Merge branch '18842-arv-mount-disk-config' refs #18842

[arvados.git] / sdk / python / arvados / collection.py

diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py
index 48fdaf03ecd685f3e420437cebb3d46fd1741085..e1138910aebfc501bdfd875c03bd568ea76c3f3e 100644 (file)
--- a/sdk/python/arvados/collection.py
+++ b/sdk/python/arvados/collection.py
@@ -7,24 +7,26 @@ from future.utils import listitems, listvalues, viewkeys
 from builtins import str
 from past.builtins import basestring
 from builtins import object
 from builtins import str
 from past.builtins import basestring
 from builtins import object

+import ciso8601
+import datetime
+import errno

 import functools
 import functools

+import hashlib
+import io

 import logging
 import os
 import re
 import logging
 import os
 import re

-import errno
-import hashlib
-import datetime
-import ciso8601
-import time
+import sys

 import threading
 import threading

+import time

 
 from collections import deque
 from stat import *
 
 
 from collections import deque
 from stat import *
 

-from .arvfile import split, _FileLikeObjectBase, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, _BlockManager, synchronized, must_be_writable, NoopLock
+from .arvfile import split, _FileLikeObjectBase, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, WrappableFile, _BlockManager, synchronized, must_be_writable, NoopLock

 from .keep import KeepLocator, KeepClient
 from .stream import StreamReader
 from .keep import KeepLocator, KeepClient
 from .stream import StreamReader

-from ._normalize_stream import normalize_stream
+from ._normalize_stream import normalize_stream, escape

 from ._ranges import Range, LocatorAndRange
 from .safeapi import ThreadSafeApiCache
 import arvados.config as config
 from ._ranges import Range, LocatorAndRange
 from .safeapi import ThreadSafeApiCache
 import arvados.config as config


@@ -35,6 +37,21 @@ from arvados.retry import retry_method
 
 _logger = logging.getLogger('arvados.collection')
 
 
 _logger = logging.getLogger('arvados.collection')
 

+
+if sys.version_info >= (3, 0):
+    TextIOWrapper = io.TextIOWrapper
+else:
+    class TextIOWrapper(io.TextIOWrapper):
+        """To maintain backward compatibility, cast str to unicode in
+        write('foo').
+
+        """
+        def write(self, data):
+            if isinstance(data, basestring):
+                data = unicode(data)
+            return super(TextIOWrapper, self).write(data)
+
+

 class CollectionBase(object):
     """Abstract base class for Collection classes."""
 
 class CollectionBase(object):
     """Abstract base class for Collection classes."""
 


@@ -266,7 +283,7 @@ class CollectionWriter(CollectionBase):
             streampath, filename = split(streampath)
         if self._last_open and not self._last_open.closed:
             raise errors.AssertionError(
             streampath, filename = split(streampath)
         if self._last_open and not self._last_open.closed:
             raise errors.AssertionError(

-                "can't open '{}' when '{}' is still open".format(
+                u"can't open '{}' when '{}' is still open".format(

                     filename, self._last_open.name))
         if streampath != self.current_stream_name():
             self.start_new_stream(streampath)
                     filename, self._last_open.name))
         if streampath != self.current_stream_name():
             self.start_new_stream(streampath)


@@ -444,22 +461,22 @@ class ResumableCollectionWriter(CollectionWriter):
                 writer._queued_file.seek(pos)
             except IOError as error:
                 raise errors.StaleWriterStateError(
                 writer._queued_file.seek(pos)
             except IOError as error:
                 raise errors.StaleWriterStateError(

-                    "failed to reopen active file {}: {}".format(path, error))
+                    u"failed to reopen active file {}: {}".format(path, error))

         return writer
 
     def check_dependencies(self):
         for path, orig_stat in listitems(self._dependencies):
             if not S_ISREG(orig_stat[ST_MODE]):
         return writer
 
     def check_dependencies(self):
         for path, orig_stat in listitems(self._dependencies):
             if not S_ISREG(orig_stat[ST_MODE]):

