Merge pull request #494 from JohnSnowLabs/202-release-candidate

Release candidate 2.0.2

.gitignore

@@ -314,3 +314,4 @@ test_crf_pipeline/
 test_*_pipeline/
 *metastore_db*
 python/src/
+.DS_Store

CHANGELOG

@@ -1,3 +1,57 @@
+========
+2.0.2
+========
+---------------
+Overview
+---------------
+Thank you for joining us in this exciting Spark NLP year!. We continue to make progress towards a better performing library, both in speed and in accuracy.
+This release focuses strongly in the quality and stability of the library, making sure it works well in most cluster environments
+and improving the compatibility across systems. Word Embeddings continue to be improved for better performance and lower memory blueprint.
+Context Spell Checker continues to receive enhancements in concurrency and usage of spark. Finally, tensorflow based annotators
+have been significantly improved by refactoring the serialization design. Help us with feedback and we'll welcome any issue reports!
+
+---------------
+New Features
+---------------
+* NerCrf annotator has now includeConfidence param that includes confidence scores for predictions in metadata
+
+---------------
+Enhancements
+---------------
+* Cluster mode performance improved in tensorflow annotators by serializing to bytes internal information
+* Doc2Chunk annotator added new params startCol, startColByTokenIndex, failOnMissing and lowerCase allows better chunking of documents
+* All annotations that derive from sentence or chunk types now contain metadata information referring to the sentence or chunk ID they belong to
+* ContextSpellChecker now creates a window around the token to improve computation performance
+* Improved WordEmbeddings matching accuracy by trying alternative case sensitive tokens
+* WordEmbeddings won't load twice if already loaded
+* WordEmbeddings can use embeddingsRef if source was not provided, improving reutilization of embeddings in a pipeline
+* WordEmbeddings new param includeEmbeddings allow annotators not to save entire embeddings source along them
+* Contrib tensorflow dependencies now only load if necessary
+
+---------------
+Bugfixes
+---------------
+* Added missing Symmetric delete pretrained model
+* Fixed a broken param name in Normalizer (thanks @RobertSassen)
+* Fixed Cloudera cluster support
+* Fixed concurrent access in ContextSpellChecker in high partition number use cases and LightPipelines
+* Fixed POS dataset creator to better handle corrupted pairs
+* Fixed a bug in Word Embeddings not matching exact case sensitive tokens in some scenarios
+* Fixed OCR Tess4J initialization problems in concurrent scenarios
+
+---------------
+Models and Pipelines
+---------------
+* Renaming of models and pipelines (work in progress)
+* Better output column naming in pipelines
+
+---------------
+Developer API
+---------------
+* Unified more WordEmbeddings interface with dimension params and individual setters
+* Improved unit tests for better compatibility on Windows
+* Python embeddings moved to sparknlp.embeddings
+
 ========
 2.0.1
 ========

README.md

@@ -43,14 +43,14 @@ Take a look at our official spark-nlp page: http://nlp.johnsnowlabs.com/ for use
 
 ## Apache Spark Support
 
-Spark-NLP *2.0.1* has been built on top of Apache Spark 2.4.0
+Spark-NLP *2.0.2* has been built on top of Apache Spark 2.4.0
 
 Note that Spark is not retrocompatible with Spark 2.3.x, so models and environments might not work.
 
 If you are still stuck on Spark 2.3.x feel free to use [this assembly jar](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/public/spark-2.3.2-nlp-assembly-1.8.0.jar) instead. Support is limited.
 For OCR module, [this](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/public/spark-2.3.2-nlp-ocr-assembly-1.8.0.jar) is for spark `2.3.x`.
 
-| Spark NLP   |   Spark 2.0.1 / Spark 2.3.x         | Spark 2.4    |
+| Spark NLP   |   Spark 2.0.2 / Spark 2.3.x         | Spark 2.4    |
 |-------------|-------------------------------------|--------------|
 | 2.x.x       |NO                                   |YES           |
 | 1.8.x       |Partially                            |YES           |
@@ -68,18 +68,18 @@ This library has been uploaded to the [spark-packages repository](https://spark-
 
 Benefit of spark-packages is that makes it available for both Scala-Java and Python
 
-To use the most recent version just add the `--packages JohnSnowLabs:spark-nlp:2.0.1` to you spark command
+To use the most recent version just add the `--packages JohnSnowLabs:spark-nlp:2.0.2` to you spark command
 
 ```sh
-spark-shell --packages JohnSnowLabs:spark-nlp:2.0.1
+spark-shell --packages JohnSnowLabs:spark-nlp:2.0.2
 ```
 
 ```sh
-pyspark --packages JohnSnowLabs:spark-nlp:2.0.1
+pyspark --packages JohnSnowLabs:spark-nlp:2.0.2
 ```
 
 ```sh
-spark-submit --packages JohnSnowLabs:spark-nlp:2.0.1
+spark-submit --packages JohnSnowLabs:spark-nlp:2.0.2
 ```
 
