SSDM-7275 : Translating properties (ongoing work)

microscopy-migration-tool/src/ethz/ch/Experiment2Sample.java

@@ -19,18 +19,10 @@ public class Experiment2Sample
     {
         return config;
     }
-    public void setConfig(ExperimentType2SampleType config)
-    {
-        this.config = config;
-    }
+
     public ExperimentPermId getExperimentPermId()
     {
         return experimentPermId;
     }
-    public void setExperimentPermId(ExperimentPermId experimentPermId)
-    {
-        this.experimentPermId = experimentPermId;
-    }
-    
     
 }

microscopy-migration-tool/src/ethz/ch/Experiment2SampleTranslator.java

@@ -30,7 +30,7 @@ import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
 public class Experiment2SampleTranslator
 {
     
-    public static void migrate(String sessionToken, 
+    public static void translate(String sessionToken, 
                                 IApplicationServerApi v3, 
                                 IDataStoreServerApi v3dss,
                                 Experiment2Sample toMigrate, 

microscopy-migration-tool/src/ethz/ch/Main.java

@@ -84,12 +84,12 @@ public class Main
         // Experiment types to migrate as samples
         //
         
-        ExperimentType2SampleType MICROSCOPY_EXPERIMENT = new ExperimentType2SampleType("MICROSCOPY_EXPERIMENT", "MICROSCOPY_EXPERIMENTS_COLLECTION", "MICROSCOPY_EXPERIMENT_NAME");
-        ExperimentType2SampleType FACS_ARIA_EXPERIMENT = new ExperimentType2SampleType("FACS_ARIA_EXPERIMENT", "FLOW_CYTOMETRY_SORTERS", "FACS_ARIA_EXPERIMENT_NAME");
-        ExperimentType2SampleType INFLUX_EXPERIMENT = new ExperimentType2SampleType("INFLUX_EXPERIMENT", "FLOW_CYTOMETRY_SORTERS", "INFLUX_EXPERIMENT_NAME");
-        ExperimentType2SampleType LSR_FORTESSA_EXPERIMENT = new ExperimentType2SampleType("LSR_FORTESSA_EXPERIMENT", "LSR_FORTESSA_ANALYZERS", "LSR_FORTESSA_EXPERIMENT_NAME");
-        ExperimentType2SampleType MOFLO_XDP_EXPERIMENT = new ExperimentType2SampleType("MOFLO_XDP_EXPERIMENT", "FLOW_CYTOMETRY_SORTERS", "MOFLO_XDP_EXPERIMENT_NAME");
-        ExperimentType2SampleType S3E_EXPERIMENT = new ExperimentType2SampleType("S3E_EXPERIMENT", "FLOW_CYTOMETRY_SORTERS", "S3E_EXPERIMENT_NAME");
+        ExperimentType2SampleType MICROSCOPY_EXPERIMENT = new ExperimentType2SampleType("MICROSCOPY_EXPERIMENT",    "MICROSCOPY_EXPERIMENTS_COLLECTION", "MICROSCOPY_EXPERIMENT_NAME");
+        ExperimentType2SampleType FACS_ARIA_EXPERIMENT = new ExperimentType2SampleType("FACS_ARIA_EXPERIMENT",      "FLOW_SORTERS_EXPERIMENTS_COLLECTION", "FACS_ARIA_EXPERIMENT_NAME");
+        ExperimentType2SampleType INFLUX_EXPERIMENT = new ExperimentType2SampleType("INFLUX_EXPERIMENT",            "FLOW_SORTERS_EXPERIMENTS_COLLECTION", "INFLUX_EXPERIMENT_NAME");
+        ExperimentType2SampleType LSR_FORTESSA_EXPERIMENT = new ExperimentType2SampleType("LSR_FORTESSA_EXPERIMENT","FLOW_ANALYZERS_EXPERIMENTS_COLLECTION", "LSR_FORTESSA_EXPERIMENT_NAME");
+        ExperimentType2SampleType MOFLO_XDP_EXPERIMENT = new ExperimentType2SampleType("MOFLO_XDP_EXPERIMENT",      "FLOW_SORTERS_EXPERIMENTS_COLLECTION", "MOFLO_XDP_EXPERIMENT_NAME");
+        ExperimentType2SampleType S3E_EXPERIMENT = new ExperimentType2SampleType("S3E_EXPERIMENT",                  "FLOW_SORTERS_EXPERIMENTS_COLLECTION", "S3E_EXPERIMENT_NAME");
         
         //
         // 1. Installing new sample types
@@ -167,6 +167,7 @@ public class Main
             }
         }
         
