Be more explicit about installing the root cert in arvbox doc

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

diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py
index 319046dc01aebbcf4d0496531be5e86c25c8f783..998481ab661105b68b0247d1a82c09211fa0d66e 100644 (file)
--- a/sdk/python/arvados/collection.py
+++ b/sdk/python/arvados/collection.py
@@ -827,7 +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):


@@ -1262,7 +1262,8 @@ class Collection(RichCollectionBase):
                  block_manager=None,
                  replication_desired=None,
                  storage_classes_desired=None,
                  block_manager=None,
                  replication_desired=None,
                  storage_classes_desired=None,

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

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


@@ -1296,17 +1297,22 @@ class Collection(RichCollectionBase):
 
         :storage_classes_desired:
           A list of storage class names where to upload the data. If None,
 
         :storage_classes_desired:
           A list of storage class names where to upload the data. If None,

-          the keepstores are expected to store the data into their default
-          storage class.
+          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
         self._block_manager = block_manager
         self.replication_desired = replication_desired
         super(Collection, self).__init__(parent)
         self._api_client = api_client
         self._keep_client = keep_client
         self._block_manager = block_manager
         self.replication_desired = replication_desired

-        self.storage_classes_desired = storage_classes_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


@@ -1340,8 +1346,11 @@ 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


@@ -1388,7 +1397,7 @@ 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))


@@ -1417,8 +1426,12 @@ 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))

-            classes = self.storage_classes_desired or []
-            self._block_manager = _BlockManager(self._my_keep(), copies=copies, put_threads=self.put_threads, num_retries=self.num_retries, storage_classes=classes)
+            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):


@@ -1442,8 +1455,8 @@ class Collection(RichCollectionBase):
         # 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)
         # 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.storage_classes_desired is None:
-            self.storage_classes_desired = self._api_response.get('storage_classes_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:


@@ -1540,7 +1553,8 @@ 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


@@ -1570,30 +1584,38 @@ 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

-        desired_classes = storage_classes
-        # Instance level storage_classes takes precedence over argument.
-        if self.storage_classes_desired:
-            if desired_classes and self.storage_classes_desired != desired_classes:
-                _logger.warning("Storage classes already set to {}".format(self.storage_classes_desired))
-            desired_classes = self.storage_classes_desired
-        if desired_classes:
-            body["storage_classes_desired"] = desired_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:


@@ -1639,7 +1661,8 @@ 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


@@ -1678,6 +1701,13 @@ 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.")


@@ -1688,11 +1718,17 @@ 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)
 


@@ -1708,17 +1744,13 @@ class Collection(RichCollectionBase):
                 body["owner_uuid"] = owner_uuid
             if properties:
                 body["properties"] = properties
                 body["owner_uuid"] = owner_uuid
             if properties:
                 body["properties"] = properties

-            desired_classes = storage_classes
-            # Instance level storage_classes takes precedence over argument.
-            if self.storage_classes_desired:
-                if desired_classes and self.storage_classes_desired != desired_classes:
-                    _logger.warning("Storage classes already set to {}".format(self.storage_classes_desired))
-                desired_classes = self.storage_classes_desired
-            if desired_classes:
-                body["storage_classes_desired"] = desired_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"]


@@ -1791,7 +1823,13 @@ 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: