sdk/cwl/arvados_cwl/fsaccess.py

   1 import fnmatch
   2 import os
   3 import errno
   4 import urlparse
   5 import re
   6 import logging
   7
   8 import ruamel.yaml as yaml
   9
  10 import cwltool.stdfsaccess
  11 from cwltool.pathmapper import abspath
  12 import cwltool.resolver
  13
  14 import arvados.util
  15 import arvados.collection
  16 import arvados.arvfile
  17 import arvados.errors
  18
  19 from schema_salad.ref_resolver import DefaultFetcher
  20
  21 logger = logging.getLogger('arvados.cwl-runner')
  22
  23 class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
  24     """Implement the cwltool FsAccess interface for Arvados Collections."""
  25
  26     def __init__(self, basedir, api_client=None, keep_client=None):
  27         super(CollectionFsAccess, self).__init__(basedir)
  28         self.api_client = api_client
  29         self.keep_client = keep_client
  30         self.collections = {}
  31
  32     def get_collection(self, path):
  33         sp = path.split("/", 1)
  34         p = sp[0]
  35         if p.startswith("keep:") and arvados.util.keep_locator_pattern.match(p[5:]):
  36             pdh = p[5:]
  37             if pdh not in self.collections:
  38                 self.collections[pdh] = arvados.collection.CollectionReader(pdh, api_client=self.api_client,
  39                                                                             keep_client=self.keep_client)
  40             return (self.collections[pdh], sp[1] if len(sp) == 2 else None)
  41         else:
  42             return (None, path)
  43
  44     def _match(self, collection, patternsegments, parent):
  45         if not patternsegments:
  46             return []
  47
  48         if not isinstance(collection, arvados.collection.RichCollectionBase):
  49             return []
  50
  51         ret = []
  52         # iterate over the files and subcollections in 'collection'
  53         for filename in collection:
  54             if patternsegments[0] == '.':
  55                 # Pattern contains something like "./foo" so just shift
  56                 # past the "./"
  57                 ret.extend(self._match(collection, patternsegments[1:], parent))
  58             elif fnmatch.fnmatch(filename, patternsegments[0]):
  59                 cur = os.path.join(parent, filename)
  60                 if len(patternsegments) == 1:
  61                     ret.append(cur)
  62                 else:
  63                     ret.extend(self._match(collection[filename], patternsegments[1:], cur))
  64         return ret
  65
  66     def glob(self, pattern):
  67         collection, rest = self.get_collection(pattern)
  68         if collection and not rest:
  69             return [pattern]
  70         patternsegments = rest.split("/")
  71         return self._match(collection, patternsegments, "keep:" + collection.manifest_locator())
  72
  73     def open(self, fn, mode):
  74         collection, rest = self.get_collection(fn)
  75         if collection:
  76             return collection.open(rest, mode)
  77         else:
  78             return super(CollectionFsAccess, self).open(self._abs(fn), mode)
  79
  80     def exists(self, fn):
  81         collection, rest = self.get_collection(fn)
  82         if collection:
  83             return collection.exists(rest)
  84         else:
  85             return super(CollectionFsAccess, self).exists(fn)
  86
  87     def isfile(self, fn):  # type: (unicode) -> bool
  88         collection, rest = self.get_collection(fn)
  89         if collection:
  90             if rest:
  91                 return isinstance(collection.find(rest), arvados.arvfile.ArvadosFile)
  92             else:
  93                 return False
  94         else:
  95             return super(CollectionFsAccess, self).isfile(fn)
  96
  97     def isdir(self, fn):  # type: (unicode) -> bool
  98         collection, rest = self.get_collection(fn)
  99         if collection:
 100             if rest:
 101                 return isinstance(collection.find(rest), arvados.collection.RichCollectionBase)
 102             else:
 103                 return True
 104         else:
 105             return super(CollectionFsAccess, self).isdir(fn)
 106
 107     def listdir(self, fn):  # type: (unicode) -> List[unicode]
 108         collection, rest = self.get_collection(fn)
 109         if collection:
 110             if rest:
 111                 dir = collection.find(rest)
 112             else:
 113                 dir = collection
 114             if dir is None:
 115                 raise IOError(errno.ENOENT, "Directory '%s' in '%s' not found" % (rest, collection.portable_data_hash()))
 116             if not isinstance(dir, arvados.collection.RichCollectionBase):