-                raise errors.StaleWriterStateError("{} not file".format(path))
+                raise errors.StaleWriterStateError(u"{} not file".format(path))

             try:
                 now_stat = tuple(os.stat(path))
             except OSError as error:
                 raise errors.StaleWriterStateError(
             try:
                 now_stat = tuple(os.stat(path))
             except OSError as error:
                 raise errors.StaleWriterStateError(

-                    "failed to stat {}: {}".format(path, error))
+                    u"failed to stat {}: {}".format(path, error))

             if ((not S_ISREG(now_stat[ST_MODE])) or
                 (orig_stat[ST_MTIME] != now_stat[ST_MTIME]) or
                 (orig_stat[ST_SIZE] != now_stat[ST_SIZE])):
             if ((not S_ISREG(now_stat[ST_MODE])) or
                 (orig_stat[ST_MTIME] != now_stat[ST_MTIME]) or
                 (orig_stat[ST_SIZE] != now_stat[ST_SIZE])):

-                raise errors.StaleWriterStateError("{} changed".format(path))
+                raise errors.StaleWriterStateError(u"{} changed".format(path))

 
     def dump_state(self, copy_func=lambda x: x):
         state = {attr: copy_func(getattr(self, attr))
 
     def dump_state(self, copy_func=lambda x: x):
         state = {attr: copy_func(getattr(self, attr))


@@ -475,7 +492,7 @@ class ResumableCollectionWriter(CollectionWriter):
         try:
             src_path = os.path.realpath(source)
         except Exception:
         try:
             src_path = os.path.realpath(source)
         except Exception:

-            raise errors.AssertionError("{} not a file path".format(source))
+            raise errors.AssertionError(u"{} not a file path".format(source))

         try:
             path_stat = os.stat(src_path)
         except OSError as stat_error:
         try:
             path_stat = os.stat(src_path)
         except OSError as stat_error:


@@ -488,10 +505,10 @@ class ResumableCollectionWriter(CollectionWriter):
             self._dependencies[source] = tuple(fd_stat)
         elif path_stat is None:
             raise errors.AssertionError(
             self._dependencies[source] = tuple(fd_stat)
         elif path_stat is None:
             raise errors.AssertionError(

-                "could not stat {}: {}".format(source, stat_error))
+                u"could not stat {}: {}".format(source, stat_error))

         elif path_stat.st_ino != fd_stat.st_ino:
             raise errors.AssertionError(
         elif path_stat.st_ino != fd_stat.st_ino:
             raise errors.AssertionError(

-                "{} changed between open and stat calls".format(source))
+                u"{} changed between open and stat calls".format(source))

         else:
             self._dependencies[src_path] = tuple(fd_stat)
 
         else:
             self._dependencies[src_path] = tuple(fd_stat)
 


@@ -545,6 +562,7 @@ class RichCollectionBase(CollectionBase):
     def stream_name(self):
         raise NotImplementedError()
 
     def stream_name(self):
         raise NotImplementedError()
 

+

     @synchronized
     def has_remote_blocks(self):
         """Recursively check for a +R segment locator signature."""
     @synchronized
     def has_remote_blocks(self):
         """Recursively check for a +R segment locator signature."""


@@ -654,7 +672,7 @@ class RichCollectionBase(CollectionBase):
 
         return self.find_or_create(path, COLLECTION)
 
 
         return self.find_or_create(path, COLLECTION)
 

-    def open(self, path, mode="r"):
+    def open(self, path, mode="r", encoding=None):

         """Open a file-like object for access.
 
         :path:
         """Open a file-like object for access.
 
         :path:


@@ -676,6 +694,7 @@ class RichCollectionBase(CollectionBase):
             opens for reading and writing.  All writes are appended to
             the end of the file.  Writing does not affect the file pointer for
             reading.
             opens for reading and writing.  All writes are appended to
             the end of the file.  Writing does not affect the file pointer for
             reading.