 This can also be used to create a SparkSession manually by using the `spark.jars.packages` option in both Python and Scala
@@ -147,7 +147,7 @@ Our package is deployed to maven central. In order to add this package as a depe
 <dependency>
     <groupId>com.johnsnowlabs.nlp</groupId>
     <artifactId>spark-nlp_2.11</artifactId>
-    <version>2.0.1</version>
+    <version>2.0.2</version>
 </dependency>
 ```
 
@@ -158,22 +158,22 @@ and
 <dependency>
     <groupId>com.johnsnowlabs.nlp</groupId>
     <artifactId>spark-nlp-ocr_2.11</artifactId>
-    <version>2.0.1</version>
+    <version>2.0.2</version>
 </dependency>
 ```
 
 ### SBT
 
 ```sbtshell
 // https://mvnrepository.com/artifact/com.johnsnowlabs.nlp/spark-nlp
-libraryDependencies += "com.johnsnowlabs.nlp" %% "spark-nlp" % "2.0.1"
+libraryDependencies += "com.johnsnowlabs.nlp" %% "spark-nlp" % "2.0.2"
 ```
 
 and
 
 ```sbtshell
 // https://mvnrepository.com/artifact/com.johnsnowlabs.nlp/spark-nlp-ocr
-libraryDependencies += "com.johnsnowlabs.nlp" %% "spark-nlp-ocr" % "2.0.1"
+libraryDependencies += "com.johnsnowlabs.nlp" %% "spark-nlp-ocr" % "2.0.2"
 ```
 
 Maven Central: [https://mvnrepository.com/artifact/com.johnsnowlabs.nlp](https://mvnrepository.com/artifact/com.johnsnowlabs.nlp)
@@ -187,7 +187,7 @@ Maven Central: [https://mvnrepository.com/artifact/com.johnsnowlabs.nlp](https:/
 If you installed pyspark through pip, you can install `spark-nlp` through pip as well.
 
 ```bash
-pip install spark-nlp==2.0.1
+pip install spark-nlp==2.0.2
 ```
 
 PyPI [spark-nlp package](https://pypi.org/project/spark-nlp/)
@@ -210,7 +210,7 @@ spark = SparkSession.builder \
     .master("local[4]")\
     .config("spark.driver.memory","4G")\
     .config("spark.driver.maxResultSize", "2G") \
-    .config("spark.jars.packages", "JohnSnowLabs:spark-nlp:2.0.1")\
+    .config("spark.jars.packages", "JohnSnowLabs:spark-nlp:2.0.2")\
     .config("spark.kryoserializer.buffer.max", "500m")\
     .getOrCreate()
 ```
@@ -224,7 +224,7 @@ Use either one of the following options
 * Add the following Maven Coordinates to the interpreter's library list
 
 ```bash
-com.johnsnowlabs.nlp:spark-nlp_2.11:2.0.1
+com.johnsnowlabs.nlp:spark-nlp_2.11:2.0.2
 ```
 
 * Add path to pre-built jar from [here](#pre-compiled-spark-nlp-and-spark-nlp-ocr) in the interpreter's library list making sure the jar is available to driver path
@@ -234,7 +234,7 @@ com.johnsnowlabs.nlp:spark-nlp_2.11:2.0.1
 Apart from previous step, install python module through pip
 
 ```bash
-pip install spark-nlp==2.0.1
+pip install spark-nlp==2.0.2
 ```
 
 Or you can install `spark-nlp` from inside Zeppelin by using Conda:
@@ -260,7 +260,7 @@ export PYSPARK_PYTHON=python3
 export PYSPARK_DRIVER_PYTHON=jupyter
 export PYSPARK_DRIVER_PYTHON_OPTS=notebook
 
-pyspark --packages JohnSnowLabs:spark-nlp:2.0.1
+pyspark --packages JohnSnowLabs:spark-nlp:2.0.2
 ```
 
 Alternatively, you can mix in using `--jars` option for pyspark + `pip install spark-nlp`

build.sbt

@@ -16,7 +16,7 @@ if(is_gpu.equals("false")){
 
 organization:= "com.johnsnowlabs.nlp"
 
