eva-sub-cli 0.4__tar.gz → 0.4.6__tar.gz

eva_sub_cli-0.4.6/.github/workflows/publish.yml

@@ -0,0 +1,51 @@
+name: Publish Python Package
+
+on:
+  push:
+    tags:
+      - '**'
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9"]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: pip
+        cache-dependency-path: '**/pyproject.toml'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest
+        python -m pip install .
+    - name: Run tests
+      run: |
+        PYTHONPATH=. pytest tests -k "not integration"
+  deploy:
+    runs-on: ubuntu-latest
+    needs: [test]
+    environment: release
+    permissions:
+      id-token: write
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.9'
+        cache: pip
+        cache-dependency-path: '**/pyproject.toml'
+    - name: Install dependencies
+      run: |
+        pip install setuptools wheel build
+    - name: Build
+      run: |
+        python -m build
+    - name: Publish
+      uses: pypa/gh-action-pypi-publish@release/v1

eva_sub_cli-0.4.6/PKG-INFO

@@ -0,0 +1,213 @@
+Metadata-Version: 2.4
+Name: eva_sub_cli
+Version: 0.4.6
+Summary: EBI EVA - validation and submission command line tool
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Communications :: File Sharing
+Classifier: License :: OSI Approved :: Apache Software License
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: ebi_eva_common_pyutils==0.*,>0.6.11
+Requires-Dist: jinja2==3.*,>=3.0.0
+Requires-Dist: jsonschema==4.*
+Requires-Dist: openpyxl==3.*
+Requires-Dist: pyyaml==6.*
+Requires-Dist: requests==2.*
+Dynamic: license-file
+
+# eva-sub-cli
+The eva-sub-cli tool is a command line interface tool for data validation and upload. The tool transforms the submission process at EVA by enabling users to take control of data validation process. Previously handled by our helpdesk team, validation can now be performed directly by users, streamlining and improving the overall submission workflow at the EVA. 
+
+
+## Installation
+
+There are currently three ways to install and run the tool : 
+- Using conda
+- From source using Docker
+- From source natively (i.e. installing dependencies yourself)
+
+### 1. Conda
+
+The most straightforward way to install eva-sub-cli and its dependencies is through conda.
+For instance, the following commands install eva-sub-cli in a new environment called `eva`, activate the environment, and print
+the help message:
+```bash
+conda create -n eva -c conda-forge -c bioconda eva-sub-cli
+conda activate eva
+eva-sub-cli.py --help
+````
+
+### 2. From source using Docker
+
+Docker provides an easy way to run eva-sub-cli without installing dependencies separately.
+This method requires just Python 3.8+ and [Docker](https://docs.docker.com/engine/install/) to be installed.
+Then you can install the most recent version from [PyPI](https://pypi.org/project/eva-sub-cli/) in a virtual environment:
+```bash
+pip install eva-sub-cli
+```
+
+To verify that the cli tool is installed correctly, run the following command, and you should see the help message displayed : 
+```bash
+eva-sub-cli.py -h
+```
+
+### 3. From source natively
+
+This installation method requires the following :
+* Python 3.8+
+* [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html) 21.10+
+* [biovalidator](https://github.com/elixir-europe/biovalidator) 2.1.0+
+* [vcf-validator](https://github.com/EBIvariation/vcf-validator) 0.9.7+
+
+Install each of these and ensure they are included in your PATH. Then install the latest release as previously described.
+
+## Getting started with the eva-sub-cli tool 
+
+The ["Getting Started" guide](docs/Getting_Started_with_eva_sub_cli.md) serves as an introduction for users of the eva-sub-cli tool. It includes instructions on how to prepare your data and metadata, ensuring that users are equipped with the necessary information to successfully submit variant data. This guide is essential for new users, offering practical advice and tips for a smooth onboarding experience with the eva-sub-cli tool.
+
+## Options and parameters guide
+
+The eva-sub-cli tool provides several options and parameters that you can use to tailor its functionality to your needs.
+You can view all the available parameters with the command `eva-sub-cli.py -h` and view detailed explanations for the
+input file requirements in the ["Getting Started" guide](docs/Getting_Started_with_eva_sub_cli.md).
+Below is an overview of the key parameters.
+
+### Submission directory
+
+This is the directory where all processing will take place, and where configuration and reports will be saved.
+Crucially, the eva-sub-cli tool requires that there be **only one submission per directory** and that the submission directory not be reused.
+Running multiple submissions from a single directory can result in data loss during validation and submission.
+
+### Metadata file
+
+Metadata can be provided in one of two files.
+
+#### The metadata spreadsheet
+
+The metadata template can be found within the [etc folder](eva_sub_cli/etc/EVA_Submission_template.xlsx). It should be populated following the instructions provided within the template.