+

         """
 
         if not re.search(r'^[rwa][bt]?\+?$', mode):
         """
 
         if not re.search(r'^[rwa][bt]?\+?$', mode):


@@ -698,7 +717,12 @@ class RichCollectionBase(CollectionBase):
         if mode[0] == 'w':
             arvfile.truncate(0)
 
         if mode[0] == 'w':
             arvfile.truncate(0)
 

-        return fclass(arvfile, mode=mode, num_retries=self.num_retries)
+        binmode = mode[0] + 'b' + re.sub('[bt]', '', mode[1:])
+        f = fclass(arvfile, mode=binmode, num_retries=self.num_retries)
+        if 'b' not in mode:
+            bufferclass = io.BufferedRandom if f.writable() else io.BufferedReader
+            f = TextIOWrapper(bufferclass(WrappableFile(f)), encoding=encoding)
+        return f

 
     def modified(self):
         """Determine if the collection has been modified since last commited."""
 
     def modified(self):
         """Determine if the collection has been modified since last commited."""


@@ -803,7 +827,7 @@ class RichCollectionBase(CollectionBase):
             self.set_committed(False)
             self.notify(DEL, self, pathcomponents[0], deleteditem)
         else:
             self.set_committed(False)
             self.notify(DEL, self, pathcomponents[0], deleteditem)
         else:

-            item.remove(pathcomponents[1])
+            item.remove(pathcomponents[1], recursive=recursive)

 
     def _clonefrom(self, source):
         for k,v in listitems(source):
 
     def _clonefrom(self, source):
         for k,v in listitems(source):


@@ -1035,7 +1059,9 @@ class RichCollectionBase(CollectionBase):
             if stream:
                 buf.append(" ".join(normalize_stream(stream_name, stream)) + "\n")
             for dirname in [s for s in sorted_keys if isinstance(self[s], RichCollectionBase)]:
             if stream:
                 buf.append(" ".join(normalize_stream(stream_name, stream)) + "\n")
             for dirname in [s for s in sorted_keys if isinstance(self[s], RichCollectionBase)]:

-                buf.append(self[dirname].manifest_text(stream_name=os.path.join(stream_name, dirname), strip=strip, normalize=True, only_committed=only_committed))
+                buf.append(self[dirname].manifest_text(
+                    stream_name=os.path.join(stream_name, dirname),
+                    strip=strip, normalize=True, only_committed=only_committed))

             return "".join(buf)
         else:
             if strip:
             return "".join(buf)
         else:
             if strip:


@@ -1235,7 +1261,9 @@ class Collection(RichCollectionBase):
                  apiconfig=None,
                  block_manager=None,
                  replication_desired=None,
                  apiconfig=None,
                  block_manager=None,
                  replication_desired=None,

-                 put_threads=None):
+                 storage_classes_desired=None,
+                 put_threads=None,
+                 get_threads=None):

         """Collection constructor.
 
         :manifest_locator_or_text:
         """Collection constructor.
 
         :manifest_locator_or_text:


@@ -1267,13 +1295,29 @@ class Collection(RichCollectionBase):
           configuration applies. If not None, this value will also be used
           for determining the number of block copies being written.
 
           configuration applies. If not None, this value will also be used
           for determining the number of block copies being written.
 

+        :storage_classes_desired:
+          A list of storage class names where to upload the data. If None,
+          the keep client is expected to store the data into the cluster's
+          default storage class(es).
+

         """
         """

+
+        if storage_classes_desired and type(storage_classes_desired) is not list:
+            raise errors.ArgumentError("storage_classes_desired must be list type.")
+

         super(Collection, self).__init__(parent)
         self._api_client = api_client
         self._keep_client = keep_client
         super(Collection, self).__init__(parent)
         self._api_client = api_client
         self._keep_client = keep_client

+
+        # Use the keep client from ThreadSafeApiCache
+        if self._keep_client is None and isinstance(self._api_client, ThreadSafeApiCache):
+            self._keep_client = self._api_client.keep
+

         self._block_manager = block_manager
         self.replication_desired = replication_desired
         self._block_manager = block_manager
         self.replication_desired = replication_desired

