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Commit c1f83e1a authored by Marco Del Tufo's avatar Marco Del Tufo
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Update reporting-plugins.md

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