Merge pull request #309 from BU-ISCIII/develop

Release v1.1.0

Author: Shettland

.github/workflows/pypi_publish.yml

@@ -1,8 +1,9 @@
 name: Publish package python distribution to Pypi
 
 on:
-  push:
-    branches: "main"
+  release:
+    types: [published]
+  workflow_dispatch:
 
 jobs:
     build:
@@ -23,14 +24,13 @@ jobs:
       - name: Build a binary wheel and a source tarball
         run: python3 -m build
       - name: Store the distribution packages
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: python-package-distributions
           path: dist/
 
     publish-to-pypi:
       name: Publish dist to PyPI
-      if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
       needs:
       - build
       runs-on: ubuntu-latest
@@ -41,7 +41,7 @@ jobs:
         id-token: write
       steps:
       - name: Download all the dists
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: python-package-distributions
           path: dist/
@@ -58,7 +58,7 @@ jobs:
           id-token: write
         steps:
         - name: Download all the dists
-          uses: actions/download-artifact@v3
+          uses: actions/download-artifact@v4
           with:
             name: python-package-distributions
             path: dist/

.github/workflows/test_modules.yml

@@ -34,7 +34,7 @@ jobs:
       env:
         OUTPUT_LOCATION: ${{ github.workspace }}/tests/
     - name: Upload output file
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         name: test-output
         path: output.txt
@@ -73,7 +73,7 @@ jobs:
       env:
         OUTPUT_LOCATION: ${{ github.workspace }}/tests/
     - name: Upload output file
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         name: test-output
         path: output.txt

.github/workflows/test_sftp_handle.yml

@@ -24,9 +24,18 @@ jobs:
         echo "Current permission level is ${{ steps.checkAccess.outputs.user-permission }}"
         echo "Job originally triggered by ${{ github.actor }}"
         exit 1
+
+  sleep_to_ensure_concurrency:
+    needs: security_check
+    runs-on: ubuntu-latest
+    steps:
+    - name: 
+      run: sleep 10s
+      shell: bash
 
   test_sftp_handle:
-    needs: security_check
+    needs: [security_check, sleep_to_ensure_concurrency]
+    if: github.repository_owner == 'BU-ISCIII'
     concurrency:
       group: ${{ github.repository }}-test_sftp_handle
       cancel-in-progress: false

CHANGELOG.md

@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [1.1.0dev] - 2024-0X-0X : https://github.com/BU-ISCIII/relecov-tools/releases/tag/1.1.X
+## [1.X.Xdev] - 2024-XX-XX : https://github.com/BU-ISCIII/relecov-tools/releases/tag/1.X.X
 
 ### Credits
 
@@ -22,7 +22,42 @@ Code contributions to the hotfix:
 
 ### Requirements
 
-## [1.0.0] - 2024-0X-0X : https://github.com/BU-ISCIII/relecov-tools/releases/tag/1.0.0
+## [1.1.0] - 2024-09-13 : https://github.com/BU-ISCIII/relecov-tools/releases/tag/1.1.0
+
+### Credits
+
+Code contributions to the hotfix:
+
+- [Pablo Mata](https://github.com/Shettland)
+- [Sara Monzón](https://github.com/saramonzon)
+
+### Modules
+
+- New logs-to-excel function to create an excel file given a list of log-summary.json files [#300](https://github.com/BU-ISCIII/relecov-tools/pull/300)
+
+#### Added enhancements
+
+- Included a way to extract pango-designation version in read-bioinfo-metadata [#299](https://github.com/BU-ISCIII/relecov-tools/pull/299)
+- Now log_summary.py also creates an excel file with the process logs [#300](https://github.com/BU-ISCIII/relecov-tools/pull/300)
+- Read-bioinfo-metadata splits files and data by batch of samples [#306](https://github.com/BU-ISCIII/relecov-tools/pull/306)
+- Included a sleep time in test_sftp-handle to avoid concurrency check failure [#308](https://github.com/BU-ISCIII/relecov-tools/pull/308)
+
+#### Fixes
+
+- Fixes in launch_pipeline including creation of samples_id.txt and joined validated json [#303](https://github.com/BU-ISCIII/relecov-tools/pull/303)
+- Fixed failing module_tests.yml workflow due to deprecated upload-artifact version [#308](https://github.com/BU-ISCIII/relecov-tools/pull/308)
+
+#### Changed
+
+- Changed pypi_publish action to publish on every release, no need to push tags [#308](https://github.com/BU-ISCIII/relecov-tools/pull/308)
+
+#### Removed
+
+- Removed only_samples argument in log_summary.py as it was not used in any module. [#300](https://github.com/BU-ISCIII/relecov-tools/pull/300)
+
+### Requirements
+
+## [1.0.0] - 2024-09-02 : https://github.com/BU-ISCIII/relecov-tools/releases/tag/1.0.0
 
