Adding log-kubectl file with changing the run logs check by using get…

…_workflow function

.gitignore

@@ -76,3 +76,4 @@ helm/reana/Chart.lock
 # Helm releases
 .cr-release-packages
 .cr-index
+helm/configurations/values-dev.yaml

scripts/log-kubectl.py

@@ -0,0 +1,96 @@
+import subprocess
+import click
+import signal
+import sys
+import os
+import time
+
+# Construct the absolute path to the reana-client directory
+current_dir = os.path.dirname(os.path.abspath(__file__))
+reana_client_path = os.path.abspath(os.path.join(current_dir, '..', '..', '..', 'reana-client'))
+
+# Add the reana-client directory to the sys.path
+if reana_client_path not in sys.path:
+    sys.path.insert(0, reana_client_path)
+
+from reana_client.api.client import get_workflow_logs
+
+# Global variable to control the loop
+continue_logging = True
+
+def signal_handler(sig, frame):
+    global continue_logging
+    continue_logging = False
+    print("Stopping log collection...")
+
+def run_command_with_retries(command, max_retries=5, delay=2):
+    attempt = 0
+    while attempt < max_retries:
+        try:
+            process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)
+            return process
+        except Exception as e:
+            print(f"An error occurred: {e}. Attempt {attempt + 1} of {max_retries}")
+            attempt += 1
+            time.sleep(delay)
+    print("All attempts to run the command have failed.")
+    return None
+
+@click.command()
+@click.option('--log-file', required=True, help='The name of the file to save the logs.')
+@click.option('--workflow', required=True, help='The name of the workflow')
+def run_command_and_save_logs(log_file, workflow):
+    global continue_logging
+
+    # Get the access token from environment variable
+    access_token = os.getenv('REANA_ACCESS_TOKEN')
+    if not access_token:
+        print("Error: REANA_ACCESS_TOKEN environment variable is not set.")
+        sys.exit(1)
+
+    # Call get_workflow_logs with the workflow and access_token
+    service = get_workflow_logs(workflow, access_token)
+    # Extract batch_id from the service response
+    batch_id = service.get('workflow_id')
+    if not batch_id:
+        print("Error: 'workflow_id' not found in the service response.")
+        sys.exit(1)
+    print("The batch_id is suppose to be this:", batch_id)
+
+    # Register the signal handler
+    signal.signal(signal.SIGINT, signal_handler)
+
+    command = (
+        "kubectl get pod -o='custom-columns=NAME:.metadata.name,PHASE:.status.phase,"
+        "CREATED:.metadata.creationTimestamp,STARTED:.status.startTime,"
+        "STARTED_CONTAINERS:.status.containerStatuses[*].state.*.startedAt,"
+        "FINISHED_CONTAINERS:.status.containerStatuses[*].state.*.finishedAt' -w"
+    )
+
+    with open(log_file, "a") as file:  # 'a' is for appending to the file without truncating it
+        # Popen - command is executed in a new shell process, standard output and standard error are redirected to pipes
+        while continue_logging:
+            process = run_command_with_retries(command)
+            if not process:
+                print("Failed to start the command")
+                break
+            try:
+                while continue_logging:
+                    line = process.stdout.readline()
+                    if not line:
+                        break
+                    line = line.strip()  # Strip the line of leading/trailing whitespace
+                    print(line)
+                    file.write(line + "\n")
+                    if f"reana-run-batch-{batch_id}" in line and "Failed" in line:
+                        file.write(line + '\n')  # Ensure newline is added when writing to file
+                        continue_logging = False
+                        break
+            except Exception as e:
+                print(f"An error occurred while reading the process output: {e}")
+            finally:
+                process.terminate()
+                process.wait()
+
+if __name__ == "__main__":
+    run_command_and_save_logs()

scripts/logs_lifetime_benchmarking_test.py

@@ -1,47 +1,78 @@
-import pandas as pd
 import subprocess
+import pandas as pd
 import matplotlib.pyplot as plt
 from matplotlib.dates import DateFormatter, SecondLocator
 import click
+import os
+import re
+import sys
+import logging
+from reana_client.api.client import get_workflow_logs
+
+# Ensure REANA_ACCESS_TOKEN is set
+access_token = os.getenv('REANA_ACCESS_TOKEN')
+if not access_token:
+    print("Error: REANA_ACCESS_TOKEN environment variable is not set.")
+    sys.exit(1)
+
+# Set up logging
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+# Function to extract job IDs from lines
+def extract_job_ids_from_lines(lines):
+    job_ids = set()
+    for line in lines:
+        match = re.search(r'reana-run-job-\w{8}-\w{4}-\w{4}-\w{4}-\w{12}', line)
+        if match:
+            job_ids.add(match.group(0))
+    return job_ids
 
-"""Run this script to generate the plots of current job status"""
-"""First compare the logs from reana-client logs command and the job pod ID's from statistics file"""
-
-def run_reana_client_logs(command):
-    command = f"reana-client logs -w {workflow}"
-    result = subprocess.run(command, shell=True, capture_output=True, text=True)
-    if result.returncode == 0:
-        return result.stdout
-    else:
-        print("Comamnd failed to run, error:")
-        print(result.stderr)
-        return None
-
+# Function to parse log file
 def parse_log_file(file_path):
     with open(file_path, 'r') as f:
         lines = f.readlines()
     return lines
 
+# Function to write filtered lines to a new file
+def write_filtered_log_file(filtered_lines, filtered_file_path):
+    with open(filtered_file_path, 'w') as f:
+        f.writelines(filtered_lines)
+
+# Function to extract unique jobs from lines
 def extract_unique_jobs(lines):
     unique_jobs = {}
     for line in lines:
-        if line.strip().startswith('reana-run-job-'):
-            job_id = line.strip().split()[0]
+        match = re.match(r'(reana-run-job-\w{8}-\w{4}-\w{4}-\w{4}-\w{12})', line)
+        if match:
+            job_id = match.group(0)
             unique_jobs[job_id] = line.strip()
     return unique_jobs.values()
 
+# Function to extract succeeded timestamps from unique jobs
 def extract_succeeded_timestamps(unique_jobs):
     succeeded_timestamps = [line.split()[5] for line in unique_jobs if line.split()[5] != "<none>"]
     succeeded_timestamps = [ts.split(',')[0] for ts in succeeded_timestamps]
     return pd.to_datetime(succeeded_timestamps, errors='coerce')
 
+# Function to get sorted data by timestamp
 def get_sorted_data(lines):
-    sorted_data = sorted(lines, key=lambda x: x.split()[1])
-    return sorted_data
-
+    sorted_lines = []
+    for line in lines:
+        parts = line.split()
+        try:
+            timestamp = pd.to_datetime(parts[2])
+            sorted_lines.append((timestamp, line))
+        except Exception as e:
+            logger.error(f"Error parsing date from line: {line}. Error: {e}")
+    sorted_lines.sort(key=lambda x: x[0])
+    return [line for _, line in sorted_lines]
+
+# Function to filter jobs based on status
 def filter_jobs(sorted_data, status):
     return [line for line in sorted_data if line.split()[1] == status]
 
+# Function to extract running timestamps
 def extract_running_timestamps(running_jobs):
     timestamps_running = []
     encountered_jobs_running = set()
@@ -64,6 +95,7 @@ def extract_running_timestamps(running_jobs):
     timestamps_running.sort()
     return timestamps_running
 
+# Function to extract pending timestamps
 def extract_pending_timestamps(pending_jobs):
     timestamps_pending = []
     encountered_jobs_pending = set()
@@ -90,6 +122,7 @@ def extract_pending_timestamps(pending_jobs):
     timestamps_pending.sort()
     return timestamps_pending
 
+# Function to calculate cumulative timestamps
 def calculate_cumulative(timestamps):
     x = []
     y = []
@@ -99,19 +132,13 @@ def calculate_cumulative(timestamps):
         x.append(timestamp[0])
         y.append(cumulative_sum)
     return x, y
-
-def plot_data(succeeded_counts, x_running, y_running, x_pending, y_pending):
-    plt.figure(figsize=figsize)
 
