draft2tool.py

import copy
import hashlib
import json
import logging
import os
import re
import shutil
import tempfile
from functools import partial
from typing import Any, Callable, Dict, Generator, Optional, Text, Union, cast

from six import string_types, u

import schema_salad.validate as validate
import shellescape
from schema_salad.ref_resolver import file_uri, uri_file_path
from schema_salad.sourceline import SourceLine, indent
from six.moves import urllib

from .builder import CONTENT_LIMIT, Builder, substitute
from .errors import WorkflowException
from .flatten import flatten
from .job import CommandLineJob, DockerCommandLineJob, JobBase
from .pathmapper import (PathMapper, adjustDirObjs, adjustFileObjs,
                         get_listing, trim_listing, visit_class)
from .process import (Process, UnsupportedRequirement,
                      _logger_validation_warnings, compute_checksums,
                      normalizeFilesDirs, shortname, uniquename)
from .stdfsaccess import StdFsAccess
from .utils import aslist

ACCEPTLIST_EN_STRICT_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")  # Accept anything
ACCEPTLIST_RE = ACCEPTLIST_EN_STRICT_RE


_logger = logging.getLogger("cwltool")


class ExpressionTool(Process):
    def __init__(self, toolpath_object, **kwargs):
        # type: (Dict[Text, Any], **Any) -> None
        super(ExpressionTool, self).__init__(toolpath_object, **kwargs)

    class ExpressionJob(object):

        def __init__(self):  # type: () -> None
            self.builder = None  # type: Builder
            self.requirements = None  # type: Dict[Text, Text]
            self.hints = None  # type: Dict[Text, Text]
            self.collect_outputs = None  # type: Callable[[Any], Any]
            self.output_callback = None  # type: Callable[[Any, Any], Any]
            self.outdir = None  # type: Text
            self.tmpdir = None  # type: Text
            self.script = None  # type: Dict[Text, Text]

        def run(self, **kwargs):  # type: (**Any) -> None
            try:
                ev = self.builder.do_eval(self.script)
                normalizeFilesDirs(ev)
                self.output_callback(ev, "success")
            except Exception as e:
                _logger.warn(u"Failed to evaluate expression:\n%s",
                             e, exc_info=kwargs.get('debug'))
                self.output_callback({}, "permanentFail")

    def job(self,
            job_order,  # type: Dict[Text, Text]
            output_callbacks,  # type: Callable[[Any, Any], Any]
            **kwargs  # type: Any
            ):
        # type: (...) -> Generator[ExpressionTool.ExpressionJob, None, None]
        builder = self._init_job(job_order, **kwargs)

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

        yield j


def remove_path(f):  # type: (Dict[Text, Any]) -> None
    if "path" in f:
        del f["path"]


def revmap_file(builder, outdir, f):
    # type: (Builder, Text, Dict[Text, Any]) -> Union[Dict[Text, Any], None]

    """Remap a file from internal path to external path.

    For Docker, this maps from the path inside tho container to the path
    outside the container. Recognizes files in the pathmapper or remaps
    internal output directories to the external directory.
    """

    split = urllib.parse.urlsplit(outdir)
    if not split.scheme:
        outdir = file_uri(str(outdir))

    if "location" in f:
        if f["location"].startswith("file://"):
            path = uri_file_path(f["location"])
            revmap_f = builder.pathmapper.reversemap(path)
            if revmap_f:
                f["location"] = revmap_f[1]
            elif path == builder.outdir:
                f["location"] = outdir
            elif path.startswith(builder.outdir):
                f["location"] = builder.fs_access.join(outdir, path[len(builder.outdir) + 1:])
        return f

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

    raise WorkflowException(u"Output File object is missing both `location` and `path` fields: %s" % f)


class CallbackJob(object):
    def __init__(self, job, output_callback, cachebuilder, jobcache):
        # type: (CommandLineTool, Callable[[Any, Any], Any], Builder, Text) -> None
        self.job = job
        self.output_callback = output_callback
        self.cachebuilder = cachebuilder
        self.outdir = jobcache

    def run(self, **kwargs):
        # type: (**Any) -> None
        self.output_callback(self.job.collect_output_ports(
            self.job.tool["outputs"],
            self.cachebuilder,
            self.outdir,
            kwargs.get("compute_checksum", True)), "success")


