fully containerize app; first full attempt and still needs testing

bamboo-specs/pom.xml

@@ -0,0 +1,40 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+
+  <parent>
+    <groupId>com.atlassian.bamboo</groupId>
+    <artifactId>bamboo-specs-parent</artifactId>
+    <version>7.1.2</version>
+    <relativePath/>
+  </parent>
+
+  <artifactId>bamboo-specs</artifactId>
+  <version>1.0.0-SNAPSHOT</version>
+  <packaging>jar</packaging>
+
+  <properties>
+    <sonar.skip>true</sonar.skip>
+  </properties>
+
+  <dependencies>
+    <dependency>
+      <groupId>com.atlassian.bamboo</groupId>
+      <artifactId>bamboo-specs-api</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>com.atlassian.bamboo</groupId>
+      <artifactId>bamboo-specs</artifactId>
+    </dependency>
+
+    <!-- Test dependencies -->
+    <dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <scope>test</scope>
+    </dependency>
+  </dependencies>
+
+  <!-- run 'mvn test' to perform offline validation of the plan -->
+  <!-- run 'mvn -Ppublish-specs' to upload the plan to your Bamboo server -->
+</project>

bamboo-specs/src/main/java/buildjob/PlanSpec.java

@@ -0,0 +1,175 @@
+package buildjob;
+
+import com.atlassian.bamboo.specs.api.BambooSpec;
+import com.atlassian.bamboo.specs.api.builders.BambooKey;
+import com.atlassian.bamboo.specs.api.builders.docker.DockerConfiguration;
+import com.atlassian.bamboo.specs.api.builders.permission.PermissionType;
+import com.atlassian.bamboo.specs.api.builders.permission.Permissions;
+import com.atlassian.bamboo.specs.api.builders.permission.PlanPermissions;
+import com.atlassian.bamboo.specs.api.builders.plan.Job;
+import com.atlassian.bamboo.specs.api.builders.plan.Plan;
+import com.atlassian.bamboo.specs.api.builders.plan.PlanIdentifier;
+import com.atlassian.bamboo.specs.api.builders.plan.Stage;
+import com.atlassian.bamboo.specs.api.builders.plan.branches.BranchCleanup;
+import com.atlassian.bamboo.specs.api.builders.plan.branches.PlanBranchManagement;
+import com.atlassian.bamboo.specs.api.builders.project.Project;
+import com.atlassian.bamboo.specs.builders.task.CheckoutItem;
+import com.atlassian.bamboo.specs.builders.task.InjectVariablesTask;
+import com.atlassian.bamboo.specs.builders.task.ScriptTask;
+import com.atlassian.bamboo.specs.builders.task.VcsCheckoutTask;
+import com.atlassian.bamboo.specs.builders.task.CleanWorkingDirectoryTask;
+import com.atlassian.bamboo.specs.builders.task.VcsTagTask;
+import com.atlassian.bamboo.specs.builders.trigger.BitbucketServerTrigger;
+import com.atlassian.bamboo.specs.model.task.InjectVariablesScope;
+import com.atlassian.bamboo.specs.api.builders.Variable;
+import com.atlassian.bamboo.specs.util.BambooServer;
+import com.atlassian.bamboo.specs.builders.task.ScriptTask;
+import com.atlassian.bamboo.specs.model.task.ScriptTaskProperties.Location;
+
+/**
+ * Plan configuration for Bamboo.
+ * Learn more on: <a href="https://confluence.atlassian.com/display/BAMBOO/Bamboo+Specs">https://confluence.atlassian.com/display/BAMBOO/Bamboo+Specs</a>
+ */
+@BambooSpec
+public class PlanSpec {
+
+    private static final String SERVICE_NAME = "vidocp-base";
+    private static final String SERVICE_NAME_BASE = "vidocp-base";
+
+    private static final String SERVICE_KEY = SERVICE_NAME.toUpperCase().replaceAll("-","").replaceAll("_","");
+
+    /**
+     * Run main to publish plan on Bamboo
+     */
+    public static void main(final String[] args) throws Exception {
+        //By default credentials are read from the '.credentials' file.
+        BambooServer bambooServer = new BambooServer("http://localhost:8085");
