CMFActivity: Use CMFActivity as a backend for joblib

This commit:

- Adds a new Activity called "SQLJoblib"
- Adds a Backend to be used by joblib
- Uses OOBTree to store results instead of ConflictFreeLog
- Adds a getResultDict API to fetch resut Dict

It uses the original work from rafael@nexedi.com and loic.esteve@inria.fr

product/CMFActivity/ActiveProcess.py

@@ -32,6 +32,7 @@ from Products.CMFCore import permissions as CMFCorePermissions
 from Products.ERP5Type.Base import Base
 from Products.ERP5Type import PropertySheet
 from Products.ERP5Type.ConflictFree import ConflictFreeLog
+from BTrees.OOBTree import OOBTree
 from BTrees.Length import Length
 from random import randrange
 from .ActiveResult import ActiveResult
@@ -87,6 +88,9 @@ class ActiveProcess(Base):
 
   security.declareProtected(CMFCorePermissions.ManagePortal, 'postResult')
   def postResult(self, result):
+    try:
+      result_id = result.id
+    except AttributeError:
       try:
         result_list = self.result_list
       except AttributeError:
@@ -103,6 +107,11 @@ class ActiveProcess(Base):
           self.result_len.change(1)
           return
       result_list.append(result)
+    else:
+      try:
+        self.result_dict[result_id] = result
+      except AttributeError:
+        self.result_dict = OOBTree({result.id: result})
 
   security.declareProtected(CMFCorePermissions.ManagePortal, 'postActiveResult')
   def postActiveResult(self, *args, **kw):
@@ -126,6 +135,17 @@ class ActiveProcess(Base):
       return result_list.values()
     return list(result_list)
 
+  security.declareProtected(CMFCorePermissions.ManagePortal, 'getResultDict')
+  def getResultDict(self, **kw):
+    """
+      Returns the result Dict
+    """
+    try:
+      return self.result_dict
+    except AttributeError:
+      self.result_dict = result_dict = OOBTree()
+      return result_dict
+
   security.declareProtected( CMFCorePermissions.View, 'hasActivity' )
   def hasActivity(self, **kw):
     """

