Merge pull request #17 from qbicsoftware/chore/examples

provide examples for property files

README.md

@@ -183,7 +183,7 @@ address) and their password, have to be provided.
 In order to interact with openBIS (transfer of data and metadata), the respective credentials need 
 to be provided, as well.
 
-**Everything but the passwords can be provided via the config file (config.txt):**
+**Everything but the passwords can be provided via the config file (e.g. config.txt):**
 
 * as=https://my-openbis-instance.de/openbis/openbis
 * dss=https://my-openbis-instance.de/datastore_server
@@ -204,6 +204,34 @@ section **Transferring Sample Types to SEEK**).
 
 * seek_openbis_sample_title=openBIS Name
 
+In order to create certain objects in SEEK, user-provided mappings need to be provided via property
+files placed in the same folder as the .jar. These are:
+
+**experiment_type_to_assay_class.properties**
+
+Here, openBIS experiment type codes are mapped to the assay class needed to create assay objects in 
+SEEK. Example entries:
+
+    PARAMETER_ESTIMATION=EXP
+    MASS_SPECTROMETRY_EXPERIMENT=EXP
+
+**experiment_type_to_assay_type.properties**
+
+Here, openBIS experiment type codes are mapped to the assay type property needed to create assay 
+objects in SEEK. Example entry:
+
+    MASS_SPECTROMETRY_EXPERIMENT=http://jermontology.org/ontology/JERMOntology#Proteomics
+
+Other fitting assay types can be found using the JERM ontology browser:
+https://bioportal.bioontology.org/ontologies/JERM/?p=classes&conceptid=http%3A%2F%2Fjermontology.org%2Fontology%2FJERMOntology%23Experimental_assay_type&lang=en
+
+**dataset_type_to_asset_type.properties**
+
+Here, openBIS dataset type codes are mapped to the asset type created in SEEK. Example entries:
+
+    SOURCE_CODE=documents
+    UNKNOWN=data_files
+
 Refer to the help of the respective command or the examples below for more details.
 
 ### Transferring Sample Types to SEEK

dataset_type_to_asset_type.properties

@@ -0,0 +1,3 @@
+SOURCE_CODE=documents
+UNKNOWN=data_files
+TEST_DAT=data_files

experiment_type_to_assay_class.properties

@@ -0,0 +1,2 @@
+PARAMETER_ESTIMATION=EXP
+MASS_SPECTROMETRY_EXPERIMENT=EXP

experiment_type_to_assay_type.properties

@@ -0,0 +1 @@
+MASS_SPECTROMETRY_EXPERIMENT=http://jermontology.org/ontology/JERMOntology#Proteomics

openbis_datatype_to_seek_attributetype.xml

@@ -0,0 +1,64 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<properties>
+	<entry type="INTEGER">
+		<seek_id>4</seek_id>
+		<seek_title>Integer</seek_title>
+		<seek_type>Integer</seek_type>
+	</entry>
+	<entry type="VARCHAR">
+		<seek_id>8</seek_id>
+		<seek_title>String</seek_title>
+		<seek_type>String</seek_type>
+	</entry>
+	<entry type="MULTILINE_VARCHAR">
+		<seek_id>7</seek_id>
+		<seek_title>Text</seek_title>
+		<seek_type>Text</seek_type>
+	</entry>
+	<entry type="REAL">
+		<seek_id>3</seek_id>
+		<seek_title>Real number</seek_title>
+		<seek_type>Float</seek_type>
+	</entry>
+	<entry type="TIMESTAMP">
+		<seek_id>1</seek_id>
+		<seek_title>Date time</seek_title>
+		<seek_type>DateTime</seek_type>
+	</entry>
+	<entry type="BOOLEAN">
+		<seek_id>16</seek_id>
+		<seek_title>Boolean</seek_title>
+		<seek_type>Boolean</seek_type>
+	</entry>
+	<entry type="CONTROLLEDVOCABULARY">
+		<seek_id>8</seek_id>
+		<seek_title>String</seek_title>
+		<seek_type>String</seek_type>
+	</entry>
+	<entry type="MATERIAL">
+		<seek_id>8</seek_id>
+		<seek_title>String</seek_title>
+		<seek_type>String</seek_type>
+	</entry>
+	<entry type="HYPERLINK">
+		<seek_id>8</seek_id>
+		<seek_title>String</seek_title>
+		<seek_type>String</seek_type>
+	</entry>
+	<entry type="XML">
+		<seek_id>7</seek_id>
+		<seek_title>Text</seek_title>
+		<seek_type>Text</seek_type>
+	</entry>
+	<entry type="SAMPLE">
+		<seek_id>5</seek_id>
+		<seek_title>Web link</seek_title>
+		<seek_type>String</seek_type>
+	</entry>
+	<entry type="DATE">
+		<seek_id>2</seek_id>
+		<seek_title>Date time</seek_title>
+		<seek_type>Date</seek_type>
+	</entry>
+</properties>
+

src/main/java/life/qbic/model/OpenbisSeekTranslator.java

@@ -138,9 +138,9 @@ public SeekStructure translateForRO(OpenbisExperimentWithDescendants experiment,
    */
   private void parseConfigs() throws IOException, ParserConfigurationException, SAXException {
     final String dataTypeToAttributeType = "openbis_datatype_to_seek_attributetype.xml";
-    final String datasetToAssaytype = "dataset_type_to_assaytype.properties";
+    final String datasetToAssaytype = "dataset_type_to_asset_type.properties";
     final String experimentTypeToAssayClass = "experiment_type_to_assay_class.properties";
-    final String experimentTypeToAssayType = "openbis_experiment_type_to_seek_assaytype.properties";
+    final String experimentTypeToAssayType = "experiment_type_to_assay_type.properties";
     this.experimentTypeToAssayType = PropertyReader.getProperties(experimentTypeToAssayType);
     this.datasetTypeToAssetType = PropertyReader.getProperties(datasetToAssaytype);
     this.experimentTypeToAssayClass = PropertyReader.getProperties(experimentTypeToAssayClass);