# 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(builder, f):
    # type: (Builder, Dict[Text, Any]) -> Dict[Text, Any]

    f["path"] = builder.pathmapper.mapper(f["location"])[1]
    f["dirname"], f["basename"] = os.path.split(f["path"])
    if f["class"] == "File":
        f["nameroot"], f["nameext"] = os.path.splitext(f["basename"])
    if not ACCEPTLIST_RE.match(f["basename"]):
        raise WorkflowException("Invalid filename: '%s' contains illegal characters" % (f["basename"]))
    return f

def check_valid_locations(fs_access, ob):
    if ob["location"].startswith("_:"):
        pass
    if ob["class"] == "File" and not fs_access.isfile(ob["location"]):
        raise validate.ValidationException("Does not exist or is not a File: '%s'" % ob["location"])
    if ob["class"] == "Directory" and not fs_access.isdir(ob["location"]):
        raise validate.ValidationException("Does not exist or is not a Directory: '%s'" % ob["location"])

class CommandLineTool(Process):
    def __init__(self, toolpath_object, **kwargs):
        # type: (Dict[Text, Any], **Any) -> None
        super(CommandLineTool, self).__init__(toolpath_object, **kwargs)
        self.find_default_container = kwargs.get("find_default_container", None)

    def makeJobRunner(self, use_container=True):  # type: (Optional[bool]) -> JobBase
        dockerReq, _ = self.get_requirement("DockerRequirement")
        if not dockerReq and use_container:
            default_container = self.find_default_container(self)
            if default_container:
                self.requirements.insert(0, {
                    "class": "DockerRequirement",
                    "dockerPull": default_container
                })
                dockerReq = self.requirements[0]

        if dockerReq and use_container:
            return DockerCommandLineJob()
        else:
            for t in reversed(self.requirements):
                if t["class"] == "DockerRequirement":
                    raise UnsupportedRequirement(
                        "--no-container, but this CommandLineTool has "
                        "DockerRequirement under 'requirements'.")
            return CommandLineJob()

    def makePathMapper(self, reffiles, stagedir, **kwargs):
        # type: (List[Any], Text, **Any) -> PathMapper
        return PathMapper(reffiles, kwargs["basedir"], stagedir)

    def job(self,
            job_order,  # type: Dict[Text, Text]
            output_callbacks,  # type: Callable[[Any, Any], Any]
            **kwargs  # type: Any
            ):
        # type: (...) -> Generator[Union[JobBase, CallbackJob], None, None]

        jobname = uniquename(kwargs.get("name", shortname(self.tool.get("id", "job"))))

        if kwargs.get("cachedir"):
            cacheargs = kwargs.copy()
            cacheargs["outdir"] = "/out"
            cacheargs["tmpdir"] = "/tmp"
            cacheargs["stagedir"] = "/stage"
            cachebuilder = self._init_job(job_order, **cacheargs)
            cachebuilder.pathmapper = PathMapper(cachebuilder.files,
                                                 kwargs["basedir"],
                                                 cachebuilder.stagedir,
                                                 separateDirs=False)
            _check_adjust = partial(check_adjust, cachebuilder)
            visit_class([cachebuilder.files, cachebuilder.bindings],
                       ("File", "Directory"), _check_adjust)

            cmdline = flatten(map(cachebuilder.generate_arg, cachebuilder.bindings))
            (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
            if docker_req and kwargs.get("use_container") is not False:
                dockerimg = docker_req.get("dockerImageId") or docker_req.get("dockerPull")
                cmdline = ["docker", "run", dockerimg] + cmdline
            keydict = {u"cmdline": cmdline}

            for location, f in cachebuilder.pathmapper.items():
                if f.type == "File":
                    checksum = next((e['checksum'] for e in cachebuilder.files
                            if 'location' in e and e['location'] == location
                            and 'checksum' in e
                            and e['checksum'] != 'sha1$hash'), None)
                    st = os.stat(f.resolved)
                    if checksum:
                        keydict[f.resolved] = [st.st_size, checksum]
                    else:
                        keydict[f.resolved] = [st.st_size, int(st.st_mtime * 1000)]

            interesting = {"DockerRequirement",
                           "EnvVarRequirement",
                           "CreateFileRequirement",
                           "ShellCommandRequirement"}
            for rh in (self.requirements, self.hints):
                for r in reversed(rh):
                    if r["class"] in interesting and r["class"] not in keydict:
                        keydict[r["class"]] = r

            keydictstr = json.dumps(keydict, separators=(',', ':'), sort_keys=True)
            cachekey = hashlib.md5(keydictstr).hexdigest()

