created SequencerRepair specific dockerfile

Signed-off-by: Javier Ron <[email protected]>

src/Docker_Images/Sequencer_Repair/Dockerfile

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+FROM openjdk:8u252-jdk-slim
+COPY --from=python:3.6-slim / /
+
+WORKDIR /root/sequencer
+
+RUN apt-get update
+RUN apt-get install -y git
+RUN git clone https://github.com/OpenNMT/OpenNMT-py.git tools/OpenNMT-py
+RUN cd tools/OpenNMT-py && python3 setup.py install
+RUN pip3 install javalang
+
+COPY ./docker-sequencer-predict.sh sequencer-predict.sh
+COPY ./tools tools/
+COPY ./models models/

src/Docker_Images/Sequencer_Repair/create-docker-image.sh

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+#!/bin/bash
+
+set -e
+
+mkdir -p tools
+cp ../../Buggy_Context_Abstraction/abstraction/lib/abstraction-1.0-SNAPSHOT-jar-with-dependencies.jar tools/abstraction.jar
+cp ../../Buggy_Context_Abstraction/tokenize.py tools
+cp ../../Buggy_Context_Abstraction/trimCon.pl tools
+cp ../../Patch_Preparation/generatePatches.py tools
+cp ../../Patch_Preparation/postProcessPredictions.py tools
+
+mkdir -p models
+cp ../../../results/Golden/golden-model.pt models/
+
+docker build . --tag javier/sequencer:2.0
+
+rm -rf tools/
+rm -rf models/