 ### Credits
 

README.md

@@ -24,9 +24,10 @@ relecov-tools is a set of helper tools for the assembly of the different element
       - [upload-to-ena](#upload-to-ena)
       - [upload-to-gisaid](#upload-to-gisaid)
       - [update-db](#update-db)
+      - [launch-pipeline](#launch-pipeline)
+      - [logs-to-excel](#logs-to-excel)
     - [build-schema](#build-schema)
       - [Mandatory Fields](#mandatory-fields)
-      - [launch-pipeline](#launch-pipeline)
       - [custom logs](#custom-logs)
     - [Python package mode](#python-package-mode)
   - [Acknowledgements](#acknowledgements)
@@ -62,7 +63,7 @@ $ relecov-tools --help
 \    \  /   |__ / |__  |    |___ |    |   |  \    /
 /    /  \   |  \  |    |    |    |    |   |   \  /
 /    |--|   |   \ |___ |___ |___ |___ |___|    \/
-RELECOV-tools version 1.0.0
+RELECOV-tools version 1.1.0
 Usage: relecov-tools [OPTIONS] COMMAND [ARGS]...
 
 Options:
@@ -160,7 +161,7 @@ Usage: relecov-tools read-bioinfo-metadata [OPTIONS]
 - Note: Software-specific configurations are available in [bioinfo_config.json](./relecov_tools/conf/bioinfo_config.json).
 
 #### validate
-`validate` commands validate the data in json format outputted by `read-metadata` command against a json schema, in this case the relecov [schema specification](./relecov_tools/schema/relecov_schema.json).
+`validate` commands validate the data in json format outputted by `read-metadata` command against a json schema, in this case the relecov [schema specification](./relecov_tools/schema/relecov_schema.json). It also creates a summary of the errors and warnings found in excel format as a report to the users.
 
 ```
 $ relecov-tools validate --help
@@ -246,6 +247,35 @@ Usage: relecov-tools upload-to-gisaid [OPTIONS]
     -t, --type                         Select the type of information to upload to database [sample,bioinfodata,variantdata]
     -d, --databaseServer               Name of the database server receiving the data [iskylims,relecov]
 
+#### launch-pipeline
+Create the folder structure to execute the given pipeline for the latest sample batches after executing download, read-lab-metadata and validate modules. This module will create symbolic links for each sample and generate the necessary files for pipeline execution using the information from validated_BATCH-NAME_DATE.json.
+```
+Usage: relecov-tools launch-pipeline [OPTIONS]
+
+  Create the symbolic links for the samples which are validated to prepare for
+  bioinformatics pipeline execution.
+
+Options:
+  -i, --input PATH          Path to the input folder where sample files are located
+  -t, --template PATH       Path to the pipeline template folder to be copied in the                       output folder
+  -c, --config PATH         Path to the the template config file
+  -o, --out_dir PATH        Path to output folder
+  --help                    Show this message and exit.
+```
+
+#### logs-to-excel
+Creates an xlsx file with all the entries found for a specified laboratory in a given set of log_summary.json files (from log-summary module). The laboratory name must match the name of one of the keys in the provided logs to work.
+```
+Usage: relecov-tools logs-to-excel [OPTIONS]
+
+  Creates a merged xlsx report from all the log summary jsons given as input
+
+Options:
+    -l, --lab_name                         Name for target laboratory in log-summary.json files
+    -o, --output_folder                    Path to output folder where xlsx file is saved
+    -f, --files                            Paths to log_summary.json files to merge into xlsx file, called once per file
+```
+
 ### build-schema
 The `build-schema` module provides functionality to generate and manage JSON Schema files based on database definitions from Excel spreadsheets. It automates the creation of JSON Schemas, including validation, drafting, and comparison with existing schemas.
 
@@ -289,22 +319,6 @@ required (Y/N): Indicates if the property is required (Y) or optional (N).
 complex_field (Y/N): Indicates if the property is a complex (nested) field (Y) or a standard field (N).
 ```
 