            _logger.debug("[job %s] keydictstr is %s -> %s", jobname,
                          keydictstr, cachekey)

            jobcache = os.path.join(kwargs["cachedir"], cachekey)
            jobcachepending = jobcache + ".pending"

            if os.path.isdir(jobcache) and not os.path.isfile(jobcachepending):
                if docker_req and kwargs.get("use_container") is not False:
                    cachebuilder.outdir = kwargs.get("docker_outdir") or "/var/spool/cwl"
                else:
                    cachebuilder.outdir = jobcache

                _logger.info("[job %s] Using cached output in %s", jobname, jobcache)
                yield CallbackJob(self, output_callbacks, cachebuilder, jobcache)
                return
            else:
                _logger.info("[job %s] Output of job will be cached in %s", jobname, jobcache)
                shutil.rmtree(jobcache, True)
                os.makedirs(jobcache)
                kwargs["outdir"] = jobcache
                open(jobcachepending, "w").close()

                def rm_pending_output_callback(output_callbacks, jobcachepending,
                                               outputs, processStatus):
                    if processStatus == "success":
                        os.remove(jobcachepending)
                    output_callbacks(outputs, processStatus)

                output_callbacks = cast(
                    Callable[..., Any],  # known bug in mypy
                    # https://github.com/python/mypy/issues/797
                    partial(rm_pending_output_callback, output_callbacks,
                            jobcachepending))

        builder = self._init_job(job_order, **kwargs)

        reffiles = copy.deepcopy(builder.files)

        j = self.makeJobRunner(kwargs.get("use_container"))
        j.builder = builder
        j.joborder = builder.job
        j.stdin = None
        j.stderr = 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 = jobname

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

        builder.pathmapper = None
        make_path_mapper_kwargs = kwargs
        if "stagedir" in make_path_mapper_kwargs:
            make_path_mapper_kwargs = make_path_mapper_kwargs.copy()
            del make_path_mapper_kwargs["stagedir"]
        builder.pathmapper = self.makePathMapper(reffiles, builder.stagedir, **make_path_mapper_kwargs)
        builder.requirements = j.requirements

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

        _check_adjust = partial(check_adjust, builder)

        visit_class([builder.files, builder.bindings], ("File", "Directory"), _check_adjust)

        if self.tool.get("stdin"):
            with SourceLine(self.tool, "stdin", validate.ValidationException):
                j.stdin = builder.do_eval(self.tool["stdin"])
                reffiles.append({"class": "File", "path": j.stdin})

        if self.tool.get("stderr"):
            with SourceLine(self.tool, "stderr", validate.ValidationException):
                j.stderr = builder.do_eval(self.tool["stderr"])
                if os.path.isabs(j.stderr) or ".." in j.stderr:
                    raise validate.ValidationException("stderr must be a relative path, got '%s'" % j.stderr)

        if self.tool.get("stdout"):
            with SourceLine(self.tool, "stdout", validate.ValidationException):
                j.stdout = builder.do_eval(self.tool["stdout"])
                if os.path.isabs(j.stdout) or ".." in j.stdout or not j.stdout:
                    raise validate.ValidationException("stdout must be a relative path, got '%s'" % j.stdout)

        if _logger.isEnabledFor(logging.DEBUG):
            _logger.debug(u"[job %s] command line bindings is %s", j.name, json.dumps(builder.bindings, indent=4))

        dockerReq = self.get_requirement("DockerRequirement")[0]
        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)
            j.stagedir = tempfile.mkdtemp(prefix=tmpdir_prefix)
        else:
            j.outdir = builder.outdir
            j.tmpdir = builder.tmpdir
            j.stagedir = builder.stagedir

