Release v1.6.0 (#62)

* Updated version.py and changelog for 1.6.0 release

* Declare support for Python 3.12 in setup.py (#60)

* Fix EPP log message duplication and missing log entries in Clarity 6+ when combining Python automations with LLTK/LITKs (#51)

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

* Fix current_minor_version failure on Python 2

* StepRunner: ignore archived reagent kits when adding default reagents to a step (#53)

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

* Fix current_minor_version failure on Python 2

* StepRunner: ignore archived reagent kits when adding default reagents to a step

* check for placement node that matches uri before creating one (#55)

* check for placement node that matches uri before creating one

* add missing quotes, fix for py2

* remove f

* Fix coveralls on Python 3.6 (#52)

* Enable automated unit testing with Python 3.12 (#56)

* Fix coveralls on Python 3.6

* Enable automated unit testing with Python 3.12

* Only trigger a production PyPi build on tags using semantic versioning (#57)

* Use latest versions of GitHub workflow actions, build with Python 3.12 (#58)

* Enable automated unit testing for Python 3.5 (#59)

* Fix coveralls parallel builds (#61)

---------

Co-authored-by: Scott Small <scott.small@semaphoresolutions.ca>

---------

Co-authored-by: Joe Rickwalder <jrickwalder@billiontoone.com>

CHANGELOG.md

@@ -1,5 +1,13 @@
 Release History
 ===============
+1.6.0
+-
+- (#60) Added support for Python 3.12.
+- (#55) Step placements can now be updated without having to clear existing placements first.
+- (#53) Fix an issue that prevented `StepRunner.add_default_reagents()` from working correctly on Clarity 6.1+ if the step being run contains an archived reagent kit.
+- (#51) Fix an issue that could cause log messages to become duplicated, or disappear, when `s4-clarity-lib` is being used in tandem with an LLTK/LITK on the same step in Clarity 6.0+.
+- (#51) Added `lims.versions` and `lims.current_minor_version` properties.
+
 1.5.0
 -
 - (#45) Added the `permitted_containers` property to `StepConfiguration`.

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)

s4/clarity/step.py

@@ -534,7 +534,9 @@ def create_placement(self, artifact, container, well_string):
         :param well_string: The location on the plate to place the artifact
         """
         placement_root = self.xml_root.find("./output-placements")
-        placement_node = ETree.SubElement(placement_root, "output-placement", {"uri": artifact.uri})
+        placement_node = self.xml_root.find("./output-placements/output-placement[@uri='" + artifact.uri + "']")
+        if not placement_node:
+            placement_node = ETree.SubElement(placement_root, "output-placement", {"uri": artifact.uri})
         location_subnode = ETree.SubElement(placement_node, "location")
         ETree.SubElement(location_subnode, "container", {"uri": container.uri})
         ETree.SubElement(location_subnode, "value").text = well_string

s4/clarity/steputils/step_runner.py

@@ -340,10 +340,15 @@ def add_default_reagents(self):
         """
         For every required reagent kit in the step, the first active lot
         will be selected. If there are no active lots it will be omitted.
+
+        Archived kits will be ignored on Clarity 6.1 (api revision 32) and later.
         """
+        revision = int(self.lims.current_minor_version[1:])
         log.info("Adding default reagent lots.")
         lots = []
         for kit in self.step.configuration.required_reagent_kits:
+            if revision >= 32 and kit.archived:
+                continue
             for lot in kit.related_reagent_lots:
                 if lot.status == "ACTIVE":
                     lots.append(lot)

s4/clarity/version.py

@@ -1,4 +1,4 @@
 # Copyright 2019 Semaphore Solutions, Inc.
 # ---------------------------------------------------------------------------
 
-__version__ = '1.5.0'
+__version__ = '1.6.0'

setup.py

@@ -39,6 +39,7 @@
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
         'Programming Language :: Python :: Implementation :: PyPy'
     ],
     install_requires=(