Merge branch '14885-ciso-and-conda-packaging-pr'

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

diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py
index e38a6bd475c7b8a4aee7787a537a40656fd93b36..cf1a36f9fdfbbfdf739fe75027d00eaa782df4f2 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)
 


@@ -520,6 +537,7 @@ class RichCollectionBase(CollectionBase):
     def __init__(self, parent=None):
         self.parent = parent
         self._committed = False
     def __init__(self, parent=None):
         self.parent = parent
         self._committed = False

+        self._has_remote_blocks = False

         self._callback = None
         self._items = {}
 
         self._callback = None
         self._items = {}
 


@@ -544,6 +562,24 @@ 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."""
+
+        if self._has_remote_blocks:
+            return True
+        for item in self:
+            if self[item].has_remote_blocks():
+                return True
+        return False
+
+    @synchronized
+    def set_has_remote_blocks(self, val):
+        self._has_remote_blocks = val
+        if self.parent:
+            self.parent.set_has_remote_blocks(val)
+

     @must_be_writable
     @synchronized
     def find_or_create(self, path, create_type):
     @must_be_writable
     @synchronized
     def find_or_create(self, path, create_type):


@@ -636,7 +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:


@@ -658,6 +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):


@@ -680,7 +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."""


@@ -832,6 +874,8 @@ class RichCollectionBase(CollectionBase):
 
         self._items[target_name] = item
         self.set_committed(False)
 
         self._items[target_name] = item
         self.set_committed(False)

+        if not self._has_remote_blocks and source_obj.has_remote_blocks():
+            self.set_has_remote_blocks(True)

 
         if modified_from:
             self.notify(MOD, self, target_name, (modified_from, item))
 
         if modified_from:
             self.notify(MOD, self, target_name, (modified_from, item))


@@ -1015,7 +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:


@@ -1023,6 +1069,24 @@ class RichCollectionBase(CollectionBase):
             else:
                 return self._manifest_text
 
             else:
                 return self._manifest_text
 

+    @synchronized
+    def _copy_remote_blocks(self, remote_blocks={}):
+        """Scan through the entire collection and ask Keep to copy remote blocks.
+
+        When accessing a remote collection, blocks will have a remote signature
+        (+R instead of +A). Collect these signatures and request Keep to copy the
+        blocks to the local cluster, returning local (+A) signatures.
+
+        :remote_blocks:
+          Shared cache of remote to local block mappings. This is used to avoid
+          doing extra work when blocks are shared by more than one file in
+          different subdirectories.
+
+        """
+        for item in self:
+            remote_blocks = self[item]._copy_remote_blocks(remote_blocks)
+        return remote_blocks
+

     @synchronized
     def diff(self, end_collection, prefix=".", holding_collection=None):
         """Generate list of add/modify/delete actions.
     @synchronized
     def diff(self, end_collection, prefix=".", holding_collection=None):
         """Generate list of add/modify/delete actions.


@@ -1257,8 +1321,12 @@ class Collection(RichCollectionBase):
                 self._manifest_locator = manifest_locator_or_text
             elif re.match(arvados.util.collection_uuid_pattern, manifest_locator_or_text):
                 self._manifest_locator = manifest_locator_or_text
                 self._manifest_locator = manifest_locator_or_text
             elif re.match(arvados.util.collection_uuid_pattern, manifest_locator_or_text):
                 self._manifest_locator = manifest_locator_or_text

+                if not self._has_local_collection_uuid():
+                    self._has_remote_blocks = True

             elif re.match(arvados.util.manifest_pattern, manifest_locator_or_text):
                 self._manifest_text = manifest_locator_or_text
             elif re.match(arvados.util.manifest_pattern, manifest_locator_or_text):
                 self._manifest_text = manifest_locator_or_text

+                if '+R' in self._manifest_text:
+                    self._has_remote_blocks = True

             else:
                 raise errors.ArgumentError(
                     "Argument to CollectionReader is not a manifest or a collection UUID")
             else:
                 raise errors.ArgumentError(
                     "Argument to CollectionReader is not a manifest or a collection UUID")


@@ -1279,7 +1347,10 @@ 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
 


@@ -1376,6 +1447,10 @@ class Collection(RichCollectionBase):
     def _has_collection_uuid(self):
         return self._manifest_locator is not None and re.match(arvados.util.collection_uuid_pattern, self._manifest_locator)
 
     def _has_collection_uuid(self):
         return self._manifest_locator is not None and re.match(arvados.util.collection_uuid_pattern, self._manifest_locator)
 

+    def _has_local_collection_uuid(self):
+        return self._has_collection_uuid and \
+            self._my_api()._rootDesc['uuidPrefix'] == self._manifest_locator.split('-')[0]
+

     def __enter__(self):
         return self
 
     def __enter__(self):
         return self
 


@@ -1505,8 +1580,14 @@ class Collection(RichCollectionBase):
             body["trash_at"] = t
 
         if not self.committed():
             body["trash_at"] = t
 
         if not self.committed():

+            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 not self._has_collection_uuid():
                 raise AssertionError("Collection manifest_locator is not a collection uuid.  Use save_new() for new collections.")
             if not self._has_collection_uuid():
                 raise AssertionError("Collection manifest_locator is not a collection uuid.  Use save_new() for new collections.")

+            elif not self._has_local_collection_uuid():
+                raise AssertionError("Collection manifest_locator is from a remote cluster. Use save_new() to save it on the local cluster.")

 
             self._my_block_manager().commit_all()
 
 
             self._my_block_manager().commit_all()
 


@@ -1591,6 +1672,11 @@ 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 self._has_remote_blocks:
+            # Copy any remote blocks to the local cluster.
+            self._copy_remote_blocks(remote_blocks={})
+            self._has_remote_blocks = False
+

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


@@ -1627,6 +1713,9 @@ class Collection(RichCollectionBase):
     _block_re = re.compile(r'[0-9a-f]{32}\+(\d+)(\+\S+)*')
     _segment_re = re.compile(r'(\d+):(\d+):(\S+)')
 
     _block_re = re.compile(r'[0-9a-f]{32}\+(\d+)(\+\S+)*')
     _segment_re = re.compile(r'(\d+):(\d+):(\S+)')
 

+    def _unescape_manifest_path(self, path):
+        return re.sub('\\\\([0-3][0-7][0-7])', lambda m: chr(int(m.group(1), 8)), path)
+

     @synchronized
     def _import_manifest(self, manifest_text):
         """Import a manifest into a `Collection`.
     @synchronized
     def _import_manifest(self, manifest_text):
         """Import a manifest into a `Collection`.


@@ -1651,7 +1740,7 @@ class Collection(RichCollectionBase):
 
             if state == STREAM_NAME:
                 # starting a new stream
 
             if state == STREAM_NAME:
                 # starting a new stream

-                stream_name = tok.replace('\\040', ' ')
+                stream_name = self._unescape_manifest_path(tok)

                 blocks = []
                 segments = []
                 streamoffset = 0
                 blocks = []
                 segments = []
                 streamoffset = 0


@@ -1673,13 +1762,18 @@ class Collection(RichCollectionBase):
                 if file_segment:
                     pos = int(file_segment.group(1))
                     size = int(file_segment.group(2))
                 if file_segment:
                     pos = int(file_segment.group(1))
                     size = int(file_segment.group(2))

-                    name = file_segment.group(3).replace('\\040', ' ')
-                    filepath = os.path.join(stream_name, name)
-                    afile = self.find_or_create(filepath, FILE)
-                    if isinstance(afile, ArvadosFile):
-                        afile.add_segment(blocks, pos, size)
+                    name = self._unescape_manifest_path(file_segment.group(3))
+                    if name.split('/')[-1] == '.':
+                        # placeholder for persisting an empty directory, not a real file
+                        if len(name) > 2:
+                            self.find_or_create(os.path.join(stream_name, name[:-2]), COLLECTION)

                     else:
                     else:

-                        raise errors.SyntaxError("File %s conflicts with stream of the same name.", filepath)
+                        filepath = os.path.join(stream_name, name)
+                        afile = self.find_or_create(filepath, FILE)
+                        if isinstance(afile, ArvadosFile):
+                            afile.add_segment(blocks, pos, size)
+                        else:
+                            raise errors.SyntaxError("File %s conflicts with stream of the same name.", filepath)

                 else:
                     # error!
                     raise errors.SyntaxError("Invalid manifest format, expected file segment but did not match format: '%s'" % tok)
                 else:
                     # error!
                     raise errors.SyntaxError("Invalid manifest format, expected file segment but did not match format: '%s'" % tok)


@@ -1745,6 +1839,16 @@ 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.