        initialWorkdir = self.get_requirement("InitialWorkDirRequirement")[0]
        j.generatefiles = {"class": "Directory", "listing": [], "basename": ""}
        if initialWorkdir:
            ls = []  # type: List[Dict[Text, Any]]
            if isinstance(initialWorkdir["listing"], (str, Text)):
                ls = builder.do_eval(initialWorkdir["listing"])
            else:
                for t in initialWorkdir["listing"]:
                    if "entry" in t:
                        et = {u"entry": builder.do_eval(t["entry"])}
                        if "entryname" in t:
                            et["entryname"] = builder.do_eval(t["entryname"])
                        else:
                            et["entryname"] = None
                        et["writable"] = t.get("writable", False)
                        ls.append(et)
                    else:
                        ls.append(builder.do_eval(t))
            for i, t in enumerate(ls):
                if "entry" in t:
                    if isinstance(t["entry"], string_types):
                        ls[i] = {
                            "class": "File",
                            "basename": t["entryname"],
                            "contents": t["entry"],
                            "writable": t.get("writable")
                        }
                    else:
                        if t["entryname"] or t["writable"]:
                            t = copy.deepcopy(t)
                            if t["entryname"]:
                                t["entry"]["basename"] = t["entryname"]
                            t["entry"]["writable"] = t.get("writable")
                        ls[i] = t["entry"]
            j.generatefiles[u"listing"] = ls

        inplaceUpdateReq = self.get_requirement("http://commonwl.org/cwltool#InplaceUpdateRequirement")[0]

        if inplaceUpdateReq:
            j.inplace_update = inplaceUpdateReq["inplaceUpdate"]
        normalizeFilesDirs(j.generatefiles)

        readers = {}
        muts = set()

        if builder.mutation_manager:
            def register_mut(f):
                muts.add(f["location"])
                builder.mutation_manager.register_mutation(j.name, f)

            def register_reader(f):
                if f["location"] not in muts:
                    builder.mutation_manager.register_reader(j.name, f)
                    readers[f["location"]] = f

            for li in j.generatefiles["listing"]:
                li = cast(Dict[Text, Any], li)
                if li.get("writable") and j.inplace_update:
                    adjustFileObjs(li, register_mut)
                    adjustDirObjs(li, register_mut)
                else:
                    adjustFileObjs(li, register_reader)
                    adjustDirObjs(li, register_reader)

            adjustFileObjs(builder.files, register_reader)
            adjustFileObjs(builder.bindings, register_reader)
            adjustDirObjs(builder.files, register_reader)
            adjustDirObjs(builder.bindings, register_reader)

        j.environment = {}
        evr = self.get_requirement("EnvVarRequirement")[0]
        if evr:
            for t in evr["envDef"]:
                j.environment[t["envName"]] = builder.do_eval(t["envValue"])

        shellcmd = self.get_requirement("ShellCommandRequirement")[0]
        if shellcmd:
            cmd = []  # type: List[Text]
            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 = partial(
            self.collect_output_ports, self.tool["outputs"], builder,
            compute_checksum=kwargs.get("compute_checksum", True),
            jobname=jobname,
            readers=readers)
        j.output_callback = output_callbacks

        yield j

    def collect_output_ports(self, ports, builder, outdir, compute_checksum=True, jobname="", readers=None):
        # type: (Set[Dict[Text, Any]], Builder, Text, bool, Text, Dict[Text, Any]) -> Dict[Text, Union[Text, List[Any], Dict[Text, Any]]]
        ret = {}  # type: Dict[Text, Union[Text, List[Any], Dict[Text, Any]]]
        try:
            fs_access = builder.make_fs_access(outdir)
            custom_output = fs_access.join(outdir, "cwl.output.json")
            if fs_access.exists(custom_output):
                with fs_access.open(custom_output, "r") as f:
                    ret = json.load(f)
                if _logger.isEnabledFor(logging.DEBUG):
                    _logger.debug(u"Raw output from %s: %s", custom_output, json.dumps(ret, indent=4))
            else:
                for i, port in enumerate(ports):
                    with SourceLine(ports, i, WorkflowException):
                        fragment = shortname(port["id"])
                        try:
                            ret[fragment] = self.collect_output(port, builder, outdir, fs_access,
                                                                compute_checksum=compute_checksum)
                        except Exception as e:
                            _logger.debug(
                                u"Error collecting output for parameter '%s'"
                                % shortname(port["id"]), exc_info=True)
                            raise WorkflowException(
                                u"Error collecting output for parameter '%s':\n%s"
                                % (shortname(port["id"]), indent(u(str(e)))))

            if ret:
                revmap = partial(revmap_file, builder, outdir)
                adjustDirObjs(ret, trim_listing)
                visit_class(ret, ("File", "Directory"), cast(Callable[[Any], Any], revmap))
                visit_class(ret, ("File", "Directory"), remove_path)
                normalizeFilesDirs(ret)
                if builder.mutation_manager:
                    adjustFileObjs(ret, builder.mutation_manager.set_generation)
                visit_class(ret, ("File", "Directory"), partial(check_valid_locations, fs_access))

                if compute_checksum:
                    adjustFileObjs(ret, partial(compute_checksums, fs_access))

            validate.validate_ex(self.names.get_name("outputs_record_schema", ""), ret,
                                 strict=False, logger=_logger_validation_warnings)
            return ret if ret is not None else {}
        except validate.ValidationException as e:
            raise WorkflowException("Error validating output record. " + Text(e) + "\n in " + json.dumps(ret, indent=4))
        finally:
            if builder.mutation_manager and readers:
                for r in readers.values():
                    builder.mutation_manager.release_reader(jobname, r)

    def collect_output(self, schema, builder, outdir, fs_access, compute_checksum=True):
        # type: (Dict[Text, Any], Builder, Text, StdFsAccess, bool) -> Union[Dict[Text, Any], List[Union[Dict[Text, Any], Text]]]
        r = []  # type: List[Any]
        if "outputBinding" in schema:
            binding = schema["outputBinding"]
            globpatterns = []  # type: List[Text]

            revmap = partial(revmap_file, builder, outdir)

            if "glob" in binding:
                with SourceLine(binding, "glob", WorkflowException):
                    for gb in aslist(binding["glob"]):
                        gb = builder.do_eval(gb)
                        if gb:
                            globpatterns.extend(aslist(gb))

                    for gb in globpatterns:
                        if gb.startswith(outdir):
                            gb = gb[len(outdir) + 1:]
                        elif gb == ".":
                            gb = outdir
                        elif gb.startswith("/"):
                            raise WorkflowException("glob patterns must not start with '/'")
                        try:
                            r.extend([{"location": g,
                                       "class": "File" if fs_access.isfile(g) else "Directory"}
                                      for g in fs_access.glob(fs_access.join(outdir, gb))])
                        except (OSError, IOError) as e:
                            _logger.warn(Text(e))
                        except:
                            _logger.error("Unexpected error from fs_access", exc_info=True)
                            raise

                for files in r:
                    if files["class"] == "Directory":
                        ll = builder.loadListing or (binding and binding.get("loadListing"))
                        if ll and ll != "no_listing":
                            get_listing(fs_access, files, (ll == "deep_listing"))
                    else:
                        with fs_access.open(files["location"], "rb") as f:
                            contents = ""
                            if binding.get("loadContents") or compute_checksum:
                                contents = f.read(CONTENT_LIMIT)
                            if binding.get("loadContents"):
                                files["contents"] = contents
                            if compute_checksum:
                                checksum = hashlib.sha1()
                                while contents != "":
                                    checksum.update(contents)
                                    contents = f.read(1024 * 1024)
                                files["checksum"] = "sha1$%s" % checksum.hexdigest()
                            f.seek(0, 2)
                            filesize = f.tell()
                        files["size"] = filesize
                        if "format" in schema:
                            files["format"] = builder.do_eval(schema["format"], context=files)

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

            if "outputEval" in binding:
                with SourceLine(binding, "outputEval", WorkflowException):
                    r = builder.do_eval(binding["outputEval"], context=r)

            if single:
                if not r and not optional:
                    with SourceLine(binding, "glob", WorkflowException):
                        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, cast(  # known bug in mypy
                # https://github.com/python/mypy/issues/797
                Callable[[Any], Any], revmap))

            if "secondaryFiles" in schema:
                with SourceLine(schema, "secondaryFiles", WorkflowException):
                    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=primary)
                                    if isinstance(sfpath, string_types):
                                        sfpath = revmap({"location": sfpath, "class": "File"})
                                else:
                                    sfpath = {"location": substitute(primary["location"], sf), "class": "File"}

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

            if not r and optional:
                r = None

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