Add metrics module to DeepVariant Runner

Dockerfile

@@ -30,6 +30,7 @@ RUN curl -L -o /usr/bin/kubectl https://storage.googleapis.com/kubernetes-releas
 ADD LICENSE /
 ADD gcp_deepvariant_runner.py /opt/deepvariant_runner/src/
 ADD gke_cluster.py /opt/deepvariant_runner/src/
+ADD metrics.py /opt/deepvariant_runner/src/
 ADD process_util.py /opt/deepvariant_runner/src/
 ADD run_and_verify.sh /opt/deepvariant_runner/bin/
 ADD cancel /opt/deepvariant_runner/bin/

metrics.py

@@ -0,0 +1,185 @@
+# Copyright 2019 Google LLC.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+#    notice, this list of conditions and the following disclaimer in the
+#    documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the copyright holder nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+"""Used to collect anonymous DeepVariant metrics."""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+
+import atexit
+import functools
+import json
+import logging
+import time
+import uuid
+
+import requests
+from typing import Dict, Optional, Text
+
+_CLEARCUT_ENDPOINT = 'https://play.googleapis.com/log'
+_CLOUD_HCLS_OSS = 'CLOUD_HCLS_OSS'
+_CONCORD = 'CONCORD'
+_DEEP_VARIANT_RUN = 'DeepVariantRun'
+_HTTP_REQUEST_TIMEOUT_SEC = 10
+_PYTHON = 'PYTHON'
+_VIRTUAL_HCLS_DEEPVARIANT = 'virtual.hcls.deepvariant'
+
+
+def capture_exceptions(func):
+  """Function decorator to capture and log any exceptions."""
+
+  @functools.wraps(func)
+  def wrapper(*args, **kwds):
+    try:
+      return func(*args, **kwds)
+    # pylint:disable=broad-except
+    except Exception as e:
+      logging.error('Exception captured in %s : %s', func.__name__, e)
+
+  return wrapper
+
+
+class _ConcordEvent(object):
+  """Encapsulates information representing a Concord event."""
+
+  def __init__(self,
+               event_name: Text,
+               event_type: Text,
+               project_number: int,
+               console_type: Text,
+               page_hostname: Text,
+               event_metadata: Optional[Dict[Text, Text]] = None) -> None:
+    self._event_name = event_name
+    self._event_type = event_type
+    self._project_number = project_number
+    self._console_type = console_type
+    self._page_hostname = page_hostname
+    self._event_metadata = event_metadata or {}
+
+  def to_json(self, **kwargs):
+    """Encodes data in json."""
+    event_dict = {
+        'project_number': str(self._project_number),
+        'event_name': self._event_name,
+        'event_type': self._event_type,
+        'console_type': self._console_type,
+        'page_hostname': self._page_hostname,
+        'event_metadata': self._event_metadata_as_kv(),
+    }
+    return json.dumps(event_dict, **kwargs)
+
+  def _event_metadata_as_kv(self):
+    kv_list = []
+    for k, v in sorted(self._event_metadata.items()):
+      kv_list.append({'key': k, 'value': str(v)})
+
+    return kv_list
+
+
+class _MetricsCollector(object):
+  """A class that collects and submits metrics.
+
+  Instances of this class share the same internal state, and thus behave the
+  same all the time.
+  """
+  _events = []
+  _session_identifier = uuid.uuid4().hex
+
+  def add_metrics(self, project_number: int,
+                  metrics_name: Text, **metrics_kw: Text) -> None:
+    concord_event = _ConcordEvent(
+        event_name=metrics_name,
+        event_type=_DEEP_VARIANT_RUN,
+        project_number=project_number,
+        console_type=_CLOUD_HCLS_OSS,
+        page_hostname=_VIRTUAL_HCLS_DEEPVARIANT,
+        event_metadata={k: v for k, v in metrics_kw.items()})
+    self._events.append(concord_event)
+
+  def submit_metrics(self):
+    """Submits all the collected metrics to Concord endpoint.
+
+    Raises:
+      HTTPError if http request doesn't succeed (status code != 200).
+    """
+    request_data = json.dumps(self._clearcut_request(), sort_keys=True)
+    requests.post(
+        url=_CLEARCUT_ENDPOINT,
+        data=request_data,
+        headers=None,
+        timeout=_HTTP_REQUEST_TIMEOUT_SEC).raise_for_status()
+
+  def _clearcut_request(self):
+    # We dont have (or want to have) any cookies.  So, using a random ID for
+    # zwieback_cookie is ok for tracking purposes.
+    return {
+        'client_info': {
+            'client_type': _PYTHON,
+        },
+        'log_source_name':
+            _CONCORD,
+        'zwieback_cookie':
+            self._session_identifier,
+        'request_time_ms':
+            _now_ms(),
+        'log_event': [{
+            'source_extension_json': e.to_json(sort_keys=True)
+        } for e in self._events]
+    }
+
+
+def _now_ms():
+  """Returns current time in milliseconds."""
+  return int(round(time.time() * 1000))
+
+
+def add(project_number: int, metrics_name: Text, **metrics_kw: Text) -> None:
+  """Adds the given metric to the metrics to be submitted to Concord.
+
+  Note: All metrics are submitted at exit.
+  Note: Do not rely on thread safety of this method.
+
+  Args:
+    project_number(int): GCP project number.
+    metrics_name(str): metrics name.
+    **metrics_kw: key-values of metrics. For example, for
+      metrics_name="MakeExamplesSuccess", metrics_kw can be
+      duration_seconds=1000, wait_duration_seconds=100.
+  """
+  metrics_collector = _MetricsCollector()
+  metrics_collector.add_metrics(project_number, metrics_name, **metrics_kw)
+
+
+# Exceptions are captured and logged to avoid crashing callers.
+@capture_exceptions
+@atexit.register
+def shutdown():
+  """Reports all metrics that were collected."""
+  metrics_collector = _MetricsCollector()
+  metrics_collector.submit_metrics()