Merge pull request #10 from Multiscale-Genomics/logger-progress

Logger progress functionality

CHANGES

@@ -11,6 +11,14 @@ Author: WHO?
 
 - Change N.
 
+**********
+31/05/2018
+**********
+Author: Mark McDowall
+
+- Added Tests for the logger
+- Changed the functionality of the PROGRESS logger so that it is more flexible and can be used within the VRE
+
 **********
 26/10/2017
 **********

tests/test_logger.py

@@ -0,0 +1,104 @@
+"""
+.. See the NOTICE file distributed with this work for additional information
+   regarding copyright ownership.
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+"""
+
+import pytest
+
+from utils import logger
+
+
+@pytest.mark.debug
+def test_debug(capsys):
+    """
+    Test the basic use of the DEBUG function
+    """
+    logger.debug("test")
+    captured = capsys.readouterr()
+    assert captured[0] == "DEBUG: test\n"
+
+
+@pytest.mark.info
+def test_info(capsys):
+    """
+    Test the basic use of the INFO function
+    """
+    logger.info("test")
+    captured = capsys.readouterr()
+    assert captured[0] == "INFO: test\n"
+
+
+@pytest.mark.warn
+def test_warn(capsys):
+    """
+    Test the basic use of the WARN function
+    """
+    logger.warn("test")
+    captured = capsys.readouterr()
+    assert captured[1] == "WARNING: test\n"
+
+
+@pytest.mark.error
+def test_error(capsys):
+    """
+    Test the basic use of the ERROR function
+    """
+    logger.error("test")
+    captured = capsys.readouterr()
+    assert captured[1] == "ERROR: test\n"
+
+
+@pytest.mark.fatal
+def test_fatal(capsys):
+    """
+    Test the basic use of the FATAL function
+    """
+    logger.fatal("test")
+    captured = capsys.readouterr()
+    assert captured[1] == "FATAL: test\n"
+
+
+@pytest.mark.progress
+def test_progress_00(capsys):
+    """
+    Test the basic use of the PROGRESS function
+    """
+    logger.progress("test")
+    captured = capsys.readouterr()
+    assert captured[0] == "PROGRESS: test\n"
+
+
+@pytest.mark.progress
+def test_progress_01(capsys):
+    """
+    Test the PROGRESS function for reporting task completion
+    """
+    logger.progress("test", status="RUNNING")
+    captured = capsys.readouterr()
+    assert captured[0] == "PROGRESS: test - RUNNING\n"
+
+    logger.progress("test", status="DONE")
+    captured = capsys.readouterr()
+    assert captured[0] == "PROGRESS: test - DONE\n"
+
+
+@pytest.mark.progress
+def test_progress_02(capsys):
+    """
+    Test the PROGRESS function for reporting tool progress
+    """
+    logger.progress("test", task_id=2, total=5)
+    captured = capsys.readouterr()
+    assert captured[0] == "PROGRESS: test (2/5)\n"

utils/logger.py

@@ -24,19 +24,18 @@
 It provides the following commonly used logging levels:
 
 DEBUG:		Detailed information, typically of interest only when
-		diagnosing problems. 
-INFO:		Confirmation that Tool execution is working as expected. 
+		diagnosing problems.
+INFO:		Confirmation that Tool execution is working as expected.
 WARNING:	An indication that something unexpected happened, but that the
 		Tool can continue working successfully.
 ERROR:		A more serious problem has occurred, and the Tool will not be
 		able to perform some function.
 FATAL:		A serious error, indicating that the Tool may be unable to
-		continue running.  
+		continue running.
 
 As well as the following non-standard levels:
 
-PROGRESS:	Provide the VRE with information about Tool execution progress,
-		in the form of a percentage (0-100)
+PROGRESS:	Provide the VRE with information about Tool execution progress
 """
 
 import sys
@@ -54,16 +53,17 @@
 STDERR_LEVELS = [WARNING, ERROR, FATAL, CRITICAL]
 
 _levelNames = {
-    FATAL : 'FATAL',
-    ERROR : 'ERROR',
-    WARNING : 'WARNING',
-    PROGRESS : 'PROGRESS',
-    INFO : 'INFO',
-    DEBUG : 'DEBUG',
-    WARN : 'WARNING',
-    CRITICAL : 'FATAL'
+    FATAL: 'FATAL',
+    ERROR: 'ERROR',
+    WARNING: 'WARNING',
+    PROGRESS: 'PROGRESS',
+    INFO: 'INFO',
+    DEBUG: 'DEBUG',
+    WARN: 'WARNING',
+    CRITICAL: 'FATAL'
 }
 
+
 def __log(level, message, *args, **kwargs):
     if level not in _levelNames:
         level = INFO
@@ -81,7 +81,7 @@ def debug(message, *args, **kwargs):
     'message' is the message format string, and the args are the arguments
     which are merged into msg using the string formatting operator. (Note that
     this means that you can use keywords in the format string, together with a
-    single dictionary argument.) 
+    single dictionary argument.)
     """
     return __log(DEBUG, message, *args, **kwargs)
 
@@ -117,15 +117,55 @@ def fatal(message, *args, **kwargs):
 critical=fatal
 
 ## Special loggers
-def progress(percentage):
+def progress(message, *args, **kwargs):
     """
-    Provides information about progress.
+    Provides information about Tool progress.
+
+    Logs a message containing information about Tool progress, with level
+    PROGRESS.
+
+    The arguments are interpreted as for debug() (see below for exceptions).
+
+    This function provides two pre-baked log message formats, that can be
+    activated by specifying the following items in **kwargs:
+
+
+        status : Status of the Tool
+            logs "MESSAGE - STATUS"
+
+
+        task_id : Current task; requires also the "total" item
+            logs "MESSAGE (TASK_ID/TOTAL)
+
+
+    Example
+    -------
+    .. code-block:: python
+       :linenos:
+
+       class TestTool(Tool):
+           # ...
+           def run(self, input_files, input_metadata, output_files):
+               logger.progress("TestTool starting", status="RUNNING")
+               total_tasks = 3
+
+               self.task1()
+               logger.progress("TestTool", task_id=1, total=total_tasks)
+
+               self.task2()
+               logger.progress("TestTool", task_id=2, total=total_tasks)
+
+               self.task3()
+               logger.progress("TestTool", task_id=3, total=total_tasks)
 
-    In fact it logs a message containing the percentage with level PERCENTAGE. 
+               logger.progress("TestTool", status="DONE")
+               return True
     """
-    if percentage > 100:
-        percentage = 100
-    if percentage < 0:
-        percentage = 0
-    return __log(PROGRESS, "{}", percentage)
+    if "status" in kwargs:
+        return __log(PROGRESS, "{} - {}", message, kwargs["status"])
+    elif "task_id" in kwargs:
+        return __log(PROGRESS, "{} ({}/{})", message, kwargs["task_id"], kwargs["total"])
+    else:
+        return __log(PROGRESS, message, *args, **kwargs)
+    return False