-    # Plot succeeded jobs
+# Function to plot data
+def plot_data(succeeded_counts, x_running, y_running, x_pending, y_pending, title, figsize):
+    plt.figure(figsize=figsize)
     plt.plot(succeeded_counts.index, succeeded_counts.cumsum(), label='Finished', linestyle='-', color='green', alpha=0.5)
-
-    # Plot running jobs
     plt.plot(x_running, y_running, linestyle='-', color='blue', alpha=0.5, linewidth=3, label='Running')
-
-    # Plot pending jobs
     plt.plot(x_pending, y_pending, linestyle='-', color='orange', alpha=0.5, linewidth=3, label='Pending')
-
     plt.xlabel('Processing time')
     plt.ylabel('Number of Jobs')
     plt.title(title)
@@ -127,39 +154,45 @@ def plot_data(succeeded_counts, x_running, y_running, x_pending, y_pending):
 @click.argument('file_path')
 @click.option('--title', default='Analysis Results', help='Title of the analysis results')
 @click.option('--figsize', nargs=2, type=float, default=(12, 8), help='Figure size as two float values')
-@click.option('--workflow', required=False, help='Name of the REANA workflow the same as the processed .txt file')
+@click.option('--workflow', required=True, help='Name of the REANA workflow')
 def main(file_path, title, figsize, workflow):
-    """Compare the reana-client logs and the jobs from the analysis results
-       Run benchmarking tests. Generate matplotlib plot
+    """ This script allows to plot the workflow lifetime statistics.
+     As a results of evaluating the logs file with pod life cycle information,
+     the statistics of how many jobe were running in parallel can be found.
 
-       The script requires matplotlib and pandas packages
-
-       Steps to run benchmarking workflow lifetime test:
 
+     Steps to run benchmarking workflow lifetime test:
         .. code-block:: console
-
         \b
         #To run this script 
         $ kubectl #To save a live logs 
         $ cd reana/scripts
-        $ python lifetime.py logs.txt # insert your .txt file with logs
-
+        $ python lifetime.py logs.txt # insert your .txt file with logs  and the name of the workflow
     """
-    reana_logs = run_reana_client_logs(workflow)
-    reana_job_ids = set()
-    for line in reana_logs.splitlines():
-        if line.strip().startswith('reana-run-job'):
-            job_id  = line.strip().split()[0]
-            reana_job_ids.add(job_id)
+    service = get_workflow_logs(workflow, access_token)
+    log_string = service['logs']
+    reana_run_job_ids = re.findall(r'reana-run-job-\w{8}-\w{4}-\w{4}-\w{4}-\w{12}', log_string)
+
     lines = parse_log_file(file_path)
+    file_job_ids = extract_job_ids_from_lines(lines)
+
+    diff_job_ids = set(reana_run_job_ids).symmetric_difference(file_job_ids)
+    if diff_job_ids:
+        print("Differing Job IDs:")
+        for job_id in diff_job_ids:
+            print(job_id)
+    else:
+        print("No differing Job IDs found.")
 
-    unique_jobs = extract_unique_jobs(lines)
+    filtered_lines = [line for line in lines if not any(job_id in line for job_id in diff_job_ids)]
+    filtered_file_path = 'filtered_' + file_path
+    write_filtered_log_file(filtered_lines, filtered_file_path)
+
+    unique_jobs = extract_unique_jobs(filtered_lines)
     succeeded_timestamps = extract_succeeded_timestamps(unique_jobs)
-    first_succeeded_timestamp = succeeded_timestamps.dropna().min()
     succeeded_counts = succeeded_timestamps.value_counts().sort_index()
 
-    sorted_data = get_sorted_data(lines)
-
+    sorted_data = get_sorted_data(filtered_lines)
     running_jobs = filter_jobs(sorted_data, 'Running')
     timestamps_running = extract_running_timestamps(running_jobs)
     x_running, y_running = calculate_cumulative(timestamps_running)
@@ -168,7 +201,7 @@ def main(file_path, title, figsize, workflow):
     timestamps_pending = extract_pending_timestamps(pending_jobs)
     x_pending, y_pending = calculate_cumulative(timestamps_pending)
 
-    plot_data(succeeded_counts, x_running, y_running, x_pending, y_pending)
+    plot_data(succeeded_counts, x_running, y_running, x_pending, y_pending, title, figsize)
 
 if __name__ == "__main__":
     main()