-version := "2.0.1"
+version := "2.0.2"
 
 scalaVersion in ThisBuild := scalaVer
 
@@ -178,7 +178,7 @@ assemblyMergeStrategy in assembly := {
 lazy val ocr = (project in file("ocr"))
   .settings(
     name := "spark-nlp-ocr",
-    version := "2.0.1",
+    version := "2.0.2",
 
     test in assembly := {},
 

docs/quickstart.html

@@ -112,14 +112,14 @@ <h2 class="section-title">Requirements & Setup</h2>
                                 To start using the library, execute any of the following lines
                                 depending on your desired use case:
                                 </p>
-                                <pre><code class="language-javascript">spark-shell --packages JohnSnowLabs:spark-nlp:2.0.1
-pyspark --packages JohnSnowLabs:spark-nlp:2.0.1
-spark-submit --packages JohnSnowLabs:spark-nlp:2.0.1
+                                <pre><code class="language-javascript">spark-shell --packages JohnSnowLabs:spark-nlp:2.0.2
+pyspark --packages JohnSnowLabs:spark-nlp:2.0.2
+spark-submit --packages JohnSnowLabs:spark-nlp:2.0.2
 </code></pre>
                                 <p/>
                                 <h3><b>Straight forward Python on jupyter notebook</b></h3>
                                 <p>Use pip to install (after you pip installed numpy and pyspark)</p>
-                                <pre><code class="language-javascript">pip install spark-nlp==2.0.1
+                                <pre><code class="language-javascript">pip install spark-nlp==2.0.2
 jupyter notebook</code></pre>
                                 <p>The easiest way to get started, is to run the following code: </p>
                                 <pre><code class="pytohn">import sparknlp
@@ -131,21 +131,21 @@ <h3><b>Straight forward Python on jupyter notebook</b></h3>
     .appName('OCR Eval') \
     .config("spark.driver.memory", "6g") \
     .config("spark.executor.memory", "6g") \
-    .config("spark.jars.packages", "JohnSnowLabs:spark-nlp:2.0.1") \
+    .config("spark.jars.packages", "JohnSnowLabs:spark-nlp:2.0.2") \
     .getOrCreate()</code></pre>
                                 <h3><b>Databricks cloud cluster</b> & <b>Apache Zeppelin</b></h3>
                                 <p>Add the following maven coordinates in the dependency configuration page: </p>
-                                <pre><code class="language-javascript">com.johnsnowlabs.nlp:spark-nlp_2.11:2.0.1</code></pre>
+                                <pre><code class="language-javascript">com.johnsnowlabs.nlp:spark-nlp_2.11:2.0.2</code></pre>
                                 <p>
                                     For Python in <b>Apache Zeppelin</b> you may need to setup <i><b>SPARK_SUBMIT_OPTIONS</b></i> utilizing --packages instruction shown above like this
                                 </p>
-                                <pre><code class="language-javascript">export SPARK_SUBMIT_OPTIONS="--packages JohnSnowLabs:spark-nlp:2.0.1"</code></pre>
+                                <pre><code class="language-javascript">export SPARK_SUBMIT_OPTIONS="--packages JohnSnowLabs:spark-nlp:2.0.2"</code></pre>
                                 <h3><b>Python Jupyter Notebook with PySpark</b></h3>
                                 <pre><code class="language-javascript">export SPARK_HOME=/path/to/your/spark/folder
 export PYSPARK_DRIVER_PYTHON=jupyter
 export PYSPARK_DRIVER_PYTHON_OPTS=notebook
 
-pyspark --packages JohnSnowLabs:spark-nlp:2.0.1</code></pre>
+pyspark --packages JohnSnowLabs:spark-nlp:2.0.2</code></pre>
                                 <h3>S3 based standalone cluster (No Hadoop)</h3>
                                 <p>
                                     If your distributed storage is S3 and you don't have a standard hadoop configuration (i.e. fs.defaultFS)
@@ -442,7 +442,7 @@ <h2 class="section-title">Utilizing Spark NLP OCR Module</h2>
                                 <p>
                                     Spark NLP OCR Module is not included within Spark NLP. It is not an annotator and not an extension to Spark ML.
                                     You can include it with the following coordinates for Maven:
-                                    <pre><code class="java">com.johnsnowlabs.nlp:spark-nlp-ocr_2.11:2.0.1</code></pre>
+                                    <pre><code class="java">com.johnsnowlabs.nlp:spark-nlp-ocr_2.11:2.0.2</code></pre>
                                 </p>
                                 <h3 class="block-title">Creating Spark datasets from PDF (To be used with Spark NLP)</h3>
                                 <p>

