Updaetd al config files to match new workflow invocation

mxcube · Jan 19, 2024 · 8645bd3 · 8645bd3
1 parent a0948d3
commit 8645bd3
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Showing 8 changed files with 3 additions and 49 deletions.
diff --git a/mxcubecore/HardwareObjects/Gphl/GphlWorkflowConnection.py b/mxcubecore/HardwareObjects/Gphl/GphlWorkflowConnection.py
@@ -129,11 +129,7 @@ def init(self):
                     raise ValueError("File path %s not recognised" % val)
             paths[tag] = val2
         paths["GPHL_INSTALLATION"] = locations["GPHL_INSTALLATION"]
-        if "java_binary" not in paths:
-            paths["java_binary"] = "java"
-        paths[
-            "runworkflow"
-        ] = "%s/ASTRAWorkflows/bin/runworkflow" % installdir
+        paths["runworkflow"] = "%s/ASTRAWorkflows/bin/runworkflow" % installdir
 
         for tag, val in properties.items():
             val2 = val.format(**locations)

diff --git a/mxcubecore/configuration/alba_xaloc13/gphl-setup.xml b/mxcubecore/configuration/alba_xaloc13/gphl-setup.xml
@@ -7,12 +7,7 @@
     </directory_locations>
 
     <software_paths>
-        <!--  OPTIONAL for java binary => defaults to just 'java' -->
-        <!-- <java_binary>/users/blissadm/bin/java</java_binary> -->
 
-        <!-- Gphl workflow Java classpath. -->
-        <!--Should point to all contents of workflow application directory-->
-        <gphl_java_classpath>/users/blissadm/local/gphl/gphl_java_classes/*</gphl_java_classpath>
     </software_paths>
 
     <!-- Software paths that are passed to global phasing workflow as java properties -->

diff --git a/mxcubecore/configuration/embl_hh_p14/gphl-setup.xml b/mxcubecore/configuration/embl_hh_p14/gphl-setup.xml
@@ -25,17 +25,9 @@
     <!-- HardwareRepository directories on the lookup path -->
 
     <software_paths>
-        <!--  OPTIONAL for java binary => defaults to just 'java' -->
-        <!-- <java_binary>/usr/bin/java</java_binary> -->
-        <!-- Debug mode:  -->
-        <!--<java_binary>ssh -i /home/rhfogh/.ssh/wf_test_id -o StrictHostKeyChecking=no lonsdale java</java_binary>-->
-
         <!-- Location of GPhL release, containing program binaries (or their wrapper scripts) -->
         <GPHL_INSTALLATION>{GPHL_RELEASE}/autoPROC/bin/linux64</GPHL_INSTALLATION>
 
-        <!-- Gphl workflow Java classpath. -->
-        <!--Should point to all contents of workflow application directory-->
-        <gphl_java_classpath>{GPHL_SETUP}/workflow/gphl_java_classes/lib/*</gphl_java_classpath>
 
         <!-- Directory with workflow config input, e.g. instrumentation.nml -->
 	<gphl_beamline_config>{GPHL_SETUP}/beamline_config_embl_hh_p14_202002</gphl_beamline_config>

diff --git a/mxcubecore/configuration/esrf_id30a2/gphl-setup.yml b/mxcubecore/configuration/esrf_id30a2/gphl-setup.yml
@@ -52,9 +52,6 @@ software_paths:
 
     GPHL_INSTALLATION: /home/opid30/GPhL_WorkFlow_beta-academic
 
-    # OPTIONAL for java binary => defaults to just 'java'
-#    java_binary: "/alt/rhfogh/Software/GPhL/mxcube_setup/jre1.8.0_144/bin/java"
-
     # gphl test samples directory - for collection emulation
 #    gphl_test_samples: gphl/test_samples
 

diff --git a/mxcubecore/configuration/esrf_id30b/gphl-setup.xml b/mxcubecore/configuration/esrf_id30b/gphl-setup.xml
@@ -7,12 +7,7 @@
     </directory_locations>
 
     <software_paths>
-        <!--  OPTIONAL for java binary => defaults to just 'java' -->
-        <!-- <java_binary>/sware/pub/java-1.8.0_91/linux_x64/bin/java</java_binary> -->
 
-        <!-- Gphl workflow Java classpath. -->
-        <!--Should point to all contents of workflow application directory-->
-        <gphl_java_classpath>/users/blissadm/local/gphl/gphl_java_classes/*</gphl_java_classpath>
     </software_paths>
 
     <!-- Software paths that are passed to global phasing workflow as java properties -->

diff --git a/mxcubecore/configuration/mockup/gphl/gphl-setup.xml b/mxcubecore/configuration/mockup/gphl/gphl-setup.xml
@@ -43,21 +43,12 @@
     <!-- HardwareRepository directories on the lookup path -->
 
     <software_paths>
-        <!--  OPTIONAL for java binary => defaults to just 'java' -->
-        <!-- <java_binary>{GPHL_SETUP}/jre1.8.0_144/bin/java</java_binary> -->
-        <!-- Debug mode:  -->
-        <!--<java_binary>ssh -i /home/rhfogh/.ssh/wf_test_id -o StrictHostKeyChecking=no lonsdale java</java_binary>-->
-
         <!-- Location of GPhL release, containing program binaries (or their wrapper scripts) -->
         <GPHL_INSTALLATION>{GPHL_RELEASE}/gphl_release/exe</GPHL_INSTALLATION>
 
         <!-- Location of CCP4 release binaries - required ot pass on to some wrapper scripts -->
         <GPHL_CCP4_PATH>/alt/rhfogh/Software/CCP4/latest/bin</GPHL_CCP4_PATH>
 
-        <!-- Gphl workflow Java classpath. -->
-        <!--Should point to all contents of workflow application directory-->
-        <gphl_java_classpath>{GPHL_SETUP}/workflow/gphl_java_classes/lib/*</gphl_java_classpath>
-
         <!-- Directory with workflow config input, e.g. instrumentation.nml -->
         <gphl_beamline_config>gphl_beamline_config</gphl_beamline_config>
 

diff --git a/mxcubecore/configuration/mockup/gphl/gphl-setup.yml b/mxcubecore/configuration/mockup/gphl/gphl-setup.yml
@@ -51,9 +51,6 @@ software_paths:
     # unless already sourced in environment
     GPHL_XDS_PATH: /alt/rhfogh/Software/XDS/latest/
 
-    # OPTIONAL for java binary => defaults to just 'java'
-#    java_binary: "/alt/rhfogh/Software/GPhL/mxcube_setup/java-11-openjdk-11/bin/java"
-
     # gphl test samples directory - for collection emulation
     gphl_test_samples: gphl/test_samples
 
@@ -87,8 +84,8 @@ software_properties:
     # co.gphl.wf.recen.bdg_licence_dir/fill/me/in
 
     # OPTIONAL. simcal *binary* For Mock collection emulation only. Not used by ASTRA workflow
-    co.gphl.wf.simcal.bin: /alt/rhfogh/Software/GPhL/nightly_20240118/Files_workflow_TRUNK_alpha-bdg/autoPROC/bin/linux64/simcal
-    co.gphl.wf.simcal.bdg_licence_dir: /alt/rhfogh/Software/GPhL/nightly_20240118/Files_workflow_TRUNK_alpha-bdg
+    co.gphl.wf.simcal.bin: /alt/rhfogh/Software/GPhL/nightly_20240119/Files_workflow_TRUNK_alpha-bdg/autoPROC/bin/linux64/simcal
+    co.gphl.wf.simcal.bdg_licence_dir: /alt/rhfogh/Software/GPhL/nightly_20240119/Files_workflow_TRUNK_alpha-bdg
 #    co.gphl.wf.simcal.bin: /alt/rhfogh/Software/GPhL/gphl_release/autoPROC/bin/linux64/simcal
 #    co.gphl.wf.simcal.bdg_licence_dir: /alt/rhfogh/Software/GPhL/gphl_release
 #    co.gphl.wf.simcal.bin: "{GPHL_INSTALLATION}/autoPROC/bin/linux64/simcal"/alt/rhfogh/Software/GPhL/gphl_release
diff --git a/mxcubecore/configuration/soleil/px2/production/singleton_objects/gphl-setup.xml b/mxcubecore/configuration/soleil/px2/production/singleton_objects/gphl-setup.xml
@@ -41,21 +41,12 @@
     <!-- HardwareRepository directories on the lookup path -->
 
     <software_paths>
-        <!--  OPTIONAL for java binary => defaults to just 'java' -->
-        <!--  <java_binary>{GPHL_SETUP}/jre1.8.0_144/bin/java</java_binary> -->
-        <!-- Debug mode:  -->
-        <!--<java_binary>ssh -i /home/rhfogh/.ssh/wf_test_id -o StrictHostKeyChecking=no lonsdale java</java_binary>-->
-
         <!-- Location of GPhL release, containing program binaries (or their wrapper scripts) -->
         <GPHL_INSTALLATION>{GPHL_RELEASE}/gphl_release/exe</GPHL_INSTALLATION>
 
         <!-- Location of CCP4 release binaries - required ot pass on to some wrapper scripts -->
         <!-- <GPHL_CCP4_PATH>/mnt/scratch/rhfogh/GPhL/ccp4-7.1/bin</GPHL_CCP4_PATH> -->
 
-        <!-- Gphl workflow Java classpath. -->
-        <!--Should point to all contents of workflow application directory-->
-        <gphl_java_classpath>{GPHL_SETUP}/workflow/gphl_java_classes/wfjars/*</gphl_java_classpath>
-
         <!-- Directory with workflow config input, e.g. instrumentation.nml -->
         <gphl_beamline_config>gphl_beamline_config</gphl_beamline_config>