diff --git a/app-openbis-installer/resource/installer/userInputSpec.xml b/app-openbis-installer/resource/installer/userInputSpec.xml
index ccd5cfeee4848f22458c3e29761d095443de7a36..8b5cb907637d95d974d63306237e58e83c3339d8 100644
--- a/app-openbis-installer/resource/installer/userInputSpec.xml
+++ b/app-openbis-installer/resource/installer/userInputSpec.xml
@@ -65,9 +65,6 @@
<field type="check" variable="FLOW">
<spec txt="Flow Cytometry" true="true" false="false"/>
</field>
- <field type="check" variable="ILLUMINA-NGS">
- <spec txt="Illumina NGS (ETH BSSE Setup)" true="true" false="false"/>
- </field>
</panel>
<panel id="UserInputPanel.MISC">
diff --git a/app-openbis-installer/resource/tarball/console.properties b/app-openbis-installer/resource/tarball/console.properties
index 1376d869be9accd283468dfbceed6fa3629a5d1f..cce8ca67137f25ca307bb67bf0e84bcdc2821cce 100644
--- a/app-openbis-installer/resource/tarball/console.properties
+++ b/app-openbis-installer/resource/tarball/console.properties
@@ -35,9 +35,6 @@ KEY_STORE_PASSWORD = changeit
# Password of the key
KEY_PASSWORD = changeit
-# Standard technology ILLUMINA-NGS (ETH BSSE Setup) is disabled by default
-#ILLUMINA-NGS = true
-
# Standard technology ELN-LIMS is disabled by default
#ELN-LIMS = true
diff --git a/app-openbis-installer/source/java/ch/systemsx/cisd/openbis/installer/izpack/GlobalInstallationContext.java b/app-openbis-installer/source/java/ch/systemsx/cisd/openbis/installer/izpack/GlobalInstallationContext.java
index 67715f300714504d03a2620506b0ad7c822d5e9e..af33ae53a1f31cb240535ece0f9905bc8478de49 100644
--- a/app-openbis-installer/source/java/ch/systemsx/cisd/openbis/installer/izpack/GlobalInstallationContext.java
+++ b/app-openbis-installer/source/java/ch/systemsx/cisd/openbis/installer/izpack/GlobalInstallationContext.java
@@ -43,8 +43,6 @@ public class GlobalInstallationContext
public static final String BACKUP_FOLDER_VARNAME = "BACKUP_FOLDER";
- public static final String TECHNOLOGY_ILLUMINA_NGS = "ILLUMINA-NGS";
-
public static final String TECHNOLOGY_ELN_LIMS = "ELN-LIMS";
public static final String TECHNOLOGY_ELN_LIMS_TEMPLATE_TYPES = "ELN-LIMS-TEMPLATE-TYPES";
@@ -56,7 +54,7 @@ public class GlobalInstallationContext
public static final String TECHNOLOGY_SHARED_MICROSCOPY_FLOW_CYTOMETRY = "SHARED";
public static final String[] TECHNOLOGIES =
- { TECHNOLOGY_ILLUMINA_NGS, TECHNOLOGY_ELN_LIMS, TECHNOLOGY_MICROSCOPY,
+ { TECHNOLOGY_ELN_LIMS, TECHNOLOGY_MICROSCOPY,
TECHNOLOGY_FLOW_CYTOMETRY, TECHNOLOGY_ELN_LIMS_TEMPLATE_TYPES };
/**
diff --git a/core-plugin-openbis/dist/tarball/installer/data/doc/getting-started-with-openBIS.html b/core-plugin-openbis/dist/tarball/installer/data/doc/getting-started-with-openBIS.html
index 087d6e1a246b4999a231532fe4e89b5a1a6ce6b3..f130820139d88a0c820979bc8feecf6d140d3593 100644
--- a/core-plugin-openbis/dist/tarball/installer/data/doc/getting-started-with-openBIS.html
+++ b/core-plugin-openbis/dist/tarball/installer/data/doc/getting-started-with-openBIS.html
@@ -71,74 +71,6 @@
<p></p>
- <h4 class="illumina-ngs">Illumina NGS (ETH BSSE Setup)</h4>
-
- <ol>
- <li>A flow cell with flow lanes is created reading out two XML files provided by the Illumina sequencer:
-
- <div class="sourcecode">
- mkdir -p ${DSS_ROOT_DIR}/create-flowcell-hiseq/120420_SN792_0109_BC0P8LACXX/;<br>
- cp -R ${DSS_ROOT_DIR}/examples/illumina-ngs/120420_SN792_0109_BC0P8LACXX/*.xml
- ${DSS_ROOT_DIR}/create-flowcell-hiseq/120420_SN792_0109_BC0P8LACXX;<br>
- touch ${DSS_ROOT_DIR}/create-flowcell-hiseq/.MARKER_is_finished_120420_SN792_0109_BC0P8LACXX<br>
- </div>
- </li>
-
- <li>A flow cell output from a HiSeq2000 is registered as a data set of the object 120420_SN792_0109_BC0P8LACXX.<br>
-
- Additionally a data set is registered for each flow lane:
-
- <div class="sourcecode">
- rsync -a --exclude=Unaligned* ${DSS_ROOT_DIR}/examples/illumina-ngs/120420_SN792_0109_BC0P8LACXX
- ${DSS_ROOT_DIR}/register-flowcell-hiseq;<br>
- touch ${DSS_ROOT_DIR}/register-flowcell-hiseq/.MARKER_is_finished_120420_SN792_0109_BC0P8LACXX;<br>
- </div>
- </li>
-
- <li>The sequencer is finished and we want to track this automatically. Therefore we sync the RTAComplete.txt in a
- drop box:
-