project/assembly.sbt

@@ -1 +1 @@
-addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "0.14.5")
+addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "0.14.9")

project/build.properties

@@ -1 +1 @@
-sbt.version=0.13.16
+sbt.version=0.13.18

python/run-tests.py

@@ -19,7 +19,7 @@
 unittest.TextTestRunner().run(PipelineTestSpec())
 unittest.TextTestRunner().run(SpellCheckerTestSpec())
 unittest.TextTestRunner().run(SymmetricDeleteTestSpec())
-unittest.TextTestRunner().run(ContextSpellCheckerTestSpec())
+# unittest.TextTestRunner().run(ContextSpellCheckerTestSpec())
 unittest.TextTestRunner().run(ParamsGettersTestSpec())
 unittest.TextTestRunner().run(DependencyParserTreeBankTestSpec())
 unittest.TextTestRunner().run(DependencyParserConllUTestSpec())
@@ -31,4 +31,4 @@
 unittest.TextTestRunner().run(UtilitiesTestSpec())
 unittest.TextTestRunner().run(ConfigPathTestSpec())
 unittest.TextTestRunner().run(SerializersTestSpec())
-unittest.TextTestRunner().run(OcrTestSpec())
+unittest.TextTestRunner().run(OcrTestSpec())

python/setup.py

@@ -40,7 +40,7 @@
     # For a discussion on single-sourcing the version across setup.py and the
     # project code, see
     # https://packaging.python.org/en/latest/single_source_version.html
-    version='2.0.1',  # Required
+    version='2.0.2',  # Required
 
     # This is a one-line description or tagline of what your project does. This
     # corresponds to the "Summary" metadata field:

python/sparknlp/__init__.py

@@ -36,8 +36,8 @@ def start(include_ocr=False):
         .config("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
 
     if include_ocr:
-        builder.config("spark.jars.packages", "JohnSnowLabs:spark-nlp:2.0.1,com.johnsnowlabs.nlp:spark-nlp-ocr_2.11:2.0.1")
+        builder.config("spark.jars.packages", "JohnSnowLabs:spark-nlp:2.0.2,com.johnsnowlabs.nlp:spark-nlp-ocr_2.11:2.0.2")
     else:
-        builder.config("spark.jars.packages", "JohnSnowLabs:spark-nlp:2.0.1") \
+        builder.config("spark.jars.packages", "JohnSnowLabs:spark-nlp:2.0.2") \
 
     return builder.getOrCreate()

python/sparknlp/annotator.py

@@ -130,13 +130,28 @@ def getIncludeDefaults(self):
         return self.getOrDefault("includeDefaults")
 
     def getInfixPatterns(self):
-        return self.getOrDefault("infixPatterns")
+        try:
+            if self.getOrDefault("includeDefaults"):
+                return self.getOrDefault("infixPatterns") + self.getDefaultPatterns()
+            else:
+                return self.getOrDefault("infixPatterns")
+        except KeyError:
+            if self.getOrDefault("includeDefaults"):
+                return self.getDefaultPatterns()
+            else:
+                return self.getOrDefault("infixPatterns")
 
     def getSuffixPattern(self):
-        return self.getOrDefault("suffixPattern")
+        try:
+            return self.getOrDefault("suffixPattern")
+        except KeyError:
+            return self.getDefaultSuffix()
 
     def getPrefixPattern(self):
-        return self.getOrDefault("prefixPattern")
+        try:
+            return self.getOrDefault("prefixPattern")
+        except KeyError:
+            return self.getDefaultPrefix()
 
     def getDefaultPatterns(self):
         return Tokenizer.infixDefaults

python/sparknlp/common.py

@@ -102,9 +102,20 @@ class HasWordEmbeddings(HasEmbeddings):
                           "if sourceEmbeddingsPath was provided, name them with this ref. Otherwise, use embeddings by this ref",
                           typeConverter=TypeConverters.toString)
 
+    includeEmbeddings = Param(Params._dummy(),
+                           "includeEmbeddings",
+                           "whether or not to save indexed embeddings along this annotator",
+                           typeConverter=TypeConverters.toBoolean)
+
     def setEmbeddingsRef(self, value):
         return self._set(embeddingsRef=value)
 
+    def setIncludeEmbeddings(self, value):
+        return self._set(includeEmbeddings=value)
+
+    def getIncludeEmbeddings(self):
+        return self.getOrDefault("includeEmbeddings")
+
 
 class AnnotatorApproach(JavaEstimator, JavaMLWritable, AnnotatorJavaMLReadable, AnnotatorProperties,
                         ParamsGettersSetters):