From c1f83e1a614dbb73d34534b83faed8a77fcd6601 Mon Sep 17 00:00:00 2001
From: Marco Del Tufo <marco.deltufo@exact-lab.it>
Date: Wed, 2 Aug 2023 15:11:01 +0000
Subject: [PATCH] Update reporting-plugins.md
---
.../reporting-plugins.md | 282 ++++++++++--------
1 file changed, 160 insertions(+), 122 deletions(-)
diff --git a/docs/software-developer-documentation/legacy-server-side-extensions/reporting-plugins.md b/docs/software-developer-documentation/legacy-server-side-extensions/reporting-plugins.md
index b93b7adc76e..8027182a02c 100644
--- a/docs/software-developer-documentation/legacy-server-side-extensions/reporting-plugins.md
+++ b/docs/software-developer-documentation/legacy-server-side-extensions/reporting-plugins.md
@@ -56,17 +56,20 @@ TABLE\_MODEL
**plugin.properties**
- class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DecoratingTableModelReportingPlugin
- label = Analysis Summary
- dataset-types = HCS_IMAGE_ANALYSIS_DATA
- reporting-plugin.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.TSVViewReportingPlugin
- reporting-plugin.separator = ,
- transformation.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.EntityLinksDecorator
- transformation.link-columns = BARCODE, GENE
- transformation.BARCODE.entity-kind = SAMPLE
- transformation.BARCODE.default-space = DEMO
- transformation.GENE.entity-kind = MATERIAL
- transformation.GENE.material-type = GENE
+```
+class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DecoratingTableModelReportingPlugin
+label = Analysis Summary
+dataset-types = HCS_IMAGE_ANALYSIS_DATA
+reporting-plugin.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.TSVViewReportingPlugin
+reporting-plugin.separator = ,
+transformation.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.EntityLinksDecorator
+transformation.link-columns = BARCODE, GENE
+transformation.BARCODE.entity-kind = SAMPLE
+transformation.BARCODE.default-space = DEMO
+transformation.GENE.entity-kind = MATERIAL
+transformation.GENE.material-type = GENE
+```
+
##### Transformations
@@ -101,12 +104,15 @@ TABLE\_MODEL
**plugin.properties**
- class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.GenericDssLinkReportingPlugin
- label = Summary
- dataset-types = MS_DATA
- download-url = https://my.domain.org:8443
- data-set-regex = summary.*
- data-set-path = report
+```
+class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.GenericDssLinkReportingPlugin
+label = Summary
+dataset-types = MS_DATA
+download-url = https://my.domain.org:8443
+data-set-regex = summary.*
+data-set-path = report
+```
+
### AggregationService
@@ -136,50 +142,56 @@ This subclass must implement the method
**ExampleAggregationServicePlugin**
- package ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard;
- import java.io.File;
- import java.util.Map;
- import java.util.Properties;
- import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
- import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
- import ch.systemsx.cisd.openbis.generic.shared.util.IRowBuilder;
- import ch.systemsx.cisd.openbis.generic.shared.util.SimpleTableModelBuilder;
+```java
+package ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard;
+import java.io.File;
+import java.util.Map;
+import java.util.Properties;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
+import ch.systemsx.cisd.openbis.generic.shared.util.IRowBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.util.SimpleTableModelBuilder;
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ExampleAggregationServicePlugin extends AggregationService
+{
+ private static final long serialVersionUID = 1L;
/**
- * @author Chandrasekhar Ramakrishnan
- */
- public class ExampleAggregationServicePlugin extends AggregationService
+ * Create a new plugin.
+ *
+ * @param properties
+ * @param storeRoot
+ */
+ public ExampleAggregationServicePlugin(Properties properties, File storeRoot)
+ {
+ super(properties, storeRoot);
+ }
+ @Override
+ public TableModel createReport(Map<String, Object> parameters, DataSetProcessingContext context)
{
- private static final long serialVersionUID = 1L;
- /**
- * Create a new plugin.
- *
- * @param properties
- * @param storeRoot
- */
- public ExampleAggregationServicePlugin(Properties properties, File storeRoot)
- {
- super(properties, storeRoot);
- }
- @Override
- public TableModel createReport(Map<String, Object> parameters, DataSetProcessingContext context)
- {
- SimpleTableModelBuilder builder = new SimpleTableModelBuilder(true);
- builder.addHeader("String");
- builder.addHeader("Integer");
- IRowBuilder row = builder.addRow();
- row.setCell("String", "Hello");
- row.setCell("Integer", 20);
- row = builder.addRow();
- row.setCell("String", parameters.get("name").toString());
- row.setCell("Integer", 30);
- return builder.getTableModel();
- }
+ SimpleTableModelBuilder builder = new SimpleTableModelBuilder(true);
+ builder.addHeader("String");
+ builder.addHeader("Integer");
+ IRowBuilder row = builder.addRow();
+ row.setCell("String", "Hello");
+ row.setCell("Integer", 20);
+ row = builder.addRow();
+ row.setCell("String", parameters.get("name").toString());
+ row.setCell("Integer", 30);
+ return builder.getTableModel();
}
+}
+```
+
**plugin.properties**
- class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.ExampleAggregationServicePlugin
- label = My Report
+```
+class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.ExampleAggregationServicePlugin
+label = My Report
+```
+
#### JythonAggregationService
@@ -200,9 +212,12 @@ Plugins](/display/openBISDoc2010/Jython-based+Reporting+and+Processing+Plugins).
**plugin.properties**
- class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonAggregationService
- label = My Report
- script-path = script.py
+```
+class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonAggregationService
+label = My Report
+script-path = script.py
+```
+
### IngestionService
@@ -232,54 +247,60 @@ This subclass must implement the methodÂ
**ExampleDbModifyingAggregationService.java**
- package ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard;
- import java.io.File;
- import java.util.Map;
- import java.util.Properties;
- import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetRegistrationTransactionV2;
- import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
- import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
- import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
- import ch.systemsx.cisd.openbis.generic.shared.util.IRowBuilder;
- import ch.systemsx.cisd.openbis.generic.shared.util.SimpleTableModelBuilder;
+```java
+package ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard;
+import java.io.File;
+import java.util.Map;
+import java.util.Properties;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetRegistrationTransactionV2;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
+import ch.systemsx.cisd.openbis.generic.shared.util.IRowBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.util.SimpleTableModelBuilder;
+/**
+ * An example aggregation service
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ExampleDbModifyingAggregationService extends IngestionService<DataSetInformation>
+{
+ private static final long serialVersionUID = 1L;
/**
- * An example aggregation service
- *
- * @author Chandrasekhar Ramakrishnan
- */
- public class ExampleDbModifyingAggregationService extends IngestionService<DataSetInformation>
+ * @param properties
+ * @param storeRoot
+ */
+ public ExampleDbModifyingAggregationService(Properties properties, File storeRoot)
+ {
+ super(properties, storeRoot);
+ }
+ @Override
+ public TableModel process(IDataSetRegistrationTransactionV2 transaction,
+ Map<String, Object> parameters, DataSetProcessingContext context)
{
- private static final long serialVersionUID = 1L;
- /**
- * @param properties
- * @param storeRoot
- */
- public ExampleDbModifyingAggregationService(Properties properties, File storeRoot)
- {
- super(properties, storeRoot);
- }
- @Override
- public TableModel process(IDataSetRegistrationTransactionV2 transaction,
- Map<String, Object> parameters, DataSetProcessingContext context)
- {
- transaction.createNewSpace("NewDummySpace", null);
- SimpleTableModelBuilder builder = new SimpleTableModelBuilder(true);
- builder.addHeader("String");
- builder.addHeader("Integer");
- IRowBuilder row = builder.addRow();
- row.setCell("String", "Hello");
- row.setCell("Integer", 20);
- row = builder.addRow();
- row.setCell("String", parameters.get("name").toString());
- row.setCell("Integer", 30);
- return builder.getTableModel();
- }
+ transaction.createNewSpace("NewDummySpace", null);
+ SimpleTableModelBuilder builder = new SimpleTableModelBuilder(true);
+ builder.addHeader("String");
+ builder.addHeader("Integer");
+ IRowBuilder row = builder.addRow();
+ row.setCell("String", "Hello");
+ row.setCell("Integer", 20);
+ row = builder.addRow();
+ row.setCell("String", parameters.get("name").toString());
+ row.setCell("Integer", 30);
+ return builder.getTableModel();
}
+}
+```
+
**plugin.properties**
- class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.ExampleDbModifyingAggregationService
- label = My Report
+```
+class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.ExampleDbModifyingAggregationService
+label = My Report
+```
+
#### JythonIngestionService
@@ -302,9 +323,12 @@ Plugins](/display/openBISDoc2010/Jython-based+Reporting+and+Processing+Plugins).
**plugin.properties**
- class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonIngestionService
- label = My Report
- script-path = script.py
+```
+class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonIngestionService
+label = My Report
+script-path = script.py
+```
+
### JythonBasedReportingPlugin
@@ -325,10 +349,13 @@ Plugins](/display/openBISDoc2010/Jython-based+Reporting+and+Processing+Plugins).
**plugin.properties**
- class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonBasedReportingPlugin
- label = My Report
- dataset-types = MS_DATA, UNKNOWN
- script-path = script.py
+```
+class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonBasedReportingPlugin
+label = My Report
+dataset-types = MS_DATA, UNKNOWN
+script-path = script.py
+```
+
### TSVViewReportingPlugin
@@ -354,10 +381,13 @@ file. This reporting plugin works only for one data set.Â
**plugin.properties**
- class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.TSVViewReportingPlugin
- label = My Report
- dataset-types = MS_DATA, UNKNOWN
- separator = ;
+```
+class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.TSVViewReportingPlugin
+label = My Report
+dataset-types = MS_DATA, UNKNOWN
+separator = ;
+```
+
Screening Reporting Plugins
---------------------------
@@ -383,10 +413,13 @@ There is some extra support for screening.
**plugin.properties**
- class = ch.systemsx.cisd.openbis.dss.screening.server.plugins.jython.ScreeningJythonBasedReportingPlugin
- label = My Report
- dataset-types = HCS_IMAGE
- script-path = script.py
+```
+class = ch.systemsx.cisd.openbis.dss.screening.server.plugins.jython.ScreeningJythonBasedReportingPlugin
+label = My Report
+dataset-types = HCS_IMAGE
+script-path = script.py
+```
+
### ScreeningJythonBasedDbModifyingAggregationServiceReportingPlugin
@@ -411,10 +444,13 @@ Plugins](/display/openBISDoc2010/Jython-based+Reporting+and+Processing+Plugins).
**plugin.properties**
- class = ch.systemsx.cisd.openbis.dss.screening.server.plugins.jython.ScreeningJythonBasedReportingPlugin
- label = My Report
- dataset-types = HCS_IMAGE
- script-path = script.py
+```
+class = ch.systemsx.cisd.openbis.dss.screening.server.plugins.jython.ScreeningJythonBasedReportingPlugin
+label = My Report
+dataset-types = HCS_IMAGE
+script-path = script.py
+```
+
### ScreeningJythonBasedReportingPlugin
@@ -436,6 +472,8 @@ There is some extra support for screening.
**plugin.properties**
- class = ch.systemsx.cisd.openbis.dss.screening.server.plugins.jython.ScreeningJythonBasedAggregationServiceReportingPlugin
- label = My Report
- script-path = script.py
+```
+class = ch.systemsx.cisd.openbis.dss.screening.server.plugins.jython.ScreeningJythonBasedAggregationServiceReportingPlugin
+label = My Report
+script-path = script.py
+```
--
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