product/CMFActivity/Activity/SQLJoblib.py

+##############################################################################
+#
+# Copyright (c) 2002,2007 Nexedi SA and Contributors. All Rights Reserved.
+#                    Jean-Paul Smets-Solanes <jp@nexedi.com>
+#
+# WARNING: This program as such is intended to be used by professional
+# programmers who take the whole responsability of assessing all potential
+# consequences resulting from its eventual inadequacies and bugs
+# End users who are looking for a ready-to-use solution with commercial
+# garantees and support are strongly adviced to contract a Free Software
+# Service Company
+#
+# This program is Free Software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+#
+##############################################################################
+
+from zLOG import LOG, TRACE, INFO, WARNING, ERROR, PANIC
+from SQLBase import SQLBase, sort_message_key, MAX_MESSAGE_LIST_SIZE
+from Products.CMFActivity.ActivityTool import Message
+
+# Stop validating more messages when this limit is reached
+MAX_VALIDATED_LIMIT = 1000
+# Read this many messages to validate.
+READ_MESSAGE_LIMIT = 1000
+
+from SQLDict import SQLDict
+
+class SQLJoblib(SQLDict):
+  """
+    An extention of SQLDict, It is non transatactional and follow always-excute paradigm.
+    It uses a dictionary to store results and with hash of arguments as keys  
+  """
+  sql_table = 'message_job'
+  uid_group = 'portal_activity_job'
+
+  def initialize(self, activity_tool, clear):
+    """
+      Initialize the message table using MYISAM Engine 
+    """
+    folder = activity_tool.getPortalObject().portal_skins.activity
+    try:
+      createMessageTable = folder.SQLJoblib_createMessageTable
+    except AttributeError:
+      return
+    if clear:
+      folder.SQLBase_dropMessageTable(table=self.sql_table)
+      createMessageTable()
+    else:
+      src = createMessageTable._upgradeSchema(create_if_not_exists=1,
+                                              initialize=self._initialize,
+                                              table=self.sql_table)
+      if src:
+        LOG('CMFActivity', INFO, "%r table upgraded\n%s"
+            % (self.sql_table, src))
+
+  def generateMessageUID(self, m):
+    return (tuple(m.object_path), m.method_id, m.activity_kw.get('signature'),
+                  m.activity_kw.get('tag'), m.activity_kw.get('group_id'))
+
+  def prepareQueueMessageList(self, activity_tool, message_list):
+    registered_message_list = [m for m in message_list if m.is_registered]
+    portal = activity_tool.getPortalObject()
+    for i in xrange(0, len(registered_message_list), MAX_MESSAGE_LIST_SIZE):
+      message_list = registered_message_list[i:i+MAX_MESSAGE_LIST_SIZE]
+      uid_list = portal.portal_ids.generateNewIdList(self.uid_group,
+        id_count=len(message_list), id_generator='uid')
+      path_list = ['/'.join(m.object_path) for m in message_list]
+      active_process_uid_list = [m.active_process_uid for m in message_list]
+      method_id_list = [m.method_id for m in message_list]
+      priority_list = [m.activity_kw.get('priority', 1) for m in message_list]
+      date_list = [m.activity_kw.get('at_date') for m in message_list]
+      group_method_id_list = [m.getGroupId() for m in message_list]
+      tag_list = [m.activity_kw.get('tag', '') for m in message_list]
+      signature_list=[m.activity_kw.get('signature', '') for m in message_list]
+      serialization_tag_list = [m.activity_kw.get('serialization_tag', '')
+                                for m in message_list]
+      processing_node_list = []
+      for m in message_list:
+        m.order_validation_text = x = self.getOrderValidationText(m)
+        processing_node_list.append(0 if x == 'none' else -1)
+      portal.SQLJoblib_writeMessage(
+        uid_list=uid_list,
+        path_list=path_list,
+        active_process_uid_list=active_process_uid_list,
+        method_id_list=method_id_list,
+        priority_list=priority_list,
+        message_list=map(Message.dump, message_list),
+        group_method_id_list=group_method_id_list,
+        date_list=date_list,
+        tag_list=tag_list,
+        processing_node_list=processing_node_list,
+        signature_list=signature_list,
+        serialization_tag_list=serialization_tag_list)
+
+  def getProcessableMessageLoader(self, activity_tool, processing_node):
+    path_and_method_id_dict = {}
+    def load(line):
+      # getProcessableMessageList already fetch messages with the same
+      # group_method_id, so what remains to be filtered on are path, method_id
+      # and signature
+      path = line.path
+      method_id = line.method_id
+      key = path, method_id
+      uid = line.uid
+      original_uid = path_and_method_id_dict.get(key)
+      if original_uid is None:
+        m = Message.load(line.message, uid=uid, line=line)
+        try:
+          result = activity_tool.SQLJoblib_selectDuplicatedLineList(
+            path=path,
+            method_id=method_id,
+            group_method_id=line.group_method_id,
+            signature=line.signature)
+          reserve_uid_list = uid_list = [x.uid for x in result]
+          if reserve_uid_list:
+            activity_tool.SQLBase_reserveMessageList(
+              table=self.sql_table,
+              processing_node=processing_node,
+              uid=reserve_uid_list)
+        except:
+          self._log(WARNING, 'getDuplicateMessageUidList got an exception')
+          raise
+        if uid_list:
+          self._log(TRACE, 'Reserved duplicate messages: %r' % uid_list)
+        path_and_method_id_dict[key] = uid
+        return m, uid, uid_list
+      # We know that original_uid != uid because caller skips lines we returned
+      # earlier.
+      return None, original_uid, [uid]
+    return load

product/CMFActivity/ActivityTool.py

@@ -288,6 +288,9 @@ class Message(BaseMessage):
   def activateResult(self, active_process, result, object):
     if not isinstance(result, ActiveResult):
       result = ActiveResult(result=result)
+    signature = self.activity_kw.get('signature')
+    if signature:
+      result.edit(id=signature)
     # XXX Allow other method_id in future
     result.edit(object_path=object, method_id=self.method_id)
     active_process.postResult(result)
@@ -459,7 +462,7 @@ allow_class(GroupedMessage)
 
 # Activity Registration
 def activity_dict():
-  from Activity import SQLDict, SQLQueue
+  from Activity import SQLDict, SQLQueue, SQLJoblib
   return {k: getattr(v, k)() for k, v in locals().iteritems()}
 activity_dict = activity_dict()
 
@@ -655,6 +658,9 @@ class ActivityTool (Folder, UniqueObject):
       for activity in activity_dict.itervalues():
         activity.initialize(self, clear=False)
 
