path": substitute(primary["path"], sf), "class": "File", "hostfs": True}

                            for sfitem in aslist(sfpath):
                                if builder.fs_access.exists(sfitem["path"]):
                                    primary["secondaryFiles"].append(sfitem)

            if not r and optional:
                r = None

        if not r and isinstance(schema["type"], dict) and schema["type"]["type"] == "record":
            r = {}
            for f in schema["type"]["fields"]:
                r[shortname(f["name"])] = self.collect_output(f, builder, outdir)

        return r