 117                 raise IOError(errno.ENOENT, "Path '%s' in '%s' is not a Directory" % (rest, collection.portable_data_hash()))
 118             return [abspath(l, fn) for l in dir.keys()]
 119         else:
 120             return super(CollectionFsAccess, self).listdir(fn)
 121
 122     def join(self, path, *paths): # type: (unicode, *unicode) -> unicode
 123         if paths and paths[-1].startswith("keep:") and arvados.util.keep_locator_pattern.match(paths[-1][5:]):
 124             return paths[-1]
 125         return os.path.join(path, *paths)
 126
 127     def realpath(self, path):
 128         if path.startswith("$(task.tmpdir)") or path.startswith("$(task.outdir)"):
 129             return path
 130         collection, rest = self.get_collection(path)
 131         if collection:
 132             return path
 133         else:
 134             return os.path.realpath(path)
 135
 136 class CollectionFetcher(DefaultFetcher):
 137     def __init__(self, cache, session, api_client=None, keep_client=None, num_retries=4):
 138         super(CollectionFetcher, self).__init__(cache, session)
 139         self.api_client = api_client
 140         self.fsaccess = CollectionFsAccess("", api_client=api_client, keep_client=keep_client)
 141         self.num_retries = num_retries
 142
 143     def fetch_text(self, url):
 144         if url.startswith("keep:"):
 145             with self.fsaccess.open(url, "r") as f:
 146                 return f.read()
 147         if url.startswith("arvwf:"):
 148             record = self.api_client.workflows().get(uuid=url[6:]).execute(num_retries=self.num_retries)
 149             definition = record["definition"] + ('\nlabel: "%s"\n' % record["name"].replace('"', '\\"'))
 150             return definition
 151         return super(CollectionFetcher, self).fetch_text(url)
 152
 153     def check_exists(self, url):
 154         try:
 155             if url.startswith("http://arvados.org/cwl"):
 156                 return True
 157             if url.startswith("keep:"):
 158                 return self.fsaccess.exists(url)
 159             if url.startswith("arvwf:"):
 160                 if self.fetch_text(url):
 161                     return True
 162         except arvados.errors.NotFoundError:
 163             return False
 164         except:
 165             logger.exception("Got unexpected exception checking if file exists:")
 166             return False
 167         return super(CollectionFetcher, self).check_exists(url)
 168
 169     def urljoin(self, base_url, url):
 170         if not url:
 171             return base_url
 172
 173         urlsp = urlparse.urlsplit(url)
 174         if urlsp.scheme or not base_url:
 175             return url
 176
 177         basesp = urlparse.urlsplit(base_url)
 178         if basesp.scheme in ("keep", "arvwf"):
 179             if not basesp.path:
 180                 raise IOError(errno.EINVAL, "Invalid Keep locator", base_url)
 181
 182             baseparts = basesp.path.split("/")
 183             urlparts = urlsp.path.split("/") if urlsp.path else []
 184
 185             pdh = baseparts.pop(0)
 186
 187             if basesp.scheme == "keep" and not arvados.util.keep_locator_pattern.match(pdh):
 188                 raise IOError(errno.EINVAL, "Invalid Keep locator", base_url)
 189
 190             if urlsp.path.startswith("/"):
 191                 baseparts = []
 192                 urlparts.pop(0)
 193
 194             if baseparts and urlsp.path:
 195                 baseparts.pop()
 196
 197             path = "/".join([pdh] + baseparts + urlparts)
 198             return urlparse.urlunsplit((basesp.scheme, "", path, "", urlsp.fragment))
 199
 200         return super(CollectionFetcher, self).urljoin(base_url, url)
 201
 202 workflow_uuid_pattern = re.compile(r'[a-z0-9]{5}-7fd4e-[a-z0-9]{15}')
 203 pipeline_template_uuid_pattern = re.compile(r'[a-z0-9]{5}-p5p6p-[a-z0-9]{15}')
 204
 205 def collectionResolver(api_client, document_loader, uri, num_retries=4):
 206     if workflow_uuid_pattern.match(uri):
 207         return "arvwf:%s#main" % (uri)
 208
 209     if pipeline_template_uuid_pattern.match(uri):
 210         pt = api_client.pipeline_templates().get(uuid=uri).execute(num_retries=num_retries)
 211         return "keep:" + pt["components"].values()[0]["script_parameters"]["cwl:tool"]
 212
 213     p = uri.split("/")
 214     if arvados.util.keep_locator_pattern.match(p[0]):
 215         return "keep:%s" % (uri)
 216
 217     if arvados.util.collection_uuid_pattern.match(p[0]):
 218         return "keep:%s%s" % (api_client.collections().
 219                               get(uuid=p[0]).execute()["portable_data_hash"],
 220                               uri[len(p[0]):])
 221
 222     return cwltool.resolver.tool_resolver(document_loader, uri)