sdk/cwl/arvados_cwl/pathmapper.py

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 from future import standard_library
   6 standard_library.install_aliases()
   7 from builtins import str
   8 from past.builtins import basestring
   9 from future.utils import viewitems
  10
  11 import re
  12 import logging
  13 import uuid
  14 import os
  15 import urllib.request, urllib.parse, urllib.error
  16
  17 import arvados_cwl.util
  18 import arvados.commands.run
  19 import arvados.collection
  20
  21 from schema_salad.sourceline import SourceLine
  22
  23 from arvados.errors import ApiError
  24 from cwltool.pathmapper import PathMapper, MapperEnt, abspath, adjustFileObjs, adjustDirObjs
  25 from cwltool.workflow import WorkflowException
  26
  27 from .http import http_to_keep
  28
  29 logger = logging.getLogger('arvados.cwl-runner')
  30
  31 def trim_listing(obj):
  32     """Remove 'listing' field from Directory objects that are keep references.
  33
  34     When Directory objects represent Keep references, it is redundant and
  35     potentially very expensive to pass fully enumerated Directory objects
  36     between instances of cwl-runner (e.g. a submitting a job, or using the
  37     RunInSingleContainer feature), so delete the 'listing' field when it is
  38     safe to do so.
  39
  40     """
  41
  42     if obj.get("location", "").startswith("keep:") and "listing" in obj:
  43         del obj["listing"]
  44
  45
  46 class ArvPathMapper(PathMapper):
  47     """Convert container-local paths to and from Keep collection ids."""
  48
  49     pdh_path = re.compile(r'^keep:[0-9a-f]{32}\+\d+/.+$')
  50     pdh_dirpath = re.compile(r'^keep:[0-9a-f]{32}\+\d+(/.*)?$')
  51
  52     def __init__(self, arvrunner, referenced_files, input_basedir,
  53                  collection_pattern, file_pattern, name=None, single_collection=False):
  54         self.arvrunner = arvrunner
  55         self.input_basedir = input_basedir
  56         self.collection_pattern = collection_pattern
  57         self.file_pattern = file_pattern
  58         self.name = name
  59         self.referenced_files = [r["location"] for r in referenced_files]
  60         self.single_collection = single_collection
  61         self.pdh_to_uuid = {}
  62         super(ArvPathMapper, self).__init__(referenced_files, input_basedir, None)
  63
  64     def visit(self, srcobj, uploadfiles):
  65         src = srcobj["location"]
  66         if "#" in src:
  67             src = src[:src.index("#")]
  68
  69         if isinstance(src, basestring) and ArvPathMapper.pdh_dirpath.match(src):
  70             self._pathmap[src] = MapperEnt(src, self.collection_pattern % urllib.parse.unquote(src[5:]), srcobj["class"], True)
  71             if arvados_cwl.util.collectionUUID in srcobj:
  72                 self.pdh_to_uuid[src.split("/", 1)[0][5:]] = srcobj[arvados_cwl.util.collectionUUID]
  73
  74         debug = logger.isEnabledFor(logging.DEBUG)
  75
  76         if src not in self._pathmap:
  77             if src.startswith("file:"):
  78                 # Local FS ref, may need to be uploaded or may be on keep
  79                 # mount.
  80                 ab = abspath(src, self.input_basedir)
  81                 st = arvados.commands.run.statfile("", ab,
  82                                                    fnPattern="keep:%s/%s",
  83                                                    dirPattern="keep:%s/%s",
  84                                                    raiseOSError=True)
  85                 with SourceLine(srcobj, "location", WorkflowException, debug):
  86                     if isinstance(st, arvados.commands.run.UploadFile):
  87                         uploadfiles.add((src, ab, st))
  88                     elif isinstance(st, arvados.commands.run.ArvFile):
  89                         self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % urllib.parse.unquote(st.fn[5:]), "File", True)
  90                     else:
  91                         raise WorkflowException("Input file path '%s' is invalid" % st)
  92             elif src.startswith("_:"):
  93                 if srcobj["class"] == "File" and "contents" not in srcobj:
  94                     raise WorkflowException("File literal '%s' is missing `contents`" % src)
  95                 if srcobj["class"] == "Directory" and "listing" not in srcobj:
  96                     raise WorkflowException("Directory literal '%s' is missing `listing`" % src)
  97             elif src.startswith("http:") or src.startswith("https:"):
  98                 keepref = http_to_keep(self.arvrunner.api, self.arvrunner.project_uuid, src)
  99                 logger.info("%s is %s", src, keepref)
 100                 self._pathmap[src] = MapperEnt(keepref, keepref, srcobj["class"], True)
 101             else:
 102                 self._pathmap[src] = MapperEnt(src, src, srcobj["class"], True)
 103
 104         with SourceLine(srcobj, "secondaryFiles", WorkflowException, debug):
 105             for l in srcobj.get("secondaryFiles", []):
 106                 self.visit(l, uploadfiles)
 107         with SourceLine(srcobj, "listing", WorkflowException, debug):
 108             for l in srcobj.get("listing", []):
 109                 self.visit(l, uploadfiles)
 110
 111     def addentry(self, obj, c, path, remap):
 112         if obj["location"] in self._pathmap:
 113             src, srcpath = self.arvrunner.fs_access.get_collection(self._pathmap[obj["location"]].resolved)
 114             if srcpath == "":
 115                 srcpath = "."
