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Posted to dev@pirk.apache.org by wraydulany <gi...@git.apache.org> on 2016/10/07 20:29:20 UTC
[GitHub] incubator-pirk pull request #107: [WIP] PIRK-45 Remove dependency on Java se...
GitHub user wraydulany opened a pull request:
https://github.com/apache/incubator-pirk/pull/107
[WIP] PIRK-45 Remove dependency on Java serialization
This is a WIP (do not merge) for adding in JSON serialization. I can't get this WIP to pass the elasticsearch spark streaming tests on my cluster.
I'm fairly sure that this is a configuration problem on my end (the errors I get appear to be such), but I'm having little luck resolving them, and would love it if some of the community could give it a test.
I've left in Java Serialization for now, but I've made JSON serialization the default.
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/wraydulany/incubator-pirk PIRK-45
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/incubator-pirk/pull/107.patch
To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:
This closes #107
----
commit c2c6af2465e21cd706c8cfd0dc4f95f7746d86f0
Author: Walter Ray-Dulany <ra...@gmail.com>
Date: 2016-09-28T15:13:12Z
Initial start on moving away from Java object serialization.
commit 66235a9c6ac07e3cec6a94c0874b40bf6624192e
Author: Walter Ray-Dulany <ra...@gmail.com>
Date: 2016-09-29T17:02:17Z
Initial work.
commit 03b4964c2b25538aaecfdcd56a408bcba8154688
Author: Walter Ray-Dulany <ra...@gmail.com>
Date: 2016-10-01T17:20:09Z
Merge branch 'master' of https://github.com/wraydulany/incubator-pirk into PIRK-45
commit de01c5ad1e670200cefa6c7dfc2b678cb245eaf6
Author: Walter Ray-Dulany <ra...@gmail.com>
Date: 2016-10-01T17:21:27Z
Merge branch 'master' of https://github.com/wraydulany/incubator-pirk into PIRK-45
commit 7b221de870f7efc8b41ec52fd5d05af06360c405
Author: Walter Ray-Dulany <ra...@gmail.com>
Date: 2016-10-04T18:24:18Z
Added deserializer for query; I think I should delete the serializer for QueryInfo.
commit fdeb7d77117691f7dda63a2a180d805861216893
Author: Walter Ray-Dulany <ra...@gmail.com>
Date: 2016-10-04T19:21:22Z
Query serialization seems to be working now; at least it doesn't fail to get recalled.
commit b31afcfe7f01ebda6a19e27b5e651f8dc8763f16
Author: Walter Ray-Dulany <ra...@gmail.com>
Date: 2016-10-04T19:42:20Z
Response deserializer compiles.
commit 42e2bb6082a601e5e503e76170499baff37fc478
Author: Walter Ray-Dulany <ra...@gmail.com>
Date: 2016-10-05T12:31:51Z
Custom deserializers complete, as are class amendments to make them work.
commit 603fcaa777f754dbf60836a8a81b7239b39ae494
Author: Walter Ray-Dulany <ra...@gmail.com>
Date: 2016-10-05T14:29:21Z
Merge remote-tracking branch 'upstream/master' into PIRK-45
commit fbebc4adafefa640e5b0339d2423abdabed9b0b3
Author: Walter Ray-Dulany <ra...@gmail.com>
Date: 2016-10-05T15:59:55Z
Needed to add a new constructor for QueryInfo so as to not depend on the existence of a populated QuerySchemaRegistry.
commit b9caf260f14405705864ba200d993057a7040416
Author: Walter Ray-Dulany <ra...@gmail.com>
Date: 2016-10-06T12:16:34Z
Move to gson breaks hdfs?
commit dc9fcfd848c89bf59310c0c12284b5bbb72caec4
Author: Walter Ray-Dulany <ra...@gmail.com>
Date: 2016-10-06T12:49:45Z
Working with Gson on two tests; time for distributed tests.
commit 99cddd1981f76569d63add70a6351ba744ca13c9
Author: Walter Ray-Dulany <ra...@gmail.com>
Date: 2016-10-07T20:19:48Z
Merge remote-tracking branch 'upstream/master' into PIRK-45
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[GitHub] incubator-pirk issue #107: [WIP] PIRK-45 Remove dependency on Java serializa...