+This is passed using the option `--metadata_xlsx`.
+
+#### The metadata JSON
+
+The metadata can also be provided via a JSON file, which should conform to the schema located [here](eva_sub_cli/etc/eva_schema.json).
+This is passed using the option `--metadata_json`.
+
+### VCF files and Reference FASTA
+
+These can be provided either in the metadata file directly, or on the command line using the `--vcf_files` and `--reference_fata` options.
+Note that if you are using more than one reference FASTA, you **cannot** use the command line options; you must specify which VCF files use which FASTA files in the metadata.
+
+VCF files can be either uncompressed or compressed using bgzip.
+Other types of compression are not allowed and will result in errors during validation.
+FASTA files must be uncompressed.
+
+## Execution
+
+### Validate only
+
+To validate and not submit, run the following command:
+
+```shell
+eva-sub-cli.py --metadata_xlsx metadata_spreadsheet.xlsx --submission_dir submission_dir --tasks VALIDATE
+```
+
+**Note for Docker users:** 
+
+Make sure that Docker is running in the background, e.g. by opening Docker Desktop.
+For each of the below commands, add the command line option `--executor docker`, which will
+fetch and manage the Docker container for you. 
+
+```shell
+eva-sub-cli.py --metadata_xlsx metadata_spreadsheet.xlsx --submission_dir submission_dir --tasks VALIDATE --executor docker 
+```
+
+### Validate and submit your dataset
+
+To validate and submit, run the following command:
+
+```shell
+eva-sub-cli.py --metadata_xlsx metadata_spreadsheet.xlsx \
+               --vcf_files vcf_file1.vcf vcf_file2.vcf --reference_fasta assembly.fa --submission_dir submission_dir
+```
+
+
+### Submit only
+
+All submissions must have been validated. You cannot run the submission without validation. Once validated, execute the following command:
+
+```shell
+eva-sub-cli.py --metadata_xlsx metadata_spreadsheet.xlsx --submission_dir submission_dir
+```
+or 
+```shell
+eva-sub-cli.py --metadata_xlsx metadata_spreadsheet.xlsx --submission_dir submission_dir --tasks SUBMIT
+```
+This will only submit the data and not validate.
+
+### Shallow validation
+
+If you are working with large VCF files and find that validation takes a very long time, you can add the
+argument `--shallow` to the command, which will validate only the first 10,000 lines in each VCF. Note that running
+shallow validation will **not** be sufficient for actual submission.
+
+
+## Leveraging Nextflow to parallelize the validation process  
+
+Nextflow is a common workflow management system that helps orchestrate tasks and interface with the execution engine (like HPC or cloud). When running natively (i.e. not using Docker), eva-sub-cli will use Nextflow to run all the validation steps. In this section we'll see how it can be parameterised to work with your compute infrastructure.
+
+When no options are provided, Nextflow will run as many tasks as there are available CPUs on the machine executing it. To modify how many tasks can start and how Nextflow will process each one, you can provide a Nextflow configuration file in several ways.
+
+From the command line you can use `--nextflow_config <path>` to specify the Nextflow config file you want to apply. The configuration can also be picked up from other places directly by Nextflow. Please refer to [the nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more details.
+
+### Basic Nextflow configuration.
+
+There are many options to configure Nextflow so we will not provide them all. Please refer to [the documentation](https://www.nextflow.io/docs/latest/reference/config.html) for advanced features.
+Below is a very basic Nextflow configuration file that will request 2 cpus for each process, essentially limiting the number of process to half the number of available CPUs 
+```
+process {
+    executor="local"
+    cpus=2
+}
+```
+In this configuration, all the process will be running on the same machine where eva-sub-cli was started as described in the schema below.
+```
+(Local machine)
+eva-sub-cli
+  |_ nextflow
+      |_ task1
+      |_ task2
+```
+
+### Basic Nextflow configuration for HPC use.
+
+If you have access to High Performance Compute (HPC) environment, Nextflow supports the main resource managers such as [SLURM](https://www.nextflow.io/docs/latest/executor.html#slurm), [SGE](https://www.nextflow.io/docs/latest/executor.html#sge), [LSF](https://www.nextflow.io/docs/latest/executor.html#lsf) and others.
+In the configuration below, we're assuming that you are using SLURM. It would work similarly with other resource managers.
+```
+process {
+    executor="slurm"
+    queue="my_production_queue"
+}
+```
+
+In this configuration, the subtasks will be performed in other machines as specified by your SLURM resource manager as described in the schema below.
+```
+(Local machine)
+eva-sub-cli
+  |_ nextflow
+(Other compute node)
+task1
+(Other compute node)
+task2
+```