+        self._storage_classes_desired = storage_classes_desired

         self.put_threads = put_threads
         self.put_threads = put_threads

+        self.get_threads = get_threads

 
         if apiconfig:
             self._config = apiconfig
 
         if apiconfig:
             self._config = apiconfig


@@ -1307,8 +1351,11 @@ class Collection(RichCollectionBase):
 
             try:
                 self._populate()
 
             try:
                 self._populate()

-            except (IOError, errors.SyntaxError) as e:
-                raise errors.ArgumentError("Error processing manifest text: %s", e)
+            except errors.SyntaxError as e:
+                raise errors.ArgumentError("Error processing manifest text: %s", str(e)) from None
+
+    def storage_classes_desired(self):
+        return self._storage_classes_desired or []

 
     def root_collection(self):
         return self
 
     def root_collection(self):
         return self


@@ -1321,7 +1368,10 @@ class Collection(RichCollectionBase):
 
     def get_trash_at(self):
         if self._api_response and self._api_response["trash_at"]:
 
     def get_trash_at(self):
         if self._api_response and self._api_response["trash_at"]:

-            return ciso8601.parse_datetime(self._api_response["trash_at"])
+            try:
+                return ciso8601.parse_datetime(self._api_response["trash_at"])
+            except ValueError:
+                return None

         else:
             return None
 
         else:
             return None
 


@@ -1352,7 +1402,7 @@ class Collection(RichCollectionBase):
                 # our tokens.
                 return
             else:
                 # our tokens.
                 return
             else:

-                self._past_versions.add((response.get("modified_at"), response.get("portable_data_hash")))
+                self._remember_api_response(response)

             other = CollectionReader(response["manifest_text"])
         baseline = CollectionReader(self._manifest_text)
         self.apply(baseline.diff(other))
             other = CollectionReader(response["manifest_text"])
         baseline = CollectionReader(self._manifest_text)
         self.apply(baseline.diff(other))


@@ -1381,7 +1431,12 @@ class Collection(RichCollectionBase):
             copies = (self.replication_desired or
                       self._my_api()._rootDesc.get('defaultCollectionReplication',
                                                    2))
             copies = (self.replication_desired or
                       self._my_api()._rootDesc.get('defaultCollectionReplication',
                                                    2))

-            self._block_manager = _BlockManager(self._my_keep(), copies=copies, put_threads=self.put_threads)
+            self._block_manager = _BlockManager(self._my_keep(),
+                                                copies=copies,
+                                                put_threads=self.put_threads,
+                                                num_retries=self.num_retries,
+                                                storage_classes_func=self.storage_classes_desired,
+                                                get_threads=self.get_threads,)

         return self._block_manager
 
     def _remember_api_response(self, response):
         return self._block_manager
 
     def _remember_api_response(self, response):


@@ -1402,9 +1457,11 @@ class Collection(RichCollectionBase):
         self._manifest_text = self._api_response['manifest_text']
         self._portable_data_hash = self._api_response['portable_data_hash']
         # If not overriden via kwargs, we should try to load the
         self._manifest_text = self._api_response['manifest_text']
         self._portable_data_hash = self._api_response['portable_data_hash']
         # If not overriden via kwargs, we should try to load the

-        # replication_desired from the API server
+        # replication_desired and storage_classes_desired from the API server

         if self.replication_desired is None:
             self.replication_desired = self._api_response.get('replication_desired', None)
         if self.replication_desired is None:
             self.replication_desired = self._api_response.get('replication_desired', None)

+        if self._storage_classes_desired is None:
+            self._storage_classes_desired = self._api_response.get('storage_classes_desired', None)

 
     def _populate(self):
         if self._manifest_text is None:
 
     def _populate(self):
         if self._manifest_text is None:


@@ -1501,7 +1558,8 @@ class Collection(RichCollectionBase):
              storage_classes=None,
              trash_at=None,
              merge=True,
              storage_classes=None,
              trash_at=None,
              merge=True,

-             num_retries=None):
+             num_retries=None,
+             preserve_version=False):

         """Save collection to an existing collection record.
 
