Merge branch 'master' of https://github.com/Multiscale-Genomics/mg-to…

…ol-api

.travis.yml

@@ -20,6 +20,7 @@ dist: trusty
 
 python:
     - "2.7"
+    - "3.6"
 
 env:
     matrix:

apps/__init__.py

@@ -15,6 +15,6 @@
    limitations under the License.
 """
 
-from pycompssapp import PyCOMPSsApp
-from localapp import LocalApp
-from workflowapp import WorkflowApp
+from apps.pycompssapp import PyCOMPSsApp
+from apps.localapp import LocalApp
+from apps.workflowapp import WorkflowApp

apps/jsonapp.py

@@ -23,6 +23,7 @@
 
 from apps.workflowapp import WorkflowApp
 from basic_modules.metadata import Metadata
+from utils import logger
 
 
 class JSONApp(WorkflowApp):  # pylint: disable=too-few-public-methods
@@ -77,7 +78,7 @@ def launch(self, tool_class,  # pylint: disable=too-many-locals,arguments-differ
         >>> # writes /path/to/results.json
         """
 
-        print "0) Unpack information from JSON"
+        logger.info("0) Unpack information from JSON")
         input_ids, arguments, output_files = self._read_config(
             config_path)
 
@@ -105,7 +106,7 @@ def launch(self, tool_class,  # pylint: disable=too-many-locals,arguments-differ
             tool_class, input_files, input_metadata,
             output_files, arguments)
 
-        print "4) Pack information to JSON"
+        logger.info("4) Pack information to JSON")
         return self._write_results(
             input_files, input_metadata,
             output_files, output_metadata,

basic_modules/app.py

@@ -18,6 +18,7 @@
 
 from __future__ import print_function
 from basic_modules.metadata import Metadata  # pylint: disable=unused-import
+from utils import logger
 
 
 # -----------------------------------------------------------------------------
@@ -98,10 +99,10 @@ def launch(self, tool_class,  # pylint: disable=too-many-arguments
         >>> app.launch(Tool, {"input": <input_file>}, {})
         """
 
-        print("1) Instantiate and configure Tool")
+        logger.info("1) Instantiate and configure Tool")
         tool_instance = self._instantiate_tool(tool_class, configuration)
 
-        print("2) Run Tool")
+        logger.info("2) Run Tool")
         input_files, input_metadata = self._pre_run(tool_instance,
                                                     input_files,
                                                     input_metadata)
@@ -114,7 +115,7 @@ def launch(self, tool_class,  # pylint: disable=too-many-arguments
                                                        output_files,
                                                        output_metadata)
 
-        print("Output_files: ", output_files)
+        logger.info("Output_files: ", output_files)
         return output_files, output_metadata
 
     def _instantiate_tool(self, tool_class, configuration):  # pylint: disable=no-self-use

tests/test_logger.py

@@ -15,6 +15,7 @@
    limitations under the License.
 """
 
+import re
 import pytest
 
 from utils import logger
@@ -27,7 +28,7 @@ def test_debug(capsys):
     """
     logger.debug("test")
     captured = capsys.readouterr()
-    assert captured[0] == "DEBUG: test\n"
+    assert re.search("DEBUG: test", captured[0])
 
 
 @pytest.mark.info
@@ -37,7 +38,7 @@ def test_info(capsys):
     """
     logger.info("test")
     captured = capsys.readouterr()
-    assert captured[0] == "INFO: test\n"
+    assert re.search("INFO: test", captured[0])
 
 
 @pytest.mark.warn
@@ -47,7 +48,7 @@ def test_warn(capsys):
     """
     logger.warn("test")
     captured = capsys.readouterr()
-    assert captured[1] == "WARNING: test\n"
+    assert re.search("WARNING: test", captured[1])
 
 
 @pytest.mark.error
@@ -57,7 +58,7 @@ def test_error(capsys):
     """
     logger.error("test")
     captured = capsys.readouterr()
-    assert captured[1] == "ERROR: test\n"
+    assert re.search("ERROR: test", captured[1])
 
 
 @pytest.mark.fatal
@@ -67,7 +68,7 @@ def test_fatal(capsys):
     """
     logger.fatal("test")
     captured = capsys.readouterr()
-    assert captured[1] == "FATAL: test\n"
+    assert re.search("FATAL: test", captured[1])
 
 
 @pytest.mark.progress
@@ -77,7 +78,7 @@ def test_progress_00(capsys):
     """
     logger.progress("test")
     captured = capsys.readouterr()
-    assert captured[0] == "PROGRESS: test\n"
+    assert re.search("PROGRESS: test", captured[0])
 
 
 @pytest.mark.progress
@@ -87,11 +88,11 @@ def test_progress_01(capsys):
     """
     logger.progress("test", status="RUNNING")
     captured = capsys.readouterr()
-    assert captured[0] == "PROGRESS: test - RUNNING\n"
+    assert re.search("PROGRESS: test - RUNNING", captured[0])
 
     logger.progress("test", status="DONE")
     captured = capsys.readouterr()
-    assert captured[0] == "PROGRESS: test - DONE\n"
+    assert re.search("PROGRESS: test - DONE", captured[0])
 
 
 @pytest.mark.progress
@@ -101,4 +102,4 @@ def test_progress_02(capsys):
     """
     logger.progress("test", task_id=2, total=5)
     captured = capsys.readouterr()
-    assert captured[0] == "PROGRESS: test (2/5)\n"
+    assert re.search("PROGRESS: test \(2\/5\)", captured[0])

utils/logger.py

@@ -17,6 +17,7 @@
 """
 
 import sys
+import datetime
 
 """
 This is the logging facility of the mg-tool-api. It is meant to provide
@@ -66,13 +67,20 @@
 
 
 def __log(level, message, *args, **kwargs):
+    """
+    Function to print out the logging input
+    """
+    log_time = datetime.datetime.now()
+    log_ts = "{}-{:02d}-{:02d} {:02d}:{:02d}:{:02d}".format(
+        log_time.year, log_time.month, log_time.day,
+        log_time.hour, log_time.minute, log_time.second)
     if level not in _levelNames:
         level = INFO
     outstream = sys.stdout
     if level in STDERR_LEVELS:
         outstream = sys.stderr
-    outstream.write("{}: {}\n".format(
-        _levelNames[level], message.format(*args, **kwargs)))
+    outstream.write("{} | {}: {}\n".format(
+        log_ts, _levelNames[level], message.format(*args, **kwargs)))
     return True