+    def _callSafeFunction(self, batch_function):
+      return batch_function()
+
     security.declareProtected(Permissions.manage_properties, 'isSubscribed')
     def isSubscribed(self):
       """

product/CMFActivity/__init__.py

@@ -41,6 +41,7 @@ document_classes = updateGlobals(this_module, globals(),
 def initialize( context ):
   # Define object classes and tools
   import ActivityTool, ActiveProcess, ActivityConnection
+  from .joblib import CMFActivityParallelBackend
   object_classes = (ActiveProcess.ActiveProcess,
                     #ActivityConnection.ActivityConnection
                     )

product/CMFActivity/dtml/manageActivities.dtml

@@ -63,7 +63,7 @@ Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
           </td>
         </dtml-if>
         <td align="left" valign="top"><dtml-var uid>
-          <dtml-var expr="{'SQLDict':'(dict)','SQLQueue':'(queue)'}[activity]">
+          <dtml-var expr="{'SQLDict':'(dict)','SQLQueue':'(queue)','SQLJoblib':'(Joblib)'}[activity]">
         </td>
         <td align="left" valign="top"><a href="<dtml-var expr="REQUEST.physicalPathToURL(path)">"><dtml-var path></a></td>
         <td align="left" valign="top"><dtml-var method_id></td>

product/CMFActivity/joblib/CMFActivityParallelBackend.py

+##############################################################################
+#
+# Copyright (c) 2016 Nexedi SA and Contributors. All Rights Reserved.
+#
+# WARNING: This program as such is intended to be used by professional
+# programmers who take the whole responsability of assessing all potential
+# consequences resulting from its eventual inadequacies and bugs
+# End users who are looking for a ready-to-use solution with commercial
+# garantees and support are strongly adviced to contract a Free Software
+# Service Company
+#
+# This program is Free Software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+#
+##############################################################################
+
+from zLOG import LOG, INFO, WARNING
+from ZODB.POSException import ConflictError
+from Products.CMFActivity.ActivityRuntimeEnvironment import \
+  getActivityRuntimeEnvironment
+
+try:
+  from sklearn.externals.joblib import register_parallel_backend
+  from sklearn.externals.joblib.parallel import ParallelBackendBase, parallel_backend
+  from sklearn.externals.joblib.parallel import FallbackToBackend, SequentialBackend
+  from sklearn.externals.joblib.hashing import hash as joblib_hash
+except ImportError:
+  LOG(__name__, WARNING, "Joblib cannot be imported, support disabled")
+else:
+  class JoblibResult(object):
+
+    def __init__(self, result, callback):
+      self.result = result
+      self.callback = callback
+
+    def get(self, timeout=None):
+      result = self.result.result
+      callback = self.callback
+      if callback is not None:
+        callback(result)
+      return result
+
+  class JoblibDispatch(object):
+
+    def __init__(self, backend):
+      self.backend = backend
+
+    def get(self, timeout=None):
+      backend = self.backend
+      def onError(exc_type, exc_value, traceback):
+        active_process = backend.active_process
+        activate = active_process.getParentValue().activate
+        kw = {
+          'active_process': active_process,
+          'activity': 'SQLJoblib',
+          'tag': "joblib_" + active_process.getId(),
+        }
+        for sig, batch in backend.job_list:
+          activate(signature=sig, **kw)._callSafeFunction(batch)
+      getActivityRuntimeEnvironment().edit(on_error_callback=onError)
+      raise ConflictError
+
+  class CMFActivityBackend(ParallelBackendBase):
+    def __init__(self, *args, **kw):
+      self.active_process = active_process = kw['active_process']
+      self.job_list = []
+      self.result_dict = active_process.getResultDict()
+
+    def effective_n_jobs(self, n_jobs):
+      """Dummy implementation to prevent n_jobs <=0
+
+      and allow (sequential) n_jobs=1 and n_jobs != 1 (parallel) behaviour
+      """
+      if n_jobs == 0:
+        raise ValueError('n_jobs == 0 in Parallel has no meaning')
+      return abs(n_jobs)
+
+    def apply_async(self, batch, callback=None):
+      """Schedule a func to be run"""
+      sig = joblib_hash(batch)
+      result = self.result_dict.get(sig)
+      if result is None:
+        self.job_list.append((sig, batch))
+        return JoblibDispatch(self)
+      return JoblibResult(result, callback)
+
+    def configure(self, n_jobs=1, parallel=None, **backend_args):
+      """Reconfigure the backend and return the number of workers. This
+      makes it possible to reuse an existing backend instance for successive
+      independent calls to Parallel with different parameters."""
+
+      if n_jobs == 1:
+        raise FallbackToBackend(SequentialBackend())
+
+      self.parallel = parallel
+      return self.effective_n_jobs(n_jobs)
+
+    def abort_everything(self, ensure_ready=True):
+      # All jobs will be aborted here while they are still processing our backend
+      if ensure_ready:
+        self.configure(n_jobs=self.parallel.n_jobs, parallel=self.parallel,
+                        **self.parallel._backend_args)
+      return
+
+  register_parallel_backend('CMFActivity', CMFActivityBackend)

