update recreate branch with updated restvv

.gitignore

@@ -0,0 +1,18 @@
+#Git ignorance file for variant validator
+#Testing script
+VariantValidator/vvTest.py
+
+# docker config
+configuration/docker.ini
+
+# Log
+rest_api.log
+
+#pycs
+rest_variantValidator/**/*.pyc
+build
+.idea
+dist
+rest_VariantValidator.egg-info
+.DS_Store
+__pycache__

Dockerfile

@@ -1,22 +1,40 @@
+FROM python:3.12.11
 
-FROM python:3.6
+# Set the working directory to /app
+WORKDIR /app
 
-#RUN seqrepo -r ${SEQREPO_DATA_DIR} pull -i ${SEQREPO_DATA_RELEASE}
-#RUN touch ${SEQREPO_DATA_DIR}/testing.txt
+# Copy the current directory contents into the container's /app directory
+COPY . /app
 
-#RUN apt update && apt install -y git
+# Create logging directory
+RUN mkdir /usr/local/share/logs
 
-WORKDIR /app
+# Update apt-get
+RUN apt update
 
-COPY . /app
+# Install apt managed sofware
+RUN apt -y install git \
+    postgresql-client \
+    sqlite3 \
+    php
 
-RUN apt-get update
+# Manage git buffer
+RUN git config http.postBuffer 500000000
 
+# Updrade pip
 RUN pip install --upgrade pip
 
-RUN pip install -r REQUIREMENTS.txt
-
+# Install the tool
 RUN pip install -e .
 
+# Copy the config file into the container home directory
 COPY configuration/docker.ini /root/.variantvalidator
-CMD gunicorn -b 0.0.0.0:8000 app --threads=5 --worker-class=gthread --chdir ./rest_variantValidator/
+
+# Install LOVD Syntax checker
+RUN python -m VariantValidator.bin.setup_lovd_syntax_checker
+
+# Define the entrypoint as an empty command
+ENTRYPOINT []
+
+# Start the container with CMD and set Gunicorn timeout to 600 seconds
+CMD ["gunicorn", "-b", "0.0.0.0:8000", "--timeout", "600", "app", "--threads=5", "--chdir", "./rest_VariantValidator/"]

Jenkinsfile

@@ -0,0 +1,104 @@
+pipeline {
+    agent {
+        docker {
+            image 'docker:24.0.6-git'
+        }
+    }
+
+    environment {
+        CODECOV_TOKEN = credentials('CODECOV_TOKEN_rest_variantvalidator')
+        CONTAINER_SUFFIX = "${BUILD_NUMBER}"
+        DATA_VOLUME = "/root/variantvalidator_data/"
+    }
+
+    stages {
+        stage("Clone Repository Remove dangling docker components and Create Docker Network") {
+            steps {
+                checkout scm
+                sh 'docker system prune --all --volumes --force'
+            }
+        }
+        stage("Switch to Git Branch") {
+            steps {
+                sh "git checkout ${BRANCH_NAME}"
+                sh "git pull"
+            }
+        }
+        stage("Install Docker Compose") {
+            steps {
+                sh 'apk update && apk add docker-compose'
+            }
+        }
+        stage("Check and Create Directories") {
+            steps {
+                script {
+                    sh """
+                        if [ ! -d "${DATA_VOLUME}seqdata" ]; then
+                            mkdir -p ${DATA_VOLUME}seqdata
+                        fi
+
+                        if [ ! -d "${DATA_VOLUME}logs" ]; then
+                            mkdir -p ${DATA_VOLUME}logs
+                        fi
+
+                        ls -l ${DATA_VOLUME}
+                    """
+                }
+            }
+        }
+        stage("Build and Run containers") {
+            steps {
+                script {
+                    sh """
+                        docker-compose --project-name rest-variantvalidator-ci build --no-cache rv-vvta rv-vdb rv-seqrepo rest-variantvalidator
+                        docker-compose --project-name rest-variantvalidator-ci up -d rv-vvta && docker-compose --project-name rest-variantvalidator-ci up -d rv-vdb && docker-compose --project-name rest-variantvalidator-ci up -d rv-seqrepo && docker-compose --project-name rest-variantvalidator-ci up -d rest-variantvalidator
+                    """
+                }
+            }
+        }
+        stage("Connect and run Pytest") {
+            steps {
+                script {
+                    def connectionSuccessful = false
+                    for (int attempt = 1; attempt <= 5; attempt++) {
+                        echo "Attempt $attempt to connect to the database..."
+                        def exitCode = sh(script: '''
+                            docker-compose exec -e PGPASSWORD=uta_admin rest-variantvalidator-${CONTAINER_SUFFIX} psql -U uta_admin -d vvta -h rv-vvta-${CONTAINER_SUFFIX} -p 54321
+                        ''', returnStatus: true)
+
+                        if (exitCode == 0) {
+                            connectionSuccessful = true
+                            echo "Connected successfully! Running tests..."
+                            break
+                        }
+
+                        echo "Connection failed. Waiting for 60 seconds before the next attempt..."
+                        sleep 60
+                    }
+
+                    if (!connectionSuccessful) {
+                        error "All connection attempts failed. Exiting..."
+                    }
+                }
+            }
+        }
+        stage("Run Pytest and Codecov") {
+            steps {
+                script {
+                    sh 'docker-compose exec rest-variantvalidator-${CONTAINER_SUFFIX} pytest --cov=rest_VariantValidator --cov-report=term tests/'
+                    sh 'docker-compose exec rest-variantvalidator-${CONTAINER_SUFFIX} codecov -t $CODECOV_TOKEN -b ${BRANCH_NAME}'
+                }
+            }
+        }
+    }
+
+    post {
+        always {
+            script {
+                sh 'docker-compose down -v'
+                sh 'docker network rm $DOCKER_NETWORK'
+                sh 'docker system prune --all --volumes --force'
+            }
+        }
+    }
+}