 116             c.copy(srcpath, path + "/" + obj["basename"], source_collection=src, overwrite=True)
 117             remap.append((obj["location"], path + "/" + obj["basename"]))
 118             for l in obj.get("secondaryFiles", []):
 119                 self.addentry(l, c, path, remap)
 120         elif obj["class"] == "Directory":
 121             for l in obj.get("listing", []):
 122                 self.addentry(l, c, path + "/" + obj["basename"], remap)
 123             remap.append((obj["location"], path + "/" + obj["basename"]))
 124         elif obj["location"].startswith("_:") and "contents" in obj:
 125             with c.open(path + "/" + obj["basename"], "w") as f:
 126                 f.write(obj["contents"])
 127             remap.append((obj["location"], path + "/" + obj["basename"]))
 128         else:
 129             raise SourceLine(obj, "location", WorkflowException).makeError("Don't know what to do with '%s'" % obj["location"])
 130
 131     def needs_new_collection(self, srcobj, prefix=""):
 132         """Check if files need to be staged into a new collection.
 133
 134         If all the files are in the same collection and in the same
 135         paths they would be staged to, return False.  Otherwise, a new
 136         collection is needed with files copied/created in the
 137         appropriate places.
 138         """
 139
 140         loc = srcobj["location"]
 141         if loc.startswith("_:"):
 142             return True
 143         if prefix:
 144             if loc != prefix+srcobj["basename"]:
 145                 return True
 146         else:
 147             i = loc.rfind("/")
 148             if i > -1:
 149                 prefix = loc[:i+1]
 150             else:
 151                 prefix = loc+"/"
 152         if srcobj["class"] == "File" and loc not in self._pathmap:
 153             return True
 154         for s in srcobj.get("secondaryFiles", []):
 155             if self.needs_new_collection(s, prefix):
 156                 return True
 157         if srcobj.get("listing"):
 158             prefix = "%s%s/" % (prefix, srcobj["basename"])
 159             for l in srcobj["listing"]:
 160                 if self.needs_new_collection(l, prefix):
 161                     return True
 162         return False
 163
 164     def setup(self, referenced_files, basedir):
 165         # type: (List[Any], unicode) -> None
 166         uploadfiles = set()
 167
 168         collection = None
 169         if self.single_collection:
 170             collection = arvados.collection.Collection(api_client=self.arvrunner.api,
 171                                                        keep_client=self.arvrunner.keep_client,
 172                                                        num_retries=self.arvrunner.num_retries)
 173
 174         for srcobj in referenced_files:
 175             self.visit(srcobj, uploadfiles)
 176
 177         arvados.commands.run.uploadfiles([u[2] for u in uploadfiles],
 178                                          self.arvrunner.api,
 179                                          dry_run=False,
 180                                          num_retries=self.arvrunner.num_retries,
 181                                          fnPattern="keep:%s/%s",
 182                                          name=self.name,
 183                                          project=self.arvrunner.project_uuid,
 184                                          collection=collection,
 185                                          packed=False)
 186
 187         for src, ab, st in uploadfiles:
 188             self._pathmap[src] = MapperEnt(urllib.parse.quote(st.fn, "/:+@"), self.collection_pattern % st.fn[5:],
 189                                            "Directory" if os.path.isdir(ab) else "File", True)
 190
 191         for srcobj in referenced_files:
 192             remap = []
 193             if srcobj["class"] == "Directory" and srcobj["location"] not in self._pathmap:
 194                 c = arvados.collection.Collection(api_client=self.arvrunner.api,
 195                                                   keep_client=self.arvrunner.keep_client,
 196                                                   num_retries=self.arvrunner.num_retries)
 197                 for l in srcobj.get("listing", []):
 198                     self.addentry(l, c, ".", remap)
 199
 200                 container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
 201                 info = arvados_cwl.util.get_intermediate_collection_info(None, container, self.arvrunner.intermediate_output_ttl)
 202
 203                 c.save_new(name=info["name"],
 204                            owner_uuid=self.arvrunner.project_uuid,
 205                            ensure_unique_name=True,
 206                            trash_at=info["trash_at"],
 207                            properties=info["properties"])
 208
 209                 ab = self.collection_pattern % c.portable_data_hash()
 210                 self._pathmap[srcobj["location"]] = MapperEnt("keep:"+c.portable_data_hash(), ab, "Directory", True)
 211             elif srcobj["class"] == "File" and (srcobj.get("secondaryFiles") or
 212                 (srcobj["location"].startswith("_:") and "contents" in srcobj)):
 213
 214                 # If all secondary files/directories are located in
 215                 # the same collection as the primary file and the
 216                 # paths and names that are consistent with staging,
 217                 # don't create a new collection.