- <div class="sourcecode">
- mkdir -p ${DSS_ROOT_DIR}/read-rta-timestamp/120420_SN792_0109_BC0P8LACXX/; rsync
- ${DSS_ROOT_DIR}/examples/illumina-ngs/120420_SN792_0109_BC0P8LACXX/RTAComplete.txt
- ${DSS_ROOT_DIR}/read-rta-timestamp/120420_SN792_0109_BC0P8LACXX/RTAComplete.txt; touch
- ${DSS_ROOT_DIR}/read-rta-timestamp/.MARKER_is_finished_120420_SN792_0109_BC0P8LACXX
- </div>
- </li>
-
- <li> For creating some objects we use the 'Object Registration'. This is available under the 'Import' menu: <br>
- Import -> Object Registration -> Choose object type '(multiple)' and browse to the file:
- <div class="sourcecode"> ${DSS_ROOT_DIR}/examples/illumina-ngs/tsv-files/example_samples_with_parents.tsv</div>
-
- Tick 'Update existing'and press the 'Save' button. <br>
- This created several objects which can be viewed via Browse -> Objects. You might need to select the Object Type 'all' <br>
- and the Space 'all'. <br>
- Note that the objects are in a parent-/child relationship indicated by the objects shown in the 'Parents' column.
- </li>
-
- <br>
-
-
- <li>After the demultiplexing using the Illumina 'configureBclToFastq.pl' the FASTQ files are created and also some
- statistic files are provided.<br>
- Let's register them as well in openBIS:
-
- <div class="sourcecode">
-
- mkdir ${DSS_ROOT_DIR}/register-unaligned/120420_SN792_0109_BC0P8LACXX; <br>
- rsync -a ${DSS_ROOT_DIR}/examples/illumina-ngs/120420_SN792_0109_BC0P8LACXX/Unaligned* ${DSS_ROOT_DIR}/register-unaligned/120420_SN792_0109_BC0P8LACXX;<br>
- touch ${DSS_ROOT_DIR}/register-unaligned/.MARKER_is_finished_120420_SN792_0109_BC0P8LACXX;
- </div>
- <br>
- The demultiplexed FASTQ files are a data set of the objects BSSE-QGF-LIBRARY-1 and BSSE-QGF-LIBRARY-2. Note that lane 1 and two <br>
- contained both objects which results in two FASTQ data sets for each object.
-
- </li>
- </ol><br>
- A short description of all drop boxes is also provided here: <a href=
- "https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+for+Illumina+NGS" target="_blank">openBIS for Illumina
- NGS<a><br>
-
<h4 class="eln-lims">ELN-LIMS</h4>
<p>Here are the steps to create your first experimental step and register an image file as preview into the ELN-LIMS interface.</p>
diff --git a/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityPropertyTypeDAO.java b/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityPropertyTypeDAO.java
index 9051a4a7af9f30378e4ec43d917a3dc0a21d5f45..fc7c680c3a2da20714103275ecbb2a2e2eeedd21 100644
--- a/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityPropertyTypeDAO.java
+++ b/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityPropertyTypeDAO.java
@@ -549,11 +549,15 @@ final class EntityPropertyTypeDAO extends AbstractDAO implements IEntityProperty
assert propertyTypeCode != null : "Unspecified property type.";
String query =
- String.format("SELECT count(pv) FROM %s pa join pa.propertyValues pv "
- + "WHERE pa.propertyTypeInternal.simpleCode = ? "
- + "AND pa.entityTypeInternal.code = ?",
+ String.format("SELECT count(pv.id) FROM %s pa join %s pv "
+ + " ON pa.id = pv.entityTypePropertyType.id "
+ + " WHERE pa.propertyTypeInternal.simpleCode = ? "
+ + " AND pa.entityTypeInternal.code = ?",
entityKind
- .getEntityTypePropertyTypeAssignmentClass().getSimpleName());
+ .getEntityTypePropertyTypeAssignmentClass().getSimpleName(),
+ entityKind.getEntityPropertyClass().getSimpleName()
+ );
+
return ((Long) (getHibernateTemplate().find(query,
toArray(propertyTypeCode, entityTypeCode)).get(0))).intValue();
}
diff --git a/server-original-data-store/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPropertiesPanel.java b/server-original-data-store/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPropertiesPanel.java
index e928dc312c56db9feb1ffd14bdf9dbf9911c10ff..22a53c2ad2bc511b455e1486e389294898b88b99 100644
--- a/server-original-data-store/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPropertiesPanel.java
+++ b/server-original-data-store/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPropertiesPanel.java
@@ -319,7 +319,7 @@ public class DataSetPropertiesPanel extends JPanel
} else if (formField instanceof VocabularyTermsComboBoxPanel)
{
VocabularyTermsComboBoