Slack

setup.py

@@ -59,7 +59,7 @@
         "psutil",
         "nbformat"
     ],
-    extras_require={"reports": ["jinja2", "networkx", "pygments", "pygraphviz"]},
+    extras_require={"reports": ["jinja2", "networkx", "pygments", "pygraphviz"], "messaging": ["slacker"]},
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Environment :: Console",

snakemake/__init__.py

@@ -21,7 +21,7 @@
 from snakemake.workflow import Workflow
 from snakemake.dag import Batch
 from snakemake.exceptions import print_exception, WorkflowError
-from snakemake.logging import setup_logger, logger
+from snakemake.logging import setup_logger, logger, SlackLogger
 from snakemake.io import load_configfile
 from snakemake.shell import shell
 from snakemake.utils import update_config, available_cpu_count
@@ -117,7 +117,7 @@ def snakemake(
     no_hooks=False,
     overwrite_shellcmd=None,
     updated_files=None,
-    log_handler=None,
+    log_handler=[],
     keep_logger=False,
     max_jobs_per_second=None,
     max_status_checks_per_second=100,
@@ -148,6 +148,7 @@ def snakemake(
     cluster_status=None,
     export_cwl=None,
     show_failed_logs=False,
+    messaging=None,
 ):
     """Run snakemake on a given snakefile.
 
@@ -253,7 +254,7 @@ def snakemake(
         assume_shared_fs (bool):    assume that cluster nodes share a common filesystem (default true).
         cluster_status (str):       status command for cluster execution. If None, Snakemake will rely on flag files. Otherwise, it expects the command to return "success", "failure" or "running" when executing with a cluster jobid as single argument.
         export_cwl (str):           Compile workflow to CWL and save to given file
-        log_handler (function):     redirect snakemake output to this custom log handler, a function that takes a log message dictionary (see below) as its only argument (default None). The log message dictionary for the log handler has to following entries:
+        log_handler (list):         redirect snakemake output to this list of custom log handler, each a function that takes a log message dictionary (see below) as its only argument (default []). The log message dictionary for the log handler has to following entries:
 
             :level:
                 the log level ("info", "error", "debug", "progress", "job_info")
@@ -1502,6 +1503,15 @@ def get_argument_parser(profile=None):
         "allowing to e.g. send notifications in the form of e.g. slack messages or emails.",
     )
 
+    group_behavior.add_argument(
+        "--log-service",
+        default=None,
+        choices=["none", "slack"],
+        help="Set a specific messaging service for logging output."
+        "Snakemake will notify the service on errors and completed execution."
+        "Currently only slack is supported.",
+    )
+
     group_cluster = parser.add_argument_group("CLUSTER")
 
     # TODO extend below description to explain the wildcards that can be used
@@ -1966,6 +1976,7 @@ def open_browser():
             # silently close
             pass
     else:
+        log_handler = []
         if args.log_handler_script is not None:
             if not os.path.exists(args.log_handler_script):
                 print(
@@ -1977,7 +1988,7 @@ def open_browser():
                 sys.exit(1)
             log_script = SourceFileLoader("log", args.log_handler_script).load_module()
             try:
-                log_handler = log_script.log_handler
+                log_handler.append(log_script.log_handler)
             except:
                 print(
                     'Error: Invalid log handler script, {}. Expect python function "log_handler(msg)".'.format(
@@ -1986,8 +1997,10 @@ def open_browser():
                     file=sys.stderr,
                 )
                 sys.exit(1)
-        else:
-            log_handler = None
+
+        if args.log_service == "slack":
+            slack_logger = logging.SlackLogger()
+            log_handler.append(slack_logger.log_handler)
 
         success = snakemake(
             args.snakefile,

snakemake/logging.py

@@ -79,6 +79,42 @@ def decorate(self, record):
         return "".join(message)
 
 
+class SlackLogger:
+    def __init__(self):
+        from slacker import Slacker
+
+        self.token = os.getenv("SLACK_TOKEN")
+        if not self.token:
+            print(
+                "The use of slack logging requires the user to set a user specific slack legacy token to the SLACK_TOKEN environment variable. Set this variable by 'export SLACK_TOKEN=your_token'. To generate your token please visit https://api.slack.com/custom-integrations/legacy-tokens."
+            )
+            exit(-1)
+        self.slack = Slacker(self.token)
+        # Check for success
+        try:
+            auth = self.slack.auth.test().body
+        except Exception:
+            print(
+                "Slack connection failed. Please compare your provided slack token exported in the SLACK_TOKEN environment variable with your online token at https://api.slack.com/custom-integrations/legacy-tokens. A different token can be set up by 'export SLACK_TOKEN=your_token'."
+            )
+            exit(-1)
+        self.own_id = auth["user_id"]
+        self.error_occured = False
+
+    def log_handler(self, msg):
+        if msg["level"] == "error" and not self.error_occured:
+            self.slack.chat.post_message(
+                self.own_id, text="At least one error occured.", username="snakemake"
+            )
+            self.error_occured = True
+
+        if msg["level"] == "progress" and msg["done"] == msg["total"]:
+            # workflow finished
+            self.slack.chat.post_message(
+                self.own_id, text="Workflow complete.", username="snakemake"
+            )
+
+
 class Logger:
     def __init__(self):
         self.logger = _logging.getLogger(__name__)
@@ -409,7 +445,7 @@ def format_resource_names(resources, omit_resources="_cores _nodes".split()):
 
 
 def setup_logger(
-    handler=None,
+    handler=[],
     quiet=False,
     printshellcmds=False,
     printreason=False,
@@ -421,9 +457,7 @@ def setup_logger(
     mode=Mode.default,
     show_failed_logs=False,
 ):
-    if handler is not None:
-        # custom log handler
-        logger.log_handler.append(handler)
+    logger.log_handler.extend(handler)
 
     # console output only if no custom logger was specified
     stream_handler = ColorizingStreamHandler(