Add docker builds for importer and webapp

docker/importer/BUILD.md

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+## How to build the importer docker image
+
+1. Build Limelight
+
+   ```
+   # go to root directory of this repo
+   cd ../..
+   
+   # use docker to build the project
+   sudo docker run --rm -it --user $(id -u):$(id -g) -v `pwd`:`pwd` -w `pwd` --env HOME=. --entrypoint ant mriffle/build-limelight -f ant__build_all_limelight.xml
+   ```
+
+   See https://github.com/yeastrc/limelight-build-docker for more information.
+
+2. Copy importer executable jars into this directory
+
+   ```
+   cd docker/importer
+   cp ../../deploy/limelightImporter_XMLFile_ScanFiles.jar ./
+   cp ../../deploy/limelightRunImporter.jar ./
+   ```
+
+3. Build the Docker image
+
+   ```
+   sudo docker image build -t mriffle/limelight-importer ./
+   ```
+
+   Tag as desired.

docker/importer/Dockerfile

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+FROM amazoncorretto:11-alpine-jdk
+
+COPY db_config_file.properties  /usr/local/bin/
+COPY run_importer_config_file.properties  /usr/local/bin/
+COPY importProxlXML.jar  /usr/local/bin/
+COPY runImportProxlXML.jar  /usr/local/bin/
+
+ENTRYPOINT ["java", "-jar", "/usr/local/bin/runImportProxlXML.jar", "-c", "/usr/local/bin/run_importer_config_file.properties"]

docker/importer/db_config_file.properties

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+
+#  db_config_file.properties
+
+#  Sample config file.
+
+#  Copy this file to the folder 'config_dir__do_not_check_contents_into_git'
+#  and configure it.
+
+#  Then build this Proxl Importer Jar
+
+#username=
+#password=
+#dbHost=
+#dbPort=
+
+
+#  override database names if changed from defaults
+
+proxl.db.name=proxl
+
+# nrseq.db.name=
+
+
+
+###################
+
+##   Non-DB Configuration. 
+
+##    !!!  These Only read if the config file location is passed in on the command line, not embedded in the JAR.
+
+###########
+
+#  Send Scan File location to Spectral Storage Service rather than the file contents
+
+# spectral.storage.send.scan.file.location=
+
+spectral.storage.send.scan.file.location=true
+
+### 
+
+#  Only send if scan file path start with this string.
+#   (Set to match configuration in spectral storage accept value of:  submitted.scan.file.path.restrictions=)
+
+spectral.storage.send.scan.file.location.if.path.starts.with=/data/proxl_upload/
+
+########### 
+

docker/importer/run_importer_config_file.properties

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+
+#  run_importer_config_file.properties
+
+#  Sample config file.
+
+
+#  Wait time until next check for an import to process, in seconds.  Defaults to 5 seconds in the program
+
+wait.time.for.next.check.for.import.to.process=60
+
+
+#  The path including the program for the Java executable.
+
+#    This is required if the java program is not on the PATH for the user that will be running this program.
+#    If java was installed using an installer or package manager, this probably is not required.
+#    If running "java -version" on the command line fails or is the wrong version, 
+
+#java.executable.with.path=
+
+#  importer jar with path
+
+importer.jar.with.path=/usr/local/bin/importProxlXML.jar
+
+
+#  optional importer config file with path if a db_config_file.properties hasn't been rolled into the importer jar 
+#     This string is passed to the importer with the "-c" command line parameter
+
+importer.db.config.file.with.path=/usr/local/bin/db_config_file.properties
+
+#  Optional PID file to track run Importer.  
+#               If used, must match filename/path in scripts:
+#                       z_run__runImportProxlXML.jar_StartBackground_ForRestartIfNotRunningScript.sh
+#                       z_restart_runImportProxlXML.jar_if_not_running.sh
+#importer.pid.file.with.path=
+
+
+#    Example for web app on same machine at TOMCAT HTTP port
+# proxl.web.app.base.url=http://localhost:8080/proxl/
+
+proxl.web.app.base.url=http://proxl:8080/proxl/
+
+#username=
+#password=
+#dbHost=
+#dbPort=
+
+
+#  override database names if changed from defaults
+
+proxl.db.name=proxl
+
+# nrseq.db.name=
+

docker/webapp/BUILD.md

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+## How to build the importer docker image
+
+1. Build Limelight
+
+   ```
+   # go to root directory of this repo
+   cd ../..
+   
+   # use docker to build the project
+   sudo docker run --rm -it --user $(id -u):$(id -g) -v `pwd`:`pwd` -w `pwd` --env HOME=. --entrypoint ant mriffle/build-limelight -f ant__build_all_limelight.xml
+   ```
+
+   See https://github.com/yeastrc/limelight-build-docker for more information.
+
+2. Copy war file into this directory
+
+   ```
+   cd docker/webapp
+   cp ../../deploy/limelight.war ./
+   ```
+
+3. Build the Docker image
+
+   ```
+   sudo docker image build -t mriffle/limelight-webapp ./
+   ```
+
+   Tag as desired.

docker/webapp/Dockerfile

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+FROM tomcat:9-jdk11-corretto
+MAINTAINER Michael Riffle <mriffle@uw.edu>
+
+COPY mysql-connector-java-8.0.26.jar /usr/local/tomcat/lib
+COPY context.xml /usr/local/tomcat/conf
+COPY setenv.sh /usr/local/tomcat/bin
+
+COPY proxl.war /usr/local/tomcat/webapps

docker/webapp/context.xml

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+<?xml version='1.0' encoding='utf-8'?>
+<!--
+  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.
+-->
+<!-- The contents of this file will be loaded for each web application -->
+<Context>
+
+    <!-- Default set of monitored resources -->
+    <WatchedResource>WEB-INF/web.xml</WatchedResource>
+
+    <Resource     name="jdbc/proxl"
+                  auth="Container"
+                  type="javax.sql.DataSource"
+                  factory="org.apache.commons.dbcp2.BasicDataSourceFactory"
+                  maxTotal="300"
+                  maxIdle="200"
+                  minIdle="200"
+                  maxWaitMillis="1000"
+
+                  minEvictableIdleTimeMillis="21600000"
+                  timeBetweenEvictionRunsMillis="30000"
+
+                  validationQuery="select 1 from dual"
+                  testOnBorrow="true"
+
+
+                  username="${PROXL_MYSQL_USER}"
+                  password="${PROXL_MYSQL_PASSWORD}"
+                  driverClassName="com.mysql.jdbc.Driver"
+
+                  url="jdbc:mysql://db:3306/${PROXL_DATABASE_NAME}?autoReconnect=true&amp;useUnicode=true&amp;characterEncoding=UTF-8&amp;characterSetResults=UTF-8"
+    />
+
+</Context>

docker/webapp/setenv.sh

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+JAVA_OPTS="-server -DPROXL_MYSQL_USER=${PROXL_MYSQL_USER}  -DPROXL_MYSQL_PASSWORD=${PROXL_MYSQL_PASSWORD}   -DPROXL_DATABASE_NAME=${PROXL_DATABASE_NAME} "
+
+CATALINA_OPTS="${WEBAPP_JAVA_OPTIONS}"