eva_sub_cli-0.4.6/README.md

@@ -0,0 +1,184 @@
+# eva-sub-cli
+The eva-sub-cli tool is a command line interface tool for data validation and upload. The tool transforms the submission process at EVA by enabling users to take control of data validation process. Previously handled by our helpdesk team, validation can now be performed directly by users, streamlining and improving the overall submission workflow at the EVA. 
+
+
+## Installation
+
+There are currently three ways to install and run the tool : 
+- Using conda
+- From source using Docker
+- From source natively (i.e. installing dependencies yourself)
+
+### 1. Conda
+
+The most straightforward way to install eva-sub-cli and its dependencies is through conda.
+For instance, the following commands install eva-sub-cli in a new environment called `eva`, activate the environment, and print
+the help message:
+```bash
+conda create -n eva -c conda-forge -c bioconda eva-sub-cli
+conda activate eva
+eva-sub-cli.py --help
+````
+
+### 2. From source using Docker
+
+Docker provides an easy way to run eva-sub-cli without installing dependencies separately.
+This method requires just Python 3.8+ and [Docker](https://docs.docker.com/engine/install/) to be installed.
+Then you can install the most recent version from [PyPI](https://pypi.org/project/eva-sub-cli/) in a virtual environment:
+```bash
+pip install eva-sub-cli
+```
+
+To verify that the cli tool is installed correctly, run the following command, and you should see the help message displayed : 
+```bash
+eva-sub-cli.py -h
+```
+
+### 3. From source natively
+
+This installation method requires the following :
+* Python 3.8+
+* [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html) 21.10+
+* [biovalidator](https://github.com/elixir-europe/biovalidator) 2.1.0+
+* [vcf-validator](https://github.com/EBIvariation/vcf-validator) 0.9.7+
+
+Install each of these and ensure they are included in your PATH. Then install the latest release as previously described.
+
+## Getting started with the eva-sub-cli tool 
+
+The ["Getting Started" guide](docs/Getting_Started_with_eva_sub_cli.md) serves as an introduction for users of the eva-sub-cli tool. It includes instructions on how to prepare your data and metadata, ensuring that users are equipped with the necessary information to successfully submit variant data. This guide is essential for new users, offering practical advice and tips for a smooth onboarding experience with the eva-sub-cli tool.
+
+## Options and parameters guide
+
+The eva-sub-cli tool provides several options and parameters that you can use to tailor its functionality to your needs.
+You can view all the available parameters with the command `eva-sub-cli.py -h` and view detailed explanations for the
+input file requirements in the ["Getting Started" guide](docs/Getting_Started_with_eva_sub_cli.md).
+Below is an overview of the key parameters.
+
+### Submission directory
+
+This is the directory where all processing will take place, and where configuration and reports will be saved.
+Crucially, the eva-sub-cli tool requires that there be **only one submission per directory** and that the submission directory not be reused.
+Running multiple submissions from a single directory can result in data loss during validation and submission.
+
+### Metadata file
+
+Metadata can be provided in one of two files.
+
+#### The metadata spreadsheet
+
+The metadata template can be found within the [etc folder](eva_sub_cli/etc/EVA_Submission_template.xlsx). It should be populated following the instructions provided within the template.
+This is passed using the option `--metadata_xlsx`.
+
+#### The metadata JSON
+
+The metadata can also be provided via a JSON file, which should conform to the schema located [here](eva_sub_cli/etc/eva_schema.json).
+This is passed using the option `--metadata_json`.
+
+### VCF files and Reference FASTA
+
+These can be provided either in the metadata file directly, or on the command line using the `--vcf_files` and `--reference_fata` options.
+Note that if you are using more than one reference FASTA, you **cannot** use the command line options; you must specify which VCF files use which FASTA files in the metadata.
+
+VCF files can be either uncompressed or compressed using bgzip.