src/Docker_Images/Sequencer_Repair/docker-sequencer-predict.sh

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+#!/bin/bash
+
+echo "sequencer-predict.sh start"
+
+CURRENT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+ROOT_DIR="$(dirname "$CURRENT_DIR")"
+
+HELP_MESSAGE=$'Usage: ./sequencer-predict.sh --model=[model path]--buggy_file=[abs path] --buggy_line=[int] --beam_size=[int] --output=[abs path]
+buggy_file: Absolute path to the buggy file
+buggy_line: Line number of buggy line
+beam_size: Beam size used in seq2seq model
+output: Absolute path for output'
+for i in "$@"
+do
+case $i in
+    --buggy_file=*)
+    BUGGY_FILE_PATH="${i#*=}"
+    shift # past argument=value
+    ;;
+    --buggy_line=*)
+    BUGGY_LINE="${i#*=}"
+    shift # past argument=value
+    ;;
+    --beam_size=*)
+    BEAM_SIZE="${i#*=}"
+    shift # past argument=value
+    ;;
+    --output=*)
+    OUTPUT="${i#*=}"
+    shift # past argument=value
+    ;;
+    --real_file_path=*)
+    REAL_FILE_PATH="${i#*=}"
+    shift # past argument=value
+    ;;
+    *)
+          # unknown option
+    ;;
+esac
+done
+
+if [ -z "$BUGGY_FILE_PATH" ]; then
+  echo "BUGGY_FILE_PATH unset!"
+  echo "$HELP_MESSAGE"
+  exit 1
+elif [[ "$BUGGY_FILE_PATH" != /* ]]; then
+  echo "BUGGY_FILE_PATH must be absolute path"
+  echo "$HELP_MESSAGE"
+  exit 1
+fi
+
+if [ -z "$BUGGY_LINE" ]; then
+  echo "BUGGY_LINE unset!"
+  echo "$HELP_MESSAGE"
+  exit 1
+fi
+
+if [ -z "$BEAM_SIZE" ]; then
+  echo "BEAM_SIZE unset!"
+  echo "$HELP_MESSAGE"
+  exit 1
+fi
+
+if [ -z "$OUTPUT" ]; then
+  echo "OUTPUT unset!"
+  echo "$HELP_MESSAGE"
+  exit 1
+elif [[ "$OUTPUT" != /* ]]; then
+  echo "OUTPUT must be absolute path"
+  echo "$HELP_MESSAGE"
+  exit 1
+fi
+
+echo "Input parameter:"
+echo "BUGGY_FILE_PATH = ${BUGGY_FILE_PATH}"
+echo "BUGGY_LINE = ${BUGGY_LINE}"
+echo "BEAM_SIZE = ${BEAM_SIZE}"
+echo "OUTPUT = ${OUTPUT}"
+echo
+
+BUGGY_FILE_NAME=${BUGGY_FILE_PATH##*/}
+BUGGY_FILE_BASENAME=${BUGGY_FILE_NAME%.*}
+
+echo "Creating temporary working folder"
+mkdir -p $CURRENT_DIR/tmp
+echo
+
+echo "Abstracting the source file"
+# the code of abstraction-1.0-SNAPSHOT-jar-with-dependencies.jar is in https://github.com/KTH/sequencer/tree/master/src/Buggy_Context_Abstraction/abstraction
+java -jar ./tools/abstraction.jar $BUGGY_FILE_PATH $BUGGY_LINE $CURRENT_DIR/tmp
+retval=$?
+if [ $retval -ne 0 ]; then
+  echo "Cannot generate abstraction for the buggy file"
+  rm -rf $CURRENT_DIR/tmp
+  exit 1
+fi
+echo
+
+echo "Tokenizing the abstraction"
+python3 ./tools/tokenize.py $CURRENT_DIR/tmp/${BUGGY_FILE_BASENAME}_abstract.java $CURRENT_DIR/tmp/${BUGGY_FILE_BASENAME}_abstract_tokenized.txt
+retval=$?
+if [ $retval -ne 0 ]; then
+  echo "Tokenization failed"
+  rm -rf $CURRENT_DIR/tmp
+  exit 1
+fi
+echo
+
+echo "Truncate the abstraction to 1000 tokens"
+perl ./tools/trimCon.pl $CURRENT_DIR/tmp/${BUGGY_FILE_BASENAME}_abstract_tokenized.txt $CURRENT_DIR/tmp/${BUGGY_FILE_BASENAME}_abstract_tokenized_truncated.txt 1000
+retval=$?
+if [ $retval -ne 0 ]; then
+  echo "Truncation failed"
+  rm -rf $CURRENT_DIR/tmp
+  exit 1
+fi
+echo
+
+echo "Generating predictions"
+python3 ./tools/OpenNMT-py/translate.py -model ./models/golden-model.pt -src $CURRENT_DIR/tmp/${BUGGY_FILE_BASENAME}_abstract_tokenized_truncated.txt -output $CURRENT_DIR/tmp/predictions.txt -beam_size $BEAM_SIZE -n_best $BEAM_SIZE 1>/dev/null
+echo
+
+echo "Post process predictions"
+python3 ./tools/postProcessPredictions.py $CURRENT_DIR/tmp/predictions.txt $CURRENT_DIR/tmp
+retval=$?
+if [ $retval -ne 0 ]; then
+  echo "Post process generates none valid predictions"
+  rm -rf $CURRENT_DIR/tmp
+  exit 1
+fi
+echo
+
+echo "Creating output directory ${OUTPUT}"
+mkdir -p $OUTPUT
+echo
+
+echo "Generating patches"
+python3 ./tools/generatePatches.py $BUGGY_FILE_PATH $BUGGY_LINE $CURRENT_DIR/tmp/predictions_JavaSource.txt $OUTPUT
+echo
+
+echo "Generating diffs"
+for patch in $OUTPUT/*; do
+  echo "--- a/$REAL_FILE_PATH" > $patch/diff
+  echo "+++ b/$REAL_FILE_PATH" >> $patch/diff
+  diff -u -w $BUGGY_FILE_PATH $patch/$BUGGY_FILE_NAME | tail -n +3 >> $patch/diff
+  chmod 777 $patch
+  chmod -R 666 $patch/diff
+done
+echo
+
+chmod 777 $OUTPUT
+
+echo "Cleaning tmp folder"
+rm -rf $CURRENT_DIR/tmp
+echo
+
+echo "Found $(ls $OUTPUT | wc -l | awk '{print $1}') patches for $BUGGY_FILE_NAME stored in $OUTPUT"
+echo "sequencer-predict.sh done"
+echo
+exit 0