+        System.out.println("3. Translate Experiment to Samples");
         
         for(ExperimentType2SampleType config:experimentMigrationConfigs) {
             int total = 0;
@@ -175,10 +176,33 @@ public class Main
             SearchResult<Experiment> experiments = v3.searchExperiments(sessionToken, experimentSearchCriteria, new ExperimentFetchOptions());
             for(Experiment experiment:experiments.getObjects()) {
                 Experiment2Sample toMigrate = new Experiment2Sample(config, experiment.getPermId());
-                Experiment2SampleTranslator.migrate(sessionToken, v3, v3dss, toMigrate, COMMIT_CHANGES_TO_OPENBIS);
+                Experiment2SampleTranslator.translate(sessionToken, v3, v3dss, toMigrate, COMMIT_CHANGES_TO_OPENBIS);
                 total++;
                 System.out.println("[DONE] " + config.getTypeCode() + "\t" + total + "/" + experiments.getTotalCount());
             }
         }
+        
+        //
+        //
+        //
+        
+        System.out.println("4. Translate Properties to Samples");
+
+        PropertyType2SampleType FACS_ARIA_TUBE =    new PropertyType2SampleType(        "FACS_ARIA_TUBE",   "FACS_ARIA_SPECIMEN",   "FACS_ARIA_SPECIMEN",   "$NAME");
+        PropertyType2SampleType FACS_ARIA_WELL =    new PropertyType2SampleType(        "FACS_ARIA_WELL",   "FACS_ARIA_SPECIMEN",   "FACS_ARIA_SPECIMEN",   "$NAME");
+        PropertyType2SampleType INFLUX_TUBE =       new PropertyType2SampleType(        "INFLUX_TUBE",      "INFLUX_SPECIMEN",      "INFLUX_SPECIMEN",      "$NAME");
+        PropertyType2SampleType LSR_FORTESSA_TUBE = new PropertyType2SampleType(        "LSR_FORTESSA_TUBE","LSR_FORTESSA_SPECIMEN","LSR_FORTESSA_SPECIMEN","$NAME");
+        PropertyType2SampleType LSR_FORTESSA_WELL = new PropertyType2SampleType(        "LSR_FORTESSA_WELL","LSR_FORTESSA_SPECIMEN","LSR_FORTESSA_SPECIMEN","$NAME");
+        PropertyType2SampleType MOFLO_XDP_TUBE =    new PropertyType2SampleType(        "MOFLO_XDP_TUBE",   "MOFLO_XDP_SPECIMEN",   "MOFLO_XDP_SPECIMEN",   "$NAME");
+        PropertyType2SampleType SE3_TUBE =          new PropertyType2SampleType(        "SE3_TUBE",         "SE3_SPECIMEN",         "SE3_SPECIMEN",         "$NAME");
+        
+        List<PropertyType2SampleType> propertiesMigrationConfigs = Arrays.asList(FACS_ARIA_TUBE,
+                FACS_ARIA_WELL,
+                INFLUX_TUBE,
+                LSR_FORTESSA_TUBE,
+                LSR_FORTESSA_WELL,
+                MOFLO_XDP_TUBE,
+                SE3_TUBE);
+        
     }
 }

microscopy-migration-tool/src/ethz/ch/Property2Sample.java

+package ethz.ch;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SamplePermId;
+
+public class Property2Sample
+{
+    private PropertyType2SampleType config;
+    private SamplePermId samplePermId;
+    
+    
+    public Property2Sample(PropertyType2SampleType config, SamplePermId samplePermId)
+    {
+        super();
+        this.config = config;
+        this.samplePermId = samplePermId;
+    }
+    
+    public PropertyType2SampleType getConfig()
+    {
+        return config;
+    }
+
+    public SamplePermId getSamplePermId()
+    {
+        return samplePermId;
+    }    
+    
+}
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microscopy-migration-tool/src/ethz/ch/Property2SampleTranslator.java

+package ethz.ch;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
+
+public class Property2SampleTranslator
+{
+    public static void translate(String sessionToken, 
+            IApplicationServerApi v3, 
+            IDataStoreServerApi v3dss,
+            Property2Sample toMigrate, 
+            boolean COMMIT_CHANGES_TO_OPENBIS) throws Exception {
+            System.out.println("[START]\t" + toMigrate.getSamplePermId());
+            
+    }
+}

microscopy-migration-tool/src/ethz/ch/PropertyType2SampleType.java

+package ethz.ch;
+
+public class PropertyType2SampleType
+{
+    private String oldSampleType;
+    private String oldPropertyCode;
+    private String newSampleType;
+    private String newPropertyCode;
+    
+    public PropertyType2SampleType(String oldSampleType, String oldPropertyCode, String newSampleType, String newPropertyCode)
+    {
+        super();
+        this.oldSampleType = oldSampleType;
+        this.oldPropertyCode = oldPropertyCode;
+        this.newSampleType = newSampleType;
+        this.newPropertyCode = newPropertyCode;
+    }
+
+    public String getOldSampleType()
+    {
+        return oldSampleType;
+    }
+
+    public String getOldPropertyCode()
+    {
+        return oldPropertyCode;
+    }
+
+    public String getNewSampleType()
+    {
+        return newSampleType;
+    }
+
+    public String getNewPropertyCode()
+    {
+        return newPropertyCode;
+    }
+    
+}
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