+Other types of compression are not allowed and will result in errors during validation.
+FASTA files must be uncompressed.
+
+## Execution
+
+### Validate only
+
+To validate and not submit, run the following command:
+
+```shell
+eva-sub-cli.py --metadata_xlsx metadata_spreadsheet.xlsx --submission_dir submission_dir --tasks VALIDATE
+```
+
+**Note for Docker users:** 
+
+Make sure that Docker is running in the background, e.g. by opening Docker Desktop.
+For each of the below commands, add the command line option `--executor docker`, which will
+fetch and manage the Docker container for you. 
+
+```shell
+eva-sub-cli.py --metadata_xlsx metadata_spreadsheet.xlsx --submission_dir submission_dir --tasks VALIDATE --executor docker 
+```
+
+### Validate and submit your dataset
+
+To validate and submit, run the following command:
+
+```shell
+eva-sub-cli.py --metadata_xlsx metadata_spreadsheet.xlsx \
+               --vcf_files vcf_file1.vcf vcf_file2.vcf --reference_fasta assembly.fa --submission_dir submission_dir
+```
+
+
+### Submit only
+
+All submissions must have been validated. You cannot run the submission without validation. Once validated, execute the following command:
+
+```shell
+eva-sub-cli.py --metadata_xlsx metadata_spreadsheet.xlsx --submission_dir submission_dir
+```
+or 
+```shell
+eva-sub-cli.py --metadata_xlsx metadata_spreadsheet.xlsx --submission_dir submission_dir --tasks SUBMIT
+```
+This will only submit the data and not validate.
+
+### Shallow validation
+
+If you are working with large VCF files and find that validation takes a very long time, you can add the
+argument `--shallow` to the command, which will validate only the first 10,000 lines in each VCF. Note that running
+shallow validation will **not** be sufficient for actual submission.
+
+
+## Leveraging Nextflow to parallelize the validation process  
+
+Nextflow is a common workflow management system that helps orchestrate tasks and interface with the execution engine (like HPC or cloud). When running natively (i.e. not using Docker), eva-sub-cli will use Nextflow to run all the validation steps. In this section we'll see how it can be parameterised to work with your compute infrastructure.
+
+When no options are provided, Nextflow will run as many tasks as there are available CPUs on the machine executing it. To modify how many tasks can start and how Nextflow will process each one, you can provide a Nextflow configuration file in several ways.
+
+From the command line you can use `--nextflow_config <path>` to specify the Nextflow config file you want to apply. The configuration can also be picked up from other places directly by Nextflow. Please refer to [the nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more details.
+
+### Basic Nextflow configuration.
+
+There are many options to configure Nextflow so we will not provide them all. Please refer to [the documentation](https://www.nextflow.io/docs/latest/reference/config.html) for advanced features.
+Below is a very basic Nextflow configuration file that will request 2 cpus for each process, essentially limiting the number of process to half the number of available CPUs 
+```
+process {
+    executor="local"
+    cpus=2
+}
+```
+In this configuration, all the process will be running on the same machine where eva-sub-cli was started as described in the schema below.
+```
+(Local machine)
+eva-sub-cli
+  |_ nextflow
+      |_ task1
+      |_ task2
+```
+
+### Basic Nextflow configuration for HPC use.
+
+If you have access to High Performance Compute (HPC) environment, Nextflow supports the main resource managers such as [SLURM](https://www.nextflow.io/docs/latest/executor.html#slurm), [SGE](https://www.nextflow.io/docs/latest/executor.html#sge), [LSF](https://www.nextflow.io/docs/latest/executor.html#lsf) and others.
+In the configuration below, we're assuming that you are using SLURM. It would work similarly with other resource managers.
+```
+process {
+    executor="slurm"
+    queue="my_production_queue"
+}
+```
+
+In this configuration, the subtasks will be performed in other machines as specified by your SLURM resource manager as described in the schema below.
+```
+(Local machine)
+eva-sub-cli
+  |_ nextflow
+(Other compute node)
+task1
+(Other compute node)
+task2
+```