         Commit pending buffer blocks to Keep, merge with remote record (if
         """Save collection to an existing collection record.
 
         Commit pending buffer blocks to Keep, merge with remote record (if


@@ -1531,24 +1589,38 @@ class Collection(RichCollectionBase):
         :num_retries:
           Retry count on API calls (if None,  use the collection default)
 
         :num_retries:
           Retry count on API calls (if None,  use the collection default)
 

+        :preserve_version:
+          If True, indicate that the collection content being saved right now
+          should be preserved in a version snapshot if the collection record is
+          updated in the future. Requires that the API server has
+          Collections.CollectionVersioning enabled, if not, setting this will
+          raise an exception.
+

         """
         if properties and type(properties) is not dict:
             raise errors.ArgumentError("properties must be dictionary type.")
 
         if storage_classes and type(storage_classes) is not list:
             raise errors.ArgumentError("storage_classes must be list type.")
         """
         if properties and type(properties) is not dict:
             raise errors.ArgumentError("properties must be dictionary type.")
 
         if storage_classes and type(storage_classes) is not list:
             raise errors.ArgumentError("storage_classes must be list type.")

+        if storage_classes:
+            self._storage_classes_desired = storage_classes

 
         if trash_at and type(trash_at) is not datetime.datetime:
             raise errors.ArgumentError("trash_at must be datetime type.")
 
 
         if trash_at and type(trash_at) is not datetime.datetime:
             raise errors.ArgumentError("trash_at must be datetime type.")
 

+        if preserve_version and not self._my_api().config()['Collections'].get('CollectionVersioning', False):
+            raise errors.ArgumentError("preserve_version is not supported when CollectionVersioning is not enabled.")
+

         body={}
         if properties:
             body["properties"] = properties
         body={}
         if properties:
             body["properties"] = properties

-        if storage_classes:
-            body["storage_classes_desired"] = storage_classes
+        if self.storage_classes_desired():
+            body["storage_classes_desired"] = self.storage_classes_desired()

         if trash_at:
             t = trash_at.strftime("%Y-%m-%dT%H:%M:%S.%fZ")
             body["trash_at"] = t
         if trash_at:
             t = trash_at.strftime("%Y-%m-%dT%H:%M:%S.%fZ")
             body["trash_at"] = t

+        if preserve_version:
+            body["preserve_version"] = preserve_version

 
         if not self.committed():
             if self._has_remote_blocks:
 
         if not self.committed():
             if self._has_remote_blocks:


@@ -1594,7 +1666,8 @@ class Collection(RichCollectionBase):
                  storage_classes=None,
                  trash_at=None,
                  ensure_unique_name=False,
                  storage_classes=None,
                  trash_at=None,
                  ensure_unique_name=False,

-                 num_retries=None):
+                 num_retries=None,
+                 preserve_version=False):

         """Save collection to a new collection record.
 
         Commit pending buffer blocks to Keep and, when create_collection_record
         """Save collection to a new collection record.
 
         Commit pending buffer blocks to Keep and, when create_collection_record


@@ -1633,6 +1706,13 @@ class Collection(RichCollectionBase):
         :num_retries:
           Retry count on API calls (if None,  use the collection default)
 
         :num_retries:
           Retry count on API calls (if None,  use the collection default)
 

+        :preserve_version:
+          If True, indicate that the collection content being saved right now
+          should be preserved in a version snapshot if the collection record is
+          updated in the future. Requires that the API server has
+          Collections.CollectionVersioning enabled, if not, setting this will
+          raise an exception.
+

         """
         if properties and type(properties) is not dict:
             raise errors.ArgumentError("properties must be dictionary type.")
         """
         if properties and type(properties) is not dict:
             raise errors.ArgumentError("properties must be dictionary type.")


@@ -1643,11 +1723,17 @@ class Collection(RichCollectionBase):
         if trash_at and type(trash_at) is not datetime.datetime:
             raise errors.ArgumentError("trash_at must be datetime type.")
 
         if trash_at and type(trash_at) is not datetime.datetime:
             raise errors.ArgumentError("trash_at must be datetime type.")
 

+        if preserve_version and not self._my_api().config()['Collections'].get('CollectionVersioning', False):
+            raise errors.ArgumentError("preserve_version is not supported when CollectionVersioning is not enabled.")
+

         if self._has_remote_blocks:
             # Copy any remote blocks to the local cluster.
             self._copy_remote_blocks(remote_blocks={})
             self._has_remote_blocks = False
 
         if self._has_remote_blocks:
             # Copy any remote blocks to the local cluster.
             self._copy_remote_blocks(remote_blocks={})
             self._has_remote_blocks = False
 

+        if storage_classes:
+            self._storage_classes_desired = storage_classes
+

         self._my_block_manager().commit_all()
         text = self.manifest_text(strip=False)
 
         self._my_block_manager().commit_all()
         text = self.manifest_text(strip=False)
 


@@ -1663,11 +1749,13 @@ class Collection(RichCollectionBase):
                 body["owner_uuid"] = owner_uuid
             if properties:
                 body["properties"] = properties
                 body["owner_uuid"] = owner_uuid
             if properties:
                 body["properties"] = properties

-            if storage_classes:
-                body["storage_classes_desired"] = storage_classes
+            if self.storage_classes_desired():
+                body["storage_classes_desired"] = self.storage_classes_desired()

             if trash_at:
                 t = trash_at.strftime("%Y-%m-%dT%H:%M:%S.%fZ")
                 body["trash_at"] = t
             if trash_at:
                 t = trash_at.strftime("%Y-%m-%dT%H:%M:%S.%fZ")
                 body["trash_at"] = t

+            if preserve_version:
+                body["preserve_version"] = preserve_version

 
             self._remember_api_response(self._my_api().collections().create(ensure_unique_name=ensure_unique_name, body=body).execute(num_retries=num_retries))
             text = self._api_response["manifest_text"]
 
             self._remember_api_response(self._my_api().collections().create(ensure_unique_name=ensure_unique_name, body=body).execute(num_retries=num_retries))
             text = self._api_response["manifest_text"]


@@ -1740,7 +1828,13 @@ class Collection(RichCollectionBase):
                             self.find_or_create(os.path.join(stream_name, name[:-2]), COLLECTION)
                     else:
                         filepath = os.path.join(stream_name, name)
                             self.find_or_create(os.path.join(stream_name, name[:-2]), COLLECTION)
                     else:
                         filepath = os.path.join(stream_name, name)

-                        afile = self.find_or_create(filepath, FILE)
+                        try:
+                            afile = self.find_or_create(filepath, FILE)
+                        except IOError as e:
+                            if e.errno == errno.ENOTDIR:
+                                raise errors.SyntaxError("Dir part of %s conflicts with file of the same name.", filepath) from None
+                            else:
+                                raise e from None

                         if isinstance(afile, ArvadosFile):
                             afile.add_segment(blocks, pos, size)
                         else:
                         if isinstance(afile, ArvadosFile):
                             afile.add_segment(blocks, pos, size)
                         else:


@@ -1810,6 +1904,16 @@ class Subcollection(RichCollectionBase):
         self.name = newname
         self.lock = self.parent.root_collection().lock
 
         self.name = newname
         self.lock = self.parent.root_collection().lock
 

+    @synchronized
+    def _get_manifest_text(self, stream_name, strip, normalize, only_committed=False):
+        """Encode empty directories by using an \056-named (".") empty file"""
+        if len(self._items) == 0:
+            return "%s %s 0:0:\\056\n" % (
+                escape(stream_name), config.EMPTY_BLOCK_LOCATOR)
+        return super(Subcollection, self)._get_manifest_text(stream_name,
+                                                             strip, normalize,
+                                                             only_committed)
+

 
 class CollectionReader(Collection):
     """A read-only collection object.
 
 class CollectionReader(Collection):
     """A read-only collection object.