product/CMFActivity/skins/activity/SQLJoblib_createMessageTable.zsql

+<dtml-comment>
+title:
+connection_id:cmf_activity_sql_connection
+max_rows:1000
+max_cache:0
+cache_time:0
+class_name:
+class_file:
+</dtml-comment>
+<params></params>
+CREATE TABLE message_job (
+  `uid` INT UNSIGNED NOT NULL,
+  `date` DATETIME NOT NULL,
+  `path` VARCHAR(255) NOT NULL,
+  `active_process_uid` INT UNSIGNED NULL,
+  `method_id` VARCHAR(255) NOT NULL,
+  `processing_node` SMALLINT NOT NULL DEFAULT -1,
+  `processing` TINYINT NOT NULL DEFAULT 0,
+  `processing_date` DATETIME,
+  `priority` TINYINT NOT NULL DEFAULT 0,
+  `group_method_id` VARCHAR(255) NOT NULL DEFAULT '',
+  `tag` VARCHAR(255) NOT NULL,
+  `signature` BINARY(16) NOT NULL,
+  `serialization_tag` VARCHAR(255) NOT NULL,
+  `retry` TINYINT UNSIGNED NOT NULL DEFAULT 0,
+  `message` LONGBLOB NOT NULL,
+  PRIMARY KEY (`uid`),
+  KEY (`path`),
+  KEY (`active_process_uid`),
+  KEY (`method_id`),
+  KEY `processing_node_processing` (`processing_node`, `processing`),
+  KEY `processing_node_priority_date` (`processing_node`, `priority`, `date`),
+  KEY `node_group_priority_date` (`processing_node`, `group_method_id`, `priority`, `date`),
+  KEY `serialization_tag_processing_node` (`serialization_tag`, `processing_node`),
+  KEY (`priority`),
+  KEY (`tag`)
+) ENGINE=InnoDB

product/CMFActivity/skins/activity/SQLJoblib_selectDuplicatedLineList.zsql

+<dtml-comment>
+title:
+connection_id:cmf_activity_sql_connection
+max_rows:0
+max_cache:0
+cache_time:0
+class_name:
+class_file:
+</dtml-comment>
+<params>
+path
+method_id
+group_method_id
+signature
+</params>
+SELECT uid FROM
+  message_job
+WHERE
+  processing_node = 0
+  AND path = <dtml-sqlvar path type="string">
+  AND method_id = <dtml-sqlvar method_id type="string">
+  AND group_method_id = <dtml-sqlvar group_method_id type="string">
+  AND signature = <dtml-sqlvar signature type="string">
+FOR UPDATE

product/CMFActivity/skins/activity/SQLJoblib_writeMessage.zsql

+<dtml-comment>
+title:
+connection_id:cmf_activity_sql_connection
+max_rows:1000
+max_cache:100
+cache_time:0
+class_name:
+class_file:
+</dtml-comment>
+<params>
+uid_list
+path_list
+active_process_uid_list
+method_id_list
+message_list
+priority_list
+processing_node_list
+date_list
+group_method_id_list
+tag_list
+signature_list
+serialization_tag_list
+</params>
+INSERT INTO message_job
+(uid, path, active_process_uid, date, method_id, processing_node, processing, priority, group_method_id, tag, signature, serialization_tag, message)
+VALUES
+<dtml-in prefix="loop" expr="_.range(_.len(path_list))">
+<dtml-if sequence-start><dtml-else>,</dtml-if>
+(
+  <dtml-sqlvar expr="uid_list[loop_item]" type="int">,
+  <dtml-sqlvar expr="path_list[loop_item]" type="string">,
+  <dtml-sqlvar expr="active_process_uid_list[loop_item]" type="int" optional>,
+  <dtml-if expr="date_list is not None"><dtml-if expr="date_list[loop_item] is not None"><dtml-sqlvar expr="date_list[loop_item]" type="datetime"><dtml-else>UTC_TIMESTAMP()</dtml-if><dtml-else>UTC_TIMESTAMP()</dtml-if>,
+  <dtml-sqlvar expr="method_id_list[loop_item]" type="string">,
+  <dtml-sqlvar expr="processing_node_list[loop_item]" type="int">,
+  0,
+  <dtml-sqlvar expr="priority_list[loop_item]" type="int">,
+  <dtml-sqlvar expr="group_method_id_list[loop_item]" type="string">,
+  <dtml-sqlvar expr="tag_list[loop_item]" type="string">,
+  <dtml-sqlvar expr="signature_list[loop_item]" type="string">,
+  <dtml-sqlvar expr="serialization_tag_list[loop_item]" type="string">,
+  <dtml-sqlvar expr="message_list[loop_item]" type="string">
+)
+</dtml-in>