eva_sub_cli-0.4.6/conda/build.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+BIOVALIDATOR_VERSION=2.2.1
+
+EVA_SUB_CLI="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}"
+mkdir -p ${EVA_SUB_CLI}
+
+# Install eva-sub-cli
+$PYTHON -m pip install .
+echo "Done with eva-sub-cli"
+
+cd ${EVA_SUB_CLI}
+
+# Install biovalidator from source
+curl -Lo biovalidator.zip https://github.com/elixir-europe/biovalidator/archive/refs/tags/v${BIOVALIDATOR_VERSION}.zip \
+    && unzip -q biovalidator.zip && rm biovalidator.zip \
+    && cd biovalidator-${BIOVALIDATOR_VERSION} \
+    && npm install && npm install -g \
+    && cd ..
+echo "Done with biovalidator"

{eva_sub_cli-0.4 → eva_sub_cli-0.4.6}/conda/meta.yaml

@@ -1,37 +1,42 @@
 {% set name = "eva-sub-cli" %}
-{% set version = "0.2" %}
+{% set version = "0.4" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  path: ../
-# For submission to bioconda recipes, replace 'path' with the following (filling in the appropriate sha256):
-#  url: https://github.com/EBIvariation/eva-sub-cli/archive/v{{version}}.tar.gz
-#  sha256:
+  url: https://github.com/EBIvariation/eva-sub-cli/archive/v{{version}}.tar.gz
+  sha256: be4d4109d9879ad94ccc01a3bd534ff6077775f126977dfb3f2d6fd9cfb251ba
 
 build:
   number: 0
   noarch: generic
-  preserve_egg_dir: True
-# For submission to bioconda recipes, replace 'preserve_egg_dir' with the following:
-#  run_exports:
-#    - {{ pin_subpackage(name, max_pin="x.x") }}
+  script_env:
+    - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }}
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
 
 requirements:
   host:
     - nextflow >=21.10.0
     - python >=3.8
     - nodejs >=10.19.1
+    - vcf-validator >=0.10.0
+    - ebi-eva-common-pyutils >=0.6.1
     - pyyaml
     - jinja2
     - openpyxl
     - requests
     - jsonschema
+    - unzip
+    - setuptools-scm
   run:
     - nextflow >=21.10.0
     - python >=3.8
+    - nodejs >=10.19.1
+    - vcf-validator >=0.9.7
+    - ebi-eva-common-pyutils >=0.6.1
     - pyyaml
     - jinja2
     - openpyxl
@@ -43,7 +48,6 @@ test:
     - eva_sub_cli
   commands:
     - biovalidator --help
-    - vcf_validator --help
     - eva-sub-cli.py --help
 
 about:
@@ -54,4 +58,6 @@ about:
 
 extra:
   recipe-maintainers:
-    - apriltuesday
+    - apriltuesday
+    - tcezard
+    - ebi-variation