-#### launch-pipeline
-Create the folder structure to execute the given pipeline for the latest sample batches after executing download, read-lab-metadata and validate modules. This module will create symbolic links for each sample and generate the necessary files for pipeline execution using the information from validated_BATCH-NAME_DATE.json.
-```
-Usage: relecov-tools launch-pipeline [OPTIONS]
-
-  Create the symbolic links for the samples which are validated to prepare for
-  bioinformatics pipeline execution.
-
-Options:
-  -i, --input PATH          Path to the input folder where sample files are located
-  -t, --template PATH       Path to the pipeline template folder to be copied in the                       output folder
-  -c, --config PATH         Path to the the template config file
-  -o, --out_dir PATH        Path to output folder
-  --help                    Show this message and exit.
-```
-
 #### custom logs
 After executing each of these modules, you may find a custom log report in json format named "DATE_EXECUTED-MODULE_log_summary.json. These custom log summaries can be useful to detect errors in metadata in order to fix them and/or notify the users.
 

relecov_tools/__main__.py

@@ -1,11 +1,12 @@
 #!/usr/bin/env python
 import logging
-
-# import re
+import os
+import json
 
 # from rich.prompt import Confirm
 import click
 import relecov_tools.download_manager
+import relecov_tools.log_summary
 import rich.console
 import rich.logging
 import rich.traceback
@@ -60,7 +61,7 @@ def run_relecov_tools():
     )
 
     # stderr.print("[green]                                          `._,._,'\n", highlight=False)
-    __version__ = "1.0.0"
+    __version__ = "1.1.0"
     stderr.print(
         "\n" "[grey39]    RELECOV-tools version {}".format(__version__), highlight=False
     )
@@ -487,7 +488,7 @@ def launch_pipeline(input, template, output, config):
 
 
 # schema builder
-@relecov_tools_cli.command(help_priority=13)
+@relecov_tools_cli.command(help_priority=14)
 @click.option(
     "-i",
     "--input_file",
@@ -523,5 +524,72 @@ def build_schema(input_file, schema_base, draft_version, diff, out_dir):
     schema_update.handle_build_schema()
 
 
+@relecov_tools_cli.command(help_priority=15)
+@click.option(
+    "-l",
+    "--lab_code",
+    type=click.Path(),
+    help="Name for target laboratory in log-summary.json files",
+    required=True,
+)
+@click.option(
+    "-o",
+    "--output_folder",
+    type=click.Path(),
+    help="Path to output folder where xlsx file is saved",
+    required=False,
+)
+@click.option(
+    "-f",
+    "--files",
+    help="Paths to log_summary.json files to merge into xlsx file, called once per file",
+    required=True,
+    multiple=True,
+)
+def logs_to_excel(lab_code, output_folder, files):
+    """Creates a merged xlsx report from all the log summary jsons given as input"""
+    all_logs = []
+    full_paths = [os.path.realpath(f) for f in files]
+    for file in full_paths:
+        if not os.path.exists(file):
+            stderr.print(f"[red]File {file} does not exist")
+            continue
+        try:
+            with open(file, "r") as f:
+                all_logs.append(json.load(f)[lab_code])
+        except Exception as e:
+            stderr.print(f"[red]Could extract data from {file}: {e}")
+    if not all_logs:
+        stderr.print("All provided files were empty.")
+        exit(1)
+    logsum = relecov_tools.log_summary.LogSum(output_location=output_folder)
+    merged_logs = logsum.merge_logs(key_name=lab_code, logs_list=all_logs)
+    final_logs = logsum.prepare_final_logs(logs=merged_logs)
+    logsum.create_logs_excel(logs=final_logs)
+
+
+@relecov_tools_cli.command(help_priority=16)
+@click.option(
+    "-c",
+    "--config_file",
+    type=click.Path(),
+    help="Path to config file in yaml format",
+    required=True,
+)
+@click.option(
+    "-o",
+    "--output_folder",
+    type=click.Path(),
+    help="Path to the base schema file. This file is used as a reference to compare it with the schema generated using this module. (Default: installed schema in 'relecov-tools/relecov_tools/schema/relecov_schema.json')",
+    required=False,
+)
+def wrapper(config_file, output_folder):
+    """Executes the modules in config file sequentially"""
+    process_wrapper = relecov_tools.dataprocess_wrapper.ProcessWrapper(
+        config_file=config_file, output_folder=output_folder
+    )
+    process_wrapper.run_wrapper()
+
+
 if __name__ == "__main__":
     run_relecov_tools()