 218                 if not self.needs_new_collection(srcobj):
 219                     continue
 220
 221                 c = arvados.collection.Collection(api_client=self.arvrunner.api,
 222                                                   keep_client=self.arvrunner.keep_client,
 223                                                   num_retries=self.arvrunner.num_retries                                                  )
 224                 self.addentry(srcobj, c, ".", remap)
 225
 226                 container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
 227                 info = arvados_cwl.util.get_intermediate_collection_info(None, container, self.arvrunner.intermediate_output_ttl)
 228
 229                 c.save_new(name=info["name"],
 230                            owner_uuid=self.arvrunner.project_uuid,
 231                            ensure_unique_name=True,
 232                            trash_at=info["trash_at"],
 233                            properties=info["properties"])
 234
 235                 ab = self.file_pattern % (c.portable_data_hash(), srcobj["basename"])
 236                 self._pathmap[srcobj["location"]] = MapperEnt("keep:%s/%s" % (c.portable_data_hash(), srcobj["basename"]),
 237                                                               ab, "File", True)
 238                 if srcobj.get("secondaryFiles"):
 239                     ab = self.collection_pattern % c.portable_data_hash()
 240                     self._pathmap["_:" + str(uuid.uuid4())] = MapperEnt("keep:"+c.portable_data_hash(), ab, "Directory", True)
 241
 242             if remap:
 243                 for loc, sub in remap:
 244                     # subdirs start with "./", strip it off
 245                     if sub.startswith("./"):
 246                         ab = self.file_pattern % (c.portable_data_hash(), sub[2:])
 247                     else:
 248                         ab = self.file_pattern % (c.portable_data_hash(), sub)
 249                     self._pathmap[loc] = MapperEnt("keep:%s/%s" % (c.portable_data_hash(), sub[2:]),
 250                                                    ab, "Directory", True)
 251
 252         self.keepdir = None
 253
 254     def reversemap(self, target):
 255         p = super(ArvPathMapper, self).reversemap(target)
 256         if p:
 257             return p
 258         elif target.startswith("keep:"):
 259             return (target, target)
 260         elif self.keepdir and target.startswith(self.keepdir):
 261             kp = "keep:" + target[len(self.keepdir)+1:]
 262             return (kp, kp)
 263         else:
 264             return None
 265
 266
 267 class StagingPathMapper(PathMapper):
 268     _follow_dirs = True
 269
 270     def __init__(self, referenced_files, basedir, stagedir, separateDirs=True):
 271         self.targets = set()
 272         super(StagingPathMapper, self).__init__(referenced_files, basedir, stagedir, separateDirs)
 273
 274     def visit(self, obj, stagedir, basedir, copy=False, staged=False):
 275         # type: (Dict[unicode, Any], unicode, unicode, bool) -> None
 276         loc = obj["location"]
 277         tgt = os.path.join(stagedir, obj["basename"])
 278         basetgt, baseext = os.path.splitext(tgt)
 279         n = 1
 280         if tgt in self.targets and (self.reversemap(tgt)[0] != loc):
 281             while tgt in self.targets:
 282                 n += 1
 283                 tgt = "%s_%i%s" % (basetgt, n, baseext)
 284         self.targets.add(tgt)
 285         if obj["class"] == "Directory":
 286             if obj.get("writable"):
 287                 self._pathmap[loc] = MapperEnt(loc, tgt, "WritableDirectory", staged)
 288             else:
 289                 self._pathmap[loc] = MapperEnt(loc, tgt, "Directory", staged)
 290             if loc.startswith("_:") or self._follow_dirs:
 291                 self.visitlisting(obj.get("listing", []), tgt, basedir)
 292         elif obj["class"] == "File":
 293             if loc in self._pathmap:
 294                 return
 295             if "contents" in obj and loc.startswith("_:"):
 296                 self._pathmap[loc] = MapperEnt(obj["contents"], tgt, "CreateFile", staged)
 297             else:
 298                 if copy or obj.get("writable"):
 299                     self._pathmap[loc] = MapperEnt(loc, tgt, "WritableFile", staged)
 300                 else:
 301                     self._pathmap[loc] = MapperEnt(loc, tgt, "File", staged)
 302                 self.visitlisting(obj.get("secondaryFiles", []), stagedir, basedir)
 303
 304
 305 class VwdPathMapper(StagingPathMapper):
 306     def setup(self, referenced_files, basedir):
 307         # type: (List[Any], unicode) -> None
 308
 309         # Go through each file and set the target to its own directory along
 310         # with any secondary files.
 311         self.visitlisting(referenced_files, self.stagedir, basedir)
 312
 313         for path, (ab, tgt, type, staged) in viewitems(self._pathmap):
 314             if type in ("File", "Directory") and ab.startswith("keep:"):
 315                 self._pathmap[path] = MapperEnt("$(task.keep)/%s" % ab[5:], tgt, type, staged)
 316
 317
 318 class NoFollowPathMapper(StagingPathMapper):
 319     _follow_dirs = False
 320     def setup(self, referenced_files, basedir):
 321         # type: (List[Any], unicode) -> None
 322         self.visitlisting(referenced_files, self.stagedir, basedir)