{eva_sub_cli-0.4 → eva_sub_cli-0.4.6}/docker/Dockerfile

@@ -1,6 +1,6 @@
 FROM python:3.10
 
-ENV vcf_validator_version=0.9.7
+ENV vcf_validator_version=0.10.0
 ENV NXF_VER=22.10.6
 
 WORKDIR /opt

{eva_sub_cli-0.4 → eva_sub_cli-0.4.6}/eva_sub_cli/__init__.py

@@ -6,6 +6,7 @@ PACKAGE_DIR = os.path.dirname(os.path.abspath(__file__))
 NEXTFLOW_DIR = os.path.join(PACKAGE_DIR, 'nextflow')
 ETC_DIR = os.path.join(PACKAGE_DIR, 'etc')
 LSRI_CLIENT_ID = "aa0fcc42-096a-4f9d-b871-aceb1a97d174"
+DEFAULT_METADATA_XLSX_TEMPLATE_VERSION = '1.1.6'
 
 SUB_CLI_CONFIG_FILE = ".eva_sub_cli_config.yml"
 

{eva_sub_cli-0.4 → eva_sub_cli-0.4.6}/eva_sub_cli/_version.py

@@ -1,8 +1,13 @@
-# file generated by setuptools_scm
+# file generated by setuptools-scm
 # don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
 TYPE_CHECKING = False
 if TYPE_CHECKING:
-    from typing import Tuple, Union
+    from typing import Tuple
+    from typing import Union
+
     VERSION_TUPLE = Tuple[Union[int, str], ...]
 else:
     VERSION_TUPLE = object
@@ -12,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.4'
-__version_tuple__ = version_tuple = (0, 4)
+__version__ = version = '0.4.6'
+__version_tuple__ = version_tuple = (0, 4, 6)

{eva_sub_cli-0.4 → eva_sub_cli-0.4.6}/eva_sub_cli/etc/spreadsheet2json_conf.yaml

@@ -32,7 +32,7 @@ Project:
     Project Title: title
     Description: description
     Center: centre
-    Tax ID: taxId
+    Taxonomy ID: taxId
   optional:
     Publication(s): publications
     Parent Project: parentProject
@@ -74,6 +74,7 @@ Analysis:
     Imputation: boolean
     Phasing: boolean
     Date: date
+    Software: list
 
 Sample:
   header_row: 3
@@ -89,7 +90,7 @@ Sample:
     Prefix: prefix
     Subject: subject
     Derived From: derivedFrom
-    Tax Id: taxId
+    Taxonomy ID: taxId
     Scientific Name: scientificName
     Common Name: commonName
     mating_type: matingType

eva_sub_cli-0.4.6/eva_sub_cli/exceptions/invalid_file_type_exception.py

@@ -0,0 +1,4 @@
+class InvalidFileTypeError(Exception):
+    def __init__(self, message):
+        self.message = message
+        super().__init__(self.message)

eva_sub_cli-0.4.6/eva_sub_cli/exceptions/metadata_template_version_exception.py

@@ -0,0 +1,10 @@
+class MetadataTemplateVersionException(Exception):
+    def __init__(self, message):
+        self.message = message
+        super().__init__(self.message)
+
+
+class MetadataTemplateVersionNotFoundException(Exception):
+    def __init__(self, message):
+        self.message = message
+        super().__init__(self.message)