+
+        Plan plan = new PlanSpec().createDockerBuildPlan();
+        bambooServer.publish(plan);
+        PlanPermissions planPermission = new PlanSpec().createPlanPermission(plan.getIdentifier());
+        bambooServer.publish(planPermission);
+    }
+
+    private PlanPermissions createPlanPermission(PlanIdentifier planIdentifier) {
+        Permissions permission = new Permissions()
+                .userPermissions("atlbamboo", PermissionType.EDIT, PermissionType.VIEW, PermissionType.ADMIN, PermissionType.CLONE, PermissionType.BUILD)
+                .groupPermissions("research", PermissionType.EDIT, PermissionType.VIEW, PermissionType.CLONE, PermissionType.BUILD)
+                .groupPermissions("Development", PermissionType.EDIT, PermissionType.VIEW, PermissionType.CLONE, PermissionType.BUILD)
+                .groupPermissions("QA", PermissionType.EDIT, PermissionType.VIEW, PermissionType.CLONE, PermissionType.BUILD)
+                .loggedInUserPermissions(PermissionType.VIEW)
+                .anonymousUserPermissionView();
+        return new PlanPermissions(planIdentifier.getProjectKey(), planIdentifier.getPlanKey()).permissions(permission);
+    }
+
+    private Project project() {
+        return new Project()
+                .name("RED")
+                .key(new BambooKey("RED"));
+    }
+
+    public Plan createDockerBuildPlan() {
+    return new Plan(
+            project(),
+            SERVICE_NAME, new BambooKey(SERVICE_KEY))
+            .description("Docker build for vidocp.")
+            // .variables()
+            .stages(new Stage("Build Stage")
+              .jobs(
+                new Job("Build Job", new BambooKey("BUILD"))
+                  .tasks(
+                    new CleanWorkingDirectoryTask()
+                        .description("Clean working directory.")
+                        .enabled(true),
+                    new VcsCheckoutTask()
+                        .description("Checkout default repository.")
+                        .checkoutItems(new CheckoutItem().defaultRepository()),
+                    new ScriptTask()
+                        .description("Set config and keys.")
+                        .inlineBody("mkdir -p ~/.ssh\n" +
+                                    "echo \"${bamboo.bamboo_agent_ssh}\" | base64 -d >> ~/.ssh/id_rsa\n" +
+                                    "echo \"host vector.iqser.com\" > ~/.ssh/config\n" +
+                                    "echo \"    user bamboo-agent\" >> ~/.ssh/config\n" +
+                                    "chmod 600 ~/.ssh/config ~/.ssh/id_rsa"),
+                    new ScriptTask()
+                        .description("Build Docker container.")
+                        .location(Location.FILE)
+                        .fileFromPath("bamboo-specs/src/main/resources/scripts/docker-build.sh")
+                        .argument(SERVICE_NAME + " " + SERVICE_NAME_BASE))
+                  .dockerConfiguration(
+                      new DockerConfiguration()
+                        .image("nexus.iqser.com:5001/infra/release_build:4.2.0")
+                        .volume("/var/run/docker.sock", "/var/run/docker.sock")),
+                new Job("Sonar Job", new BambooKey("SONAR"))
+                  .tasks(
+                    new CleanWorkingDirectoryTask()
+                        .description("Clean working directory.")
+                        .enabled(true),
+                    new VcsCheckoutTask()
+                        .description("Checkout default repository.")
+                        .checkoutItems(new CheckoutItem().defaultRepository()),
+                    new ScriptTask()
+                        .description("Set config and keys.")
+                        .inlineBody("mkdir -p ~/.ssh\n" +
+                                    "echo \"${bamboo.bamboo_agent_ssh}\" | base64 -d >> ~/.ssh/id_rsa\n" +
+                                    "echo \"host vector.iqser.com\" > ~/.ssh/config\n" +
+                                    "echo \"    user bamboo-agent\" >> ~/.ssh/config\n" +
+                                    "chmod 600 ~/.ssh/config ~/.ssh/id_rsa"),
+                    new ScriptTask()
+                        .description("Run Sonarqube scan.")
+                        .location(Location.FILE)
+                        .fileFromPath("bamboo-specs/src/main/resources/scripts/sonar-scan.sh")
+                        .argument(SERVICE_NAME))
+                  .dockerConfiguration(
+                      new DockerConfiguration()
+                        .image("nexus.iqser.com:5001/infra/release_build:4.2.0")
+                        .volume("/var/run/docker.sock", "/var/run/docker.sock"))),
+            new Stage("Licence Stage")
+              .jobs(
+                new Job("Git Tag Job", new BambooKey("GITTAG"))
+                  .tasks(
+                    new VcsCheckoutTask()
+                        .description("Checkout default repository.")
+                        .checkoutItems(new CheckoutItem().defaultRepository()),
+                    new ScriptTask()
+                        .description("Build git tag.")
+                        .location(Location.FILE)
+                        .fileFromPath("bamboo-specs/src/main/resources/scripts/git-tag.sh"),
+                    new InjectVariablesTask()
+                        .description("Inject git tag.")
+                        .path("git.tag")
+                        .namespace("g")
+                        .scope(InjectVariablesScope.LOCAL),
+                    new VcsTagTask()
+                        .description("${bamboo.g.gitTag}")
+                        .tagName("${bamboo.g.gitTag}")
+                        .defaultRepository())
+                .dockerConfiguration(
+                    new DockerConfiguration()
+                        .image("nexus.iqser.com:5001/infra/release_build:2.7.0")),
+                new Job("Licence Job", new BambooKey("LICENCE"))
+                  .enabled(false)
+                  .tasks(
+                    new VcsCheckoutTask()
+                        .description("Checkout default repository.")
+                        .checkoutItems(new CheckoutItem().defaultRepository()),
+                    new ScriptTask()
+                        .description("Build licence.")
+                        .location(Location.FILE)
+                        .fileFromPath("bamboo-specs/src/main/resources/scripts/create-licence.sh"))
+                  .dockerConfiguration(
+                    new DockerConfiguration()
+                        .image("nexus.iqser.com:5001/infra/maven:3.6.2-jdk-13-3.0.0")
+                        .volume("/etc/maven/settings.xml", "/usr/share/maven/ref/settings.xml")
+                        .volume("/var/run/docker.sock", "/var/run/docker.sock"))))
+            .linkedRepositories("RR / " + SERVICE_NAME)
+            .triggers(new BitbucketServerTrigger())
+            .planBranchManagement(new PlanBranchManagement()
+              .createForVcsBranch()
+              .delete(new BranchCleanup()
+                  .whenInactiveInRepositoryAfterDays(14))
+              .notificationForCommitters());
+    }
+
+
+}

bamboo-specs/src/main/resources/scripts/create-licence.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+set -e
+
+if [[ \"${bamboo_version_tag}\" != \"dev\" ]]
+then
+    ${bamboo_capability_system_builder_mvn3_Maven_3}/bin/mvn \
+                    -f ${bamboo_build_working_directory}/pom.xml \
+                    versions:set  \
+                    -DnewVersion=${bamboo_version_tag}
+
+    ${bamboo_capability_system_builder_mvn3_Maven_3}/bin/mvn \
+                    -f ${bamboo_build_working_directory}/pom.xml \
+                    -B clean deploy \
+                    -e -DdeployAtEnd=true \
+                    -Dmaven.wagon.http.ssl.insecure=true \
+                    -Dmaven.wagon.http.ssl.allowall=true \
+                    -Dmaven.wagon.http.ssl.ignore.validity.dates=true \
+                    -DaltDeploymentRepository=iqser_release::default::https://nexus.iqser.com/repository/gin4-platform-releases
+fi

bamboo-specs/src/main/resources/scripts/docker-build.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+set -e
+
+SERVICE_NAME=$1
+SERVICE_NAME_BASE=$2
+
+python3 -m venv build_venv
+source build_venv/bin/activate
+python3 -m pip install --upgrade pip
+
+pip install dvc
+pip install 'dvc[ssh]'
+dvc pull
+
+echo "index-url = https://${bamboo_nexus_user}:${bamboo_nexus_password}@nexus.iqser.com/repository/python-combind/simple" >> pip.conf
+docker build -f Dockerfile_base  -t nexus.iqser.com:5001/red/$SERVICE_NAME_BASE:${bamboo_version_tag} .
+docker build -f Dockerfile  -t nexus.iqser.com:5001/red/$SERVICE_NAME:${bamboo_version_tag} --build-arg VERSION_TAG=${bamboo_version_tag} .
+echo "${bamboo_nexus_password}" | docker login --username "${bamboo_nexus_user}" --password-stdin nexus.iqser.com:5001
+docker push nexus.iqser.com:5001/red/$SERVICE_NAME:${bamboo_version_tag}

bamboo-specs/src/main/resources/scripts/git-tag.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+set -e
+
+if [[ "${bamboo_version_tag}" = "dev" ]]
+then
+    echo "gitTag=${bamboo_planRepository_1_branch}_${bamboo_buildNumber}" > git.tag
+else
+    echo "gitTag=${bamboo_version_tag}" > git.tag
+fi

bamboo-specs/src/main/resources/scripts/sonar-scan.sh

@@ -0,0 +1,61 @@
+#!/bin/bash
+set -e
+
+export JAVA_HOME=/usr/bin/sonar-scanner/jre
+
+python3 -m venv build_venv
+source build_venv/bin/activate
+python3 -m pip install --upgrade pip
+
+echo "dev setup for unit test and coverage"
+
+pip install -e .
+pip install -r requirements.txt
+
+
+echo "DVC pull step"
+dvc pull
+
+echo "coverage calculation"
+coverage run -m pytest
+echo "coverage report generation"
+coverage report -m
+coverage xml
+
+SERVICE_NAME=$1
+
+echo "dependency-check:aggregate"
+mkdir -p reports
+dependency-check --enableExperimental -f JSON -f HTML -f XML \
+  --disableAssembly -s . -o reports --project $SERVICE_NAME --exclude ".git/**" --exclude "venv/**" \
+  --exclude "build_venv/**" --exclude "**/__pycache__/**"
+
+if [[ -z "${bamboo_repository_pr_key}" ]]
+then
+    echo "Sonar Scan for branch: ${bamboo_planRepository_1_branch}"
+    /usr/bin/sonar-scanner/bin/sonar-scanner -X\
+      -Dsonar.projectKey=RED_$SERVICE_NAME \
+      -Dsonar.sources=src,ner \
+      -Dsonar.host.url=https://sonarqube.iqser.com \
+      -Dsonar.login=${bamboo_sonarqube_api_token_secret} \
+      -Dsonar.branch.name=${bamboo_planRepository_1_branch} \
+      -Dsonar.dependencyCheck.jsonReportPath=reports/dependency-check-report.json \
+      -Dsonar.dependencyCheck.xmlReportPath=reports/dependency-check-report.xml \
+      -Dsonar.dependencyCheck.htmlReportPath=reports/dependency-check-report.html \
+      -Dsonar.python.coverage.reportPaths=reports/coverage.xml
+
+else
+    echo "Sonar Scan for PR with key1: ${bamboo_repository_pr_key}"
+    /usr/bin/sonar-scanner/bin/sonar-scanner \
+      -Dsonar.projectKey=RED_$SERVICE_NAME \
+      -Dsonar.sources=src,ner \
+      -Dsonar.host.url=https://sonarqube.iqser.com \
+      -Dsonar.login=${bamboo_sonarqube_api_token_secret} \
+      -Dsonar.pullrequest.key=${bamboo_repository_pr_key} \
+      -Dsonar.pullrequest.branch=${bamboo_repository_pr_sourceBranch} \
+      -Dsonar.pullrequest.base=${bamboo_repository_pr_targetBranch} \
+      -Dsonar.dependencyCheck.jsonReportPath=reports/dependency-check-report.json \
+      -Dsonar.dependencyCheck.xmlReportPath=reports/dependency-check-report.xml \
+      -Dsonar.dependencyCheck.htmlReportPath=reports/dependency-check-report.html \
+      -Dsonar.python.coverage.reportPaths=reports/coverage.xml
+fi

bamboo-specs/src/test/java/buildjob/PlanSpecTest.java

@@ -0,0 +1,16 @@
+package buildjob;
+
+
+import com.atlassian.bamboo.specs.api.builders.plan.Plan;
+import com.atlassian.bamboo.specs.api.exceptions.PropertiesValidationException;
+import com.atlassian.bamboo.specs.api.util.EntityPropertiesBuilders;
+import org.junit.Test;
+
+public class PlanSpecTest {
+    @Test
+    public void checkYourPlanOffline() throws PropertiesValidationException {
+        Plan plan = new PlanSpec().createDockerBuildPlan();
+
+        EntityPropertiesBuilders.build(plan);
+    }
+}

bamboo-specs/target/classes/scripts/create-licence.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+set -e
+
+if [[ \"${bamboo_version_tag}\" != \"dev\" ]]
+then
+    ${bamboo_capability_system_builder_mvn3_Maven_3}/bin/mvn \
+                    -f ${bamboo_build_working_directory}/pom.xml \
+                    versions:set  \
+                    -DnewVersion=${bamboo_version_tag}
+
+    ${bamboo_capability_system_builder_mvn3_Maven_3}/bin/mvn \
+                    -f ${bamboo_build_working_directory}/pom.xml \
+                    -B clean deploy \
+                    -e -DdeployAtEnd=true \
+                    -Dmaven.wagon.http.ssl.insecure=true \
+                    -Dmaven.wagon.http.ssl.allowall=true \
+                    -Dmaven.wagon.http.ssl.ignore.validity.dates=true \
+                    -DaltDeploymentRepository=iqser_release::default::https://nexus.iqser.com/repository/gin4-platform-releases
+fi

bamboo-specs/target/classes/scripts/docker-build.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+set -e
+
+SERVICE_NAME=$1
+SERVICE_NAME_BASE=$2
+
+python3 -m venv build_venv
+source build_venv/bin/activate
+python3 -m pip install --upgrade pip
+
+pip install dvc
+pip install 'dvc[ssh]'
+dvc pull
+
+echo "index-url = https://${bamboo_nexus_user}:${bamboo_nexus_password}@nexus.iqser.com/repository/python-combind/simple" >> pip.conf
+docker build -f Dockerfile_base  -t nexus.iqser.com:5001/red/$SERVICE_NAME_BASE:${bamboo_version_tag} .
+docker build -f Dockerfile  -t nexus.iqser.com:5001/red/$SERVICE_NAME:${bamboo_version_tag} --build-arg VERSION_TAG=${bamboo_version_tag} .
+echo "${bamboo_nexus_password}" | docker login --username "${bamboo_nexus_user}" --password-stdin nexus.iqser.com:5001
+docker push nexus.iqser.com:5001/red/$SERVICE_NAME:${bamboo_version_tag}

bamboo-specs/target/classes/scripts/git-tag.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+set -e
+
+if [[ "${bamboo_version_tag}" = "dev" ]]
+then
+    echo "gitTag=${bamboo_planRepository_1_branch}_${bamboo_buildNumber}" > git.tag
+else
+    echo "gitTag=${bamboo_version_tag}" > git.tag
+fi

bamboo-specs/target/classes/scripts/sonar-scan.sh

@@ -0,0 +1,61 @@
+#!/bin/bash
+set -e
+
+export JAVA_HOME=/usr/bin/sonar-scanner/jre
+
+python3 -m venv build_venv
+source build_venv/bin/activate
+python3 -m pip install --upgrade pip
+
+echo "dev setup for unit test and coverage"
+
+pip install -e .
+pip install -r requirements.txt
+
+
+echo "DVC pull step"
+dvc pull
+
+echo "coverage calculation"
+coverage run -m pytest
+echo "coverage report generation"
+coverage report -m
+coverage xml
+
+SERVICE_NAME=$1
+
+echo "dependency-check:aggregate"
+mkdir -p reports
+dependency-check --enableExperimental -f JSON -f HTML -f XML \
+  --disableAssembly -s . -o reports --project $SERVICE_NAME --exclude ".git/**" --exclude "venv/**" \
+  --exclude "build_venv/**" --exclude "**/__pycache__/**"
+
+if [[ -z "${bamboo_repository_pr_key}" ]]
+then
+    echo "Sonar Scan for branch: ${bamboo_planRepository_1_branch}"
+    /usr/bin/sonar-scanner/bin/sonar-scanner -X\
+      -Dsonar.projectKey=RED_$SERVICE_NAME \
+      -Dsonar.sources=src,ner \
+      -Dsonar.host.url=https://sonarqube.iqser.com \
+      -Dsonar.login=${bamboo_sonarqube_api_token_secret} \
+      -Dsonar.branch.name=${bamboo_planRepository_1_branch} \
+      -Dsonar.dependencyCheck.jsonReportPath=reports/dependency-check-report.json \
+      -Dsonar.dependencyCheck.xmlReportPath=reports/dependency-check-report.xml \
+      -Dsonar.dependencyCheck.htmlReportPath=reports/dependency-check-report.html \
+      -Dsonar.python.coverage.reportPaths=reports/coverage.xml
+
+else
+    echo "Sonar Scan for PR with key1: ${bamboo_repository_pr_key}"
+    /usr/bin/sonar-scanner/bin/sonar-scanner \
+      -Dsonar.projectKey=RED_$SERVICE_NAME \
+      -Dsonar.sources=src,ner \
+      -Dsonar.host.url=https://sonarqube.iqser.com \
+      -Dsonar.login=${bamboo_sonarqube_api_token_secret} \
+      -Dsonar.pullrequest.key=${bamboo_repository_pr_key} \
+      -Dsonar.pullrequest.branch=${bamboo_repository_pr_sourceBranch} \
+      -Dsonar.pullrequest.base=${bamboo_repository_pr_targetBranch} \
+      -Dsonar.dependencyCheck.jsonReportPath=reports/dependency-check-report.json \
+      -Dsonar.dependencyCheck.xmlReportPath=reports/dependency-check-report.xml \
+      -Dsonar.dependencyCheck.htmlReportPath=reports/dependency-check-report.html \
+      -Dsonar.python.coverage.reportPaths=reports/coverage.xml
+fi

requirements.txt

@@ -2,8 +2,13 @@ opencv-python~=4.5.5.62
 numpy~=1.22.1
 pdf2image~=1.16.0
 matplotlib~=3.5.1
-imutils==0.5.4
-iteration-utilities==0.11.0
+imutils~=0.5.4
+iteration-utilities~=0.11.0
 dvc==2.9.3
 dvc[ssh]
 scipy~=1.8.0
+PyYAML~=6.0
+Flask~=2.0
+waitress~=2.0
+pytest~=6.2
+envyaml~=1.8

