Fix EPP log message duplication and missing log entries in Clarity 6+ when combining Python automations with LLTK/LITKs

s4/clarity/lims.py

@@ -3,6 +3,12 @@
 import logging
 import re
 import time
+
+try:
+    import urllib.parse as urlparse  # Python 3
+except ImportError:
+    import urlparse  # Python 2
+
 from xml.etree import cElementTree as ETree
 
 import requests
@@ -247,6 +253,31 @@ def properties(self):
         properties = root.findall("property")
         return dict( (property.get("name"), property.get("value")) for property in properties )
 
+    @lazy_property
+    def versions(self):
+        """
+        :type: list[dict]
+        """
+        root = self.request("get", self.root_uri + "/..")
+        versions = root.findall("version")
+        return list({
+            "uri": version.get("uri"),
+            "major": version.get("major"),
+            "minor": version.get("minor")
+        } for version in versions)
+
+    @lazy_property
+    def current_minor_version(self):
+        """
+        :type: str
+        """
+        path = urlparse.urlparse(self.root_uri).path
+        current_major_version = [x for x in path.split("/") if x][-1]
+        root = self.request("get", self.root_uri + "/..")
+        xpath = "version[@major='%s']" % current_major_version
+        version = root.findall(xpath)[0]
+        return version.get("minor")
+
     def raw_request(self, method, uri, **kwargs):
         """
         :type method: str

s4/clarity/scripts/stepepp.py

@@ -53,11 +53,24 @@ def open_log_output_stream(self):
         Use step's logfile.
         """
         if self.options.logfile:
+
+            # Log files that are shared by Python and LLTK/LITKs on a step must
+            # use the same file name in order to prevent bugs. In Clarity 5 and
+            # earlier, the file name used by LLTK/LITKs is simply the limsid of
+            # the ResultFile. But in Clarity 6 and later it has "LogFile"
+            # appended to the name, and so we need to check the active Clarity
+            # version and adjust our behaviour accordingly.
+
+            filename = self.options.logfile
+            revision = int(self.lims.current_minor_version[1:])
+            if revision >= 31:  # Clarity 6.0 has an API minor version of 31
+                filename = "%s-LogFile" % filename
+
             if self.options.log_type == 'html':
-                filename = "%s.html" % self.options.logfile
+                filename = "%s.html" % filename
                 content_type = 'text/html'
             elif self.options.log_type == 'text':
-                filename = "%s.log" % self.options.logfile
+                filename = "%s.log" % filename
                 content_type = 'text/plain'
             else:
                 raise Exception("Unrecognized log type %s", self.options.log_type)