README.md

@@ -1,8 +1,12 @@
-# About rest_variantValidator
+# rest_VariantValidator
+[![Build Status](http://127.0.0.1:8080/job/rest_VariantValidator%20CI/job/master/badge/icon)](http://127.0.0.1:8080/job/rest_VariantValidator%20CI/job/master/)
+[![codecov](https://codecov.io/gh/openvar/rest_variantValidator/graph/badge.svg?token=DE92ZVZT3F)](https://codecov.io/gh/openvar/rest_variantValidator)
+
+## About rest_variantValidator
 
 rest_variantValidator is a rest web interface for VariantValidator
 
-# About VariantValidator
+## About VariantValidator
 
 VariantValidator is a user-friendly software tool designed to validate the syntax and 
 parameters of DNA variant descriptions according to the HGVS Sequence Variant 
@@ -47,14 +51,21 @@ Optional software:
 
 For installation instructions please see [INSTALLATION.md](./docs/INSTALLATION.md)
 
-# Operation and configuration
+## Operation and configuration
 
 Please see [MANUAL.md](./docs/MANUAL.md)
 
+# Running in docker
+
+Please see [DOCKER.md](https://github.com/openvar/rest_variantValidator/blob/master/docs/DOCKER.md)
+
 ## License
 
 Please see [LICENSE.txt](LICENSE.txt)
 
+## Terms and conditions of use
+[Terms and conditions can be found here](https://github.com/openvar/variantValidator/blob/master/README.md)
+
 ## Cite us
 
 Hum Mutat. 2017 Oct 1. doi: 10.1002/humu.23348

bin/batch_validator.py

@@ -0,0 +1,101 @@
+import os
+import sys
+import VariantValidator
+vval = VariantValidator.Validator()
+cwd = os.path.dirname(os.path.abspath(__file__))
+
+
+# Check Args
+if len(sys.argv) != 3:
+    print('Too few arguments. The command required is: python bin/batch_validator.py genome_build select_transcripts')
+    exit()
+
+# Check genome_build
+genome_build = sys.argv[1]
+genomes = ['GRCh38', 'hg38', 'GRCh37', 'hg19']
+if genome_build not in genomes:
+    warn = '%s is not a supported genome build' % genome_build
+    print(warn)
+    exit()
+
+select_transcripts = sys.argv[2]
+
+# Loop through file and detect fails
+filepath = cwd.replace('bin', 'batch')
+infile = filepath + '/input.txt'
+outfile = open(filepath + "/output.txt", "w")
+counter = 0
+with open(infile) as fp:
+    variants = fp.readlines()
+    for variant in variants:
+        variant = variant.strip()
+        print(variant)
+        try:
+            validate = vval.validate(variant, genome_build, select_transcripts)
+            validation = validate.format_as_table(with_meta=True)
+            if counter == 0:
+                line_counter = 0
+                for line in validation:
+                    if line_counter == 0:
+                        outfile.write(line + '\n')
+                    elif line_counter == 1:
+                        ln_cat = '\t'.join(line)
+                        outfile.write(ln_cat + '\n')
+                    else:
+                        copy_line = []
+                        for element in line:
+                            if element == '':
+                                copy_line.append('None')
+                            elif element is None:
+                                copy_line.append('None')
+                            else:
+                                copy_line.append(element)
+                        ln_cat = '\t'.join(copy_line)
+                        outfile.write(ln_cat + '\n')
+                    line_counter = line_counter + 1
+            else:
+                line_counter = 0
+                for line in validation:
+                    if line_counter == 0:
+                        pass
+                    elif line_counter == 1:
+                        ln_cat = '\t'.join(line)
+                        pass
+                    else:
+                        copy_line = []
+                        for element in line:
+                            if element == '':
+                                copy_line.append('None')
+                            elif element is None:
+                                copy_line.append('None')
+                            else:
+                                copy_line.append(element)
+                        ln_cat = '\t'.join(copy_line)
+                        outfile.write(ln_cat + '\n')
+                    line_counter = line_counter + 1
+        except VariantValidator.modules.utils.VariantValidatorError as e:
+            outfile.close()
+            print(variant)
+            print(e)
+            exit()
+        counter = counter + 1
+
+print('Processing complete')
+outfile.close()
+
+# <LICENSE>
+# Copyright (C) 2016-2025 VariantValidator Contributors
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+# </LICENSE>

bin/update_vdb.py

@@ -0,0 +1,33 @@
+#! /usr/bin/env python
+
+from VariantValidator import update_vv_db
+import argparse
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--delete', '-d', action='store_true', help='Delete the contents of the current database '
+                                                                    'before updating')
+
+    args = parser.parse_args()
+    if args.delete:
+        print("Deleting current database contents")
+        update_vv_db.delete()
+
+    update_vv_db.update()
+
+# <LICENSE>
+# Copyright (C) 2016-2025 VariantValidator Contributors
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+# </LICENSE>