src/run_service.py

@@ -1,6 +1,87 @@
 import argparse
 import json
 import logging
+from flask import Flask, request, jsonify
+from waitress import serve
+
+from vidocp.utils import preprocess #TODO
+from vidocp.table_parsing import parse_table#, detect_tables_in_pdf
+from vidocp.redaction_detection import find_redactions#, detect_redactions_in_pdf
+from vidocp.layout_parsing import parse_layout#, detect_layout_in_pdf #TODO
+from vidocp.figure_detection import detect_figures#, detect_figures_in_pdf #TODO
+from vidocp.utils.logging import logger
+from vidocp.config import CONFIG
+
+
+def suppress_user_warnings():
+    import warnings
+    warnings.filterwarnings("ignore")
+
+
+def parse_args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--warnings", action="store_true", default=False)
+    args = parser.parse_args()
+
+    return args
+
+
+def main(args):
+
+    if not args.warnings:
+        suppress_user_warnings()
+
+    run_server()
+
+
+def run_server():
+    app = Flask(__name__)
+
+    @app.route("/", methods=["POST"])
+    def predict_request():
+        def inner():
+            data = request.data
+            logger.info(f"<3 Received data.")
+            #section_text = json.loads(data)
+            logger.info(f"Processing data. <3")
+            predictions = make_predictions(data)
+            return jsonify({"result": predictions})
+        try:
+            return inner()
+        except Exception as err:
+            logger.warning("Analysis failed")
+            logger.exception(err)
+            resp = jsonify("Analysis failed")
+            resp.status_code = 500
+            return resp
+
+    @app.route("/status", methods=["GET"])
+    def status():
+        response = "OK"
+        return jsonify(response)
+
+    #predictor = initialize_predictor()
+    #logger.info("<3 Predictor ready.")
+
+    mode = CONFIG.webserver.mode
+    if mode == "development":
+        app.run(host=CONFIG.webserver.host, port=CONFIG.webserver.port, debug=True)
+    elif mode == "production":
+        serve(app, host=CONFIG.webserver.host, port=CONFIG.webserver.port)
+
+
+def make_predictions(pdf_data, page_index):
+    pdf = preprocess(pdf_data[page_index])
+    tables = parse_table(pdf)
+    redactions = find_redactions(pdf)
+    layout = parse_layout(pdf)
+    figure = detect_figures(pdf)
+    return jsonify({"tables": tables,
+                    "redactions": redactions,
+                    "layout": layout,
+                    "figure": figure})
+
+
 """
 from tkinter import W
 

vidocp/config.py

@@ -0,0 +1,36 @@
+"""Implements a config object with dot-indexing syntax."""
+
+
+from envyaml import EnvYAML
+from vidocp.locations import CONFIG_FILE
+
+
+def _get_item_and_maybe_make_dotindexable(container, item):
+    ret = container[item]
+    return DotIndexable(ret) if isinstance(ret, dict) else ret
+
+
+class DotIndexable:
+    def __init__(self, x):
+        self.x = x
+
+    def __getattr__(self, item):
+        return _get_item_and_maybe_make_dotindexable(self.x, item)
+
+    def __setitem__(self, key, value):
+        self.x[key] = value
+
+    def __repr__(self):
+        return self.x.__repr__()
+
+
+class Config:
+    def __init__(self, config_path):
+        self.__config = EnvYAML(config_path)
+
+    def __getattr__(self, item):
+        if item in self.__config:
+            return _get_item_and_maybe_make_dotindexable(self.__config, item)
+
+    def __getitem__(self, item):
+        return self.__getattr__(item)

vidocp/locations.py

@@ -0,0 +1,14 @@
+"""Defines constant paths relative to the module root path."""
+
+
+from os import path
+
+MODULE_DIR = path.dirname(path.abspath(__file__))
+PACKAGE_ROOT_DIR = path.dirname(MODULE_DIR)
+
+CONFIG_FILE = path.join(PACKAGE_ROOT_DIR, "config.yaml")
+LOG_FILE = "/tmp/log.log"
+
+DVC_DATA_DIR = path.join(PACKAGE_ROOT_DIR, "data")
+
+TEST_DATA_DIR = path.join(PACKAGE_ROOT_DIR, "test", "test_data")

vidocp/table_parsig.py

@@ -75,7 +75,6 @@ def annotate_table(image, parsed_tables):
     return image
 
 
-
 def filter_unconnected_cells(stats):
     filtered_cells = []
     # print(stats)

vidocp/utils/logging.py

@@ -0,0 +1,22 @@
+"""Defines the default logger for the service."""
+
+
+import sys
+import logging
+
+from vidocp.config import CONFIG
+
+def get_logger():
+    logger = logging.getLogger(__name__)
+    logger.setLevel(logging.getLevelName(CONFIG.service.logging_level))
+    formatter = logging.Formatter(fmt="%(asctime)s %(levelname)s: %(message)s", datefmt="%d.%m.%Y - %H:%M:%S")
+
+    ch = logging.StreamHandler(sys.stdout)
+    ch.setLevel(logging.getLevelName(CONFIG.service.logging_level))
+    ch.setFormatter(formatter)
+
+    logger.addHandler(ch)
+    logger.propagate = False
+    return logger
+
+logger = get_logger()