Posted by wraydulany <gi...@git.apache.org>.
Github user wraydulany commented on the issue:
https://github.com/apache/incubator-pirk/pull/107
Ok, I've expurgated references (import and comment) to jackson in the code, and I've run the style checker against the code i touched.
Additionally, I've investigated the problems with the 1:ES and 1:ESS tests that I'm having, and I'm convinced that they are due to misconfiguration of the cluster I'm testing on.
This passes the build tests and distributed tests 1:J, 1:JS, 1:JSS, 1:SS, and 1:E for me. If anyone has been able to successfully execute the 1:ES and/or 1:ESS tests with this PR *and* fail them, please comment and kill this PR. Otherwise, I'm going to move this from WIP to full PR in the late morning on the US East Coast tomorrow.
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[GitHub] incubator-pirk issue #107: [WIP] PIRK-45 Remove dependency on Java serializa...
Posted by ellisonanne <gi...@git.apache.org>.
Github user ellisonanne commented on the issue:
https://github.com/apache/incubator-pirk/pull/107
A couple of general comments - (1) need to remove the Jackson imports and dependency as it GSON is being used (2) need to format with the Pirk codestyle file.
I'll take a look at the ES issues...
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[GitHub] incubator-pirk pull request #107: [WIP] PIRK-45 Remove dependency on Java se...
Posted by wraydulany <gi...@git.apache.org>.
Github user wraydulany commented on a diff in the pull request:
https://github.com/apache/incubator-pirk/pull/107#discussion_r82467602
--- Diff: src/main/java/org/apache/pirk/query/wideskies/QueryDeserializer.java ---
@@ -0,0 +1,265 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.pirk.query.wideskies;
+
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.deser.std.StdDeserializer;
+import com.google.gson.*;
+import com.google.gson.reflect.TypeToken;
+import org.apache.pirk.schema.query.QuerySchema;
+import org.apache.pirk.schema.query.filter.DataFilter;
+import org.apache.pirk.schema.query.filter.FilterFactory;
+import org.apache.pirk.utils.PIRException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.lang.reflect.Type;
+import java.math.BigInteger;
+import java.util.*;
--- End diff --
Yeah, there are 8 of those. Fixing.
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[GitHub] incubator-pirk pull request #107: [WIP] PIRK-45 Remove dependency on Java se...
Posted by ellisonanne <gi...@git.apache.org>.
Github user ellisonanne commented on a diff in the pull request:
https://github.com/apache/incubator-pirk/pull/107#discussion_r82505750
--- Diff: src/main/java/org/apache/pirk/querier/wideskies/QuerierDeserializer.java ---
@@ -0,0 +1,80 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.pirk.querier.wideskies;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+import com.google.gson.Gson;
+import com.google.gson.JsonDeserializationContext;
+import com.google.gson.JsonDeserializer;
+import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonParseException;
+import com.google.gson.reflect.TypeToken;
+import org.apache.pirk.encryption.Paillier;
+import org.apache.pirk.query.wideskies.Query;
+
+
+import java.lang.reflect.Type;
+import java.math.BigInteger;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Custom deserializer for Querier class for Jackson.
--- End diff --
Need to remove Jackson reference since using GSON
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[GitHub] incubator-pirk pull request #107: PIRK-45 Remove dependency on Java serializ...
Posted by tellison <gi...@git.apache.org>.
