sdk/cwl/arvados_cwl/pathmapper.py

   1 import re
   2 import logging
   3 import uuid
   4 import os
   5
   6 import arvados.commands.run
   7 import arvados.collection
   8
   9 from schema_salad.sourceline import SourceLine
  10
  11 from cwltool.pathmapper import PathMapper, MapperEnt, abspath, adjustFileObjs, adjustDirObjs
  12 from cwltool.workflow import WorkflowException
  13
  14 logger = logging.getLogger('arvados.cwl-runner')
  15
  16 class ArvPathMapper(PathMapper):
  17     """Convert container-local paths to and from Keep collection ids."""
  18
  19     pdh_path = re.compile(r'^keep:[0-9a-f]{32}\+\d+/.+$')
  20     pdh_dirpath = re.compile(r'^keep:[0-9a-f]{32}\+\d+(/.+)?$')
  21
  22     def __init__(self, arvrunner, referenced_files, input_basedir,
  23                  collection_pattern, file_pattern, name=None, **kwargs):
  24         self.arvrunner = arvrunner
  25         self.input_basedir = input_basedir
  26         self.collection_pattern = collection_pattern
  27         self.file_pattern = file_pattern
  28         self.name = name
  29         super(ArvPathMapper, self).__init__(referenced_files, input_basedir, None)
  30
  31     def visit(self, srcobj, uploadfiles):
  32         src = srcobj["location"]
  33         if srcobj["class"] == "File":
  34             if "#" in src:
  35                 src = src[:src.index("#")]
  36             if isinstance(src, basestring) and ArvPathMapper.pdh_path.match(src):
  37                 self._pathmap[src] = MapperEnt(src, self.collection_pattern % src[5:], "File")
  38             if src not in self._pathmap:
  39                 # Local FS ref, may need to be uploaded or may be on keep
  40                 # mount.
  41                 ab = abspath(src, self.input_basedir)
  42                 st = arvados.commands.run.statfile("", ab, fnPattern="keep:%s/%s")
  43                 with SourceLine(srcobj, "location", WorkflowException):
  44                     if isinstance(st, arvados.commands.run.UploadFile):
  45                         uploadfiles.add((src, ab, st))
  46                     elif isinstance(st, arvados.commands.run.ArvFile):
  47                         self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % st.fn[5:], "File")
  48                     elif src.startswith("_:"):
  49                         if "contents" in srcobj:
  50                             pass
  51                         else:
  52                             raise WorkflowException("File literal '%s' is missing contents" % src)
  53                     elif src.startswith("arvwf:"):
  54                         self._pathmap[src] = MapperEnt(src, src, "File")
  55                     else:
  56                         raise WorkflowException("Input file path '%s' is invalid" % st)
  57             if "secondaryFiles" in srcobj:
  58                 for l in srcobj["secondaryFiles"]:
  59                     self.visit(l, uploadfiles)
  60         elif srcobj["class"] == "Directory":
  61             if isinstance(src, basestring) and ArvPathMapper.pdh_dirpath.match(src):
  62                 self._pathmap[src] = MapperEnt(src, self.collection_pattern % src[5:], "Directory")
  63             for l in srcobj.get("listing", []):
  64                 self.visit(l, uploadfiles)
  65
  66     def addentry(self, obj, c, path, subdirs):
  67         if obj["location"] in self._pathmap:
  68             src, srcpath = self.arvrunner.fs_access.get_collection(self._pathmap[obj["location"]].resolved)
  69             if srcpath == "":
  70                 srcpath = "."
  71             c.copy(srcpath, path + "/" + obj["basename"], source_collection=src, overwrite=True)
  72             for l in obj.get("secondaryFiles", []):
  73                 self.addentry(l, c, path, subdirs)
  74         elif obj["class"] == "Directory":
  75             for l in obj["listing"]:
  76                 self.addentry(l, c, path + "/" + obj["basename"], subdirs)
  77             subdirs.append((obj["location"], path + "/" + obj["basename"]))
  78         elif obj["location"].startswith("_:") and "contents" in obj:
  79             with c.open(path + "/" + obj["basename"], "w") as f:
  80                 f.write(obj["contents"].encode("utf-8"))
  81         else:
  82             raise SourceLine(obj, "location", WorkflowException).makeError("Don't know what to do with '%s'" % obj["location"])
  83
  84     def setup(self, referenced_files, basedir):
  85         # type: (List[Any], unicode) -> None
  86         uploadfiles = set()
  87
  88         for k,v in self.arvrunner.get_uploaded().iteritems():
  89             self._pathmap[k] = MapperEnt(v.resolved, self.collection_pattern % v.resolved[5:], "File")
  90
  91         for srcobj in referenced_files:
  92             self.visit(srcobj, uploadfiles)
  93
  94         if uploadfiles:
  95             arvados.commands.run.uploadfiles([u[2] for u in uploadfiles],
  96                                              self.arvrunner.api,
  97                                              dry_run=False,
  98                                              num_retries=self.arvrunner.num_retries,
  99                                              fnPattern="keep:%s/%s",
 100                                              name=self.name,
 101                                              project=self.arvrunner.project_uuid)
 102
 103         for src, ab, st in uploadfiles:
 104             self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % st.fn[5:], "File")
 105             self.arvrunner.add_uploaded(src, self._pathmap[src])
 106
 107         for srcobj in referenced_files:
 108             if srcobj["class"] == "Directory":
 109                 if srcobj["location"] not in self._pathmap:
 110                     c = arvados.collection.Collection(api_client=self.arvrunner.api,
 111                                                       keep_client=self.arvrunner.keep_client,
 112                                                       num_retries=self.arvrunner.num_retries)
 113                     subdirs = []
 114                     for l in srcobj["listing"]:
 115                         self.addentry(l, c, ".", subdirs)
 116
 117                     check = self.arvrunner.api.collections().list(filters=[["portable_data_hash", "=", c.portable_data_hash()]], limit=1).execute(num_retries=self.arvrunner.num_retries)
 118                     if not check["items"]:
 119                         c.save_new(owner_uuid=self.arvrunner.project_uuid)
 120
 121                     ab = self.collection_pattern % c.portable_data_hash()
 122                     self._pathmap[srcobj["location"]] = MapperEnt(ab, ab, "Directory")
 123                     for loc, sub in subdirs:
 124                         ab = self.file_pattern % (c.portable_data_hash(), sub[2:])
 125                         self._pathmap[loc] = MapperEnt(ab, ab, "Directory")
 126             elif srcobj["class"] == "File" and (srcobj.get("secondaryFiles") or
 127                 (srcobj["location"].startswith("_:") and "contents" in srcobj)):
 128
 129                 c = arvados.collection.Collection(api_client=self.arvrunner.api,
 130                                                   keep_client=self.arvrunner.keep_client,
 131                                                   num_retries=self.arvrunner.num_retries                                                  )
 132                 subdirs = []
 133                 self.addentry(srcobj, c, ".", subdirs)
 134
 135                 check = self.arvrunner.api.collections().list(filters=[["portable_data_hash", "=", c.portable_data_hash()]], limit=1).execute(num_retries=self.arvrunner.num_retries)
 136                 if not check["items"]:
 137                     c.save_new(owner_uuid=self.arvrunner.project_uuid)
 138
 139                 ab = self.file_pattern % (c.portable_data_hash(), srcobj["basename"])
 140                 self._pathmap[srcobj["location"]] = MapperEnt(ab, ab, "File")
 141                 if srcobj.get("secondaryFiles"):
 142                     ab = self.collection_pattern % c.portable_data_hash()
 143                     self._pathmap["_:" + unicode(uuid.uuid4())] = MapperEnt(ab, ab, "Directory")
 144                 for loc, sub in subdirs:
 145                     ab = self.file_pattern % (c.portable_data_hash(), sub[2:])
 146                     self._pathmap[loc] = MapperEnt(ab, ab, "Directory")
 147
 148         self.keepdir = None
 149
 150     def reversemap(self, target):
 151         if target.startswith("keep:"):
 152             return (target, target)
 153         elif self.keepdir and target.startswith(self.keepdir):
 154             return (target, "keep:" + target[len(self.keepdir)+1:])
 155         else:
 156             return super(ArvPathMapper, self).reversemap(target)
 157
 158 class StagingPathMapper(PathMapper):
 159     _follow_dirs = True
 160
 161     def visit(self, obj, stagedir, basedir, copy=False):
 162         # type: (Dict[unicode, Any], unicode, unicode, bool) -> None
 163         loc = obj["location"]
 164         tgt = os.path.join(stagedir, obj["basename"])
 165         if obj["class"] == "Directory":
 166             self._pathmap[loc] = MapperEnt(loc, tgt, "Directory")
 167             if loc.startswith("_:") or self._follow_dirs:
 168                 self.visitlisting(obj.get("listing", []), tgt, basedir)
 169         elif obj["class"] == "File":
 170             if loc in self._pathmap:
 171                 return
 172             if "contents" in obj and loc.startswith("_:"):
 173                 self._pathmap[loc] = MapperEnt(obj["contents"], tgt, "CreateFile")
 174             else:
 175                 if copy:
 176                     self._pathmap[loc] = MapperEnt(loc, tgt, "WritableFile")
 177                 else:
 178                     self._pathmap[loc] = MapperEnt(loc, tgt, "File")
 179                 self.visitlisting(obj.get("secondaryFiles", []), stagedir, basedir)
 180
 181
 182 class InitialWorkDirPathMapper(StagingPathMapper):
 183     def setup(self, referenced_files, basedir):
 184         # type: (List[Any], unicode) -> None
 185
 186         # Go through each file and set the target to its own directory along
 187         # with any secondary files.
 188         self.visitlisting(referenced_files, self.stagedir, basedir)
 189
 190         for path, (ab, tgt, type) in self._pathmap.items():
 191             if type in ("File", "Directory") and ab.startswith("keep:"):
 192                 self._pathmap[path] = MapperEnt("$(task.keep)/%s" % ab[5:], tgt, type)
 193
 194
 195 class FinalOutputPathMapper(StagingPathMapper):
 196     _follow_dirs = False
 197     def setup(self, referenced_files, basedir):
 198         # type: (List[Any], unicode) -> None
 199         self.visitlisting(referenced_files, self.stagedir, basedir)