Github user tellison commented on a diff in the pull request:
https://github.com/apache/incubator-pirk/pull/107#discussion_r82813654
--- Diff: src/main/java/org/apache/pirk/query/wideskies/Query.java ---
@@ -26,41 +26,51 @@
import java.util.concurrent.ConcurrentHashMap;
import java.util.function.Consumer;
+import com.google.gson.annotations.Expose;
import org.apache.pirk.encryption.ModPowAbstraction;
import org.apache.pirk.serialization.Storable;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Class to hold the PIR query vectors
- *
*/
+
public class Query implements Serializable, Storable
--- End diff --
I assume we can also drop ```implements Serializable``` now too, right?
This instance, and friends elsewhere.
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[GitHub] incubator-pirk pull request #107: [WIP] PIRK-45 Remove dependency on Java se...
Posted by smarthi <gi...@git.apache.org>.
Github user smarthi commented on a diff in the pull request:
https://github.com/apache/incubator-pirk/pull/107#discussion_r82467067
--- Diff: src/main/java/org/apache/pirk/querier/wideskies/QuerierDeserializer.java ---
@@ -0,0 +1,117 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.pirk.querier.wideskies;
+
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.deser.std.StdDeserializer;
+import com.google.gson.*;
--- End diff --
Please avoid using import *.
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[GitHub] incubator-pirk issue #107: [WIP] PIRK-45 Remove dependency on Java serializa...
Posted by wraydulany <gi...@git.apache.org>.
Github user wraydulany commented on the issue:
https://github.com/apache/incubator-pirk/pull/107
Ok, changing to full PR. I should note for the record that the previously-working-for-me Pirk Releases also no longer pass the ES and ESS tests for me, another sign that It's Not My Fault.
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[GitHub] incubator-pirk issue #107: [WIP] PIRK-45 Remove dependency on Java serializa...
Posted by wraydulany <gi...@git.apache.org>.
Github user wraydulany commented on the issue:
https://github.com/apache/incubator-pirk/pull/107
Fixed the `import...*` and also removed some code garbage that i'd commented out, from an earlier attempt to use jackson, an attempt killed by spark and its ancient version of jackson.
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[GitHub] incubator-pirk pull request #107: PIRK-45 Remove dependency on Java serializ...
Posted by tellison <gi...@git.apache.org>.
Github user tellison commented on a diff in the pull request:
https://github.com/apache/incubator-pirk/pull/107#discussion_r82813992
--- Diff: src/main/java/org/apache/pirk/query/wideskies/Query.java ---
@@ -26,41 +26,51 @@
import java.util.concurrent.ConcurrentHashMap;
import java.util.function.Consumer;
+import com.google.gson.annotations.Expose;
import org.apache.pirk.encryption.ModPowAbstraction;
import org.apache.pirk.serialization.Storable;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Class to hold the PIR query vectors
- *
*/
+
public class Query implements Serializable, Storable
{
- private static final long serialVersionUID = 1L;
+ public static final long querySerialVersionUID = 1L;
+
+ // So that we can serialize the version number in gson.
+ @Expose public final long queryVersion = querySerialVersionUID;
private static final Logger logger = LoggerFactory.getLogger(Query.class);
- private final QueryInfo queryInfo; // holds all query info
+ @Expose private final QueryInfo queryInfo; // holds all query info
- private final SortedMap<Integer,BigInteger> queryElements; // query elements - ordered on insertion
+ @Expose private final SortedMap<Integer,BigInteger> queryElements; // query elements - ordered on insertion
// lookup table for exponentiation of query vectors - based on dataPartitionBitSize
// element -> <power, element^power mod N^2>
private Map<BigInteger,Map<Integer,BigInteger>> expTable = new ConcurrentHashMap<>();
// File based lookup table for modular exponentiation
// element hash -> filename containing it's <power, element^power mod N^2> modular exponentiations
- private Map<Integer,String> expFileBasedLookup = new HashMap<>();
+ @Expose private Map<Integer,String> expFileBasedLookup = new HashMap<>();
--- End diff --
Should the hash -> filename map be serialized?
AFAIK it is only used by the responder to compute the results, so I don't think it needs serializing.
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[GitHub] incubator-pirk pull request #107: [WIP] PIRK-45 Remove dependency on Java se...
Posted by wraydulany <gi...@git.apache.org>.
Github user wraydulany commented on a diff in the pull request:
https://github.com/apache/incubator-pirk/pull/107#discussion_r82467453
--- Diff: src/main/java/org/apache/pirk/query/wideskies/QueryDeserializer.java ---
@@ -0,0 +1,265 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.pirk.query.wideskies;
+
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.deser.std.StdDeserializer;
+import com.google.gson.*;
+import com.google.gson.reflect.TypeToken;
+import org.apache.pirk.schema.query.QuerySchema;
+import org.apache.pirk.schema.query.filter.DataFilter;
+import org.apache.pirk.schema.query.filter.FilterFactory;
+import org.apache.pirk.utils.PIRException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.lang.reflect.Type;
+import java.math.BigInteger;
+import java.util.*;
--- End diff --
Yes, indeed, sorry; my IDE has been doing that automatically. Let me go fix all of those.
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[GitHub] incubator-pirk issue #107: PIRK-45 Remove dependency on Java serialization
Posted by ellisonanne <gi...@git.apache.org>.
Github user ellisonanne commented on the issue:
https://github.com/apache/incubator-pirk/pull/107
+1 - looks good to merge
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[GitHub] incubator-pirk pull request #107: [WIP] PIRK-45 Remove dependency on Java se...
Posted by ellisonanne <gi...@git.apache.org>.
Github user ellisonanne commented on a diff in the pull request:
https://github.com/apache/incubator-pirk/pull/107#discussion_r82505758
--- Diff: src/main/java/org/apache/pirk/query/wideskies/Query.java ---
@@ -26,100 +26,103 @@
import java.util.concurrent.ConcurrentHashMap;
import java.util.function.Consumer;
+import com.fasterxml.jackson.annotation.JsonIgnore;
--- End diff --
Need to remove Jackson imports
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[GitHub] incubator-pirk pull request #107: PIRK-45 Remove dependency on Java serializ...
Posted by tellison <gi...@git.apache.org>.
Github user tellison commented on a diff in the pull request:
https://github.com/apache/incubator-pirk/pull/107#discussion_r82814228
--- Diff: src/main/java/org/apache/pirk/query/wideskies/Query.java ---
@@ -114,8 +124,7 @@ public void generateExpTable()
queryElements.values().parallelStream().forEach(new Consumer<BigInteger>()
{
- @Override
- public void accept(BigInteger element)
+ @Override public void accept(BigInteger element)
--- End diff --
IDE formatting wars ;-)
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[GitHub] incubator-pirk pull request #107: [WIP] PIRK-45 Remove dependency on Java se...
Posted by smarthi <gi...@git.apache.org>.
Github user smarthi commented on a diff in the pull request:
https://github.com/apache/incubator-pirk/pull/107#discussion_r82467151
--- Diff: src/main/java/org/apache/pirk/query/wideskies/QueryDeserializer.java ---
@@ -0,0 +1,265 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.pirk.query.wideskies;
+
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.deser.std.StdDeserializer;
+import com.google.gson.*;
+import com.google.gson.reflect.TypeToken;
+import org.apache.pirk.schema.query.QuerySchema;
+import org.apache.pirk.schema.query.filter.DataFilter;
+import org.apache.pirk.schema.query.filter.FilterFactory;
+import org.apache.pirk.utils.PIRException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.lang.reflect.Type;
+import java.math.BigInteger;
+import java.util.*;
--- End diff --
avoid using import *
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[GitHub] incubator-pirk pull request #107: PIRK-45 Remove dependency on Java serializ...
Posted by asfgit <gi...@git.apache.org>.
Github user asfgit closed the pull request at:
https://github.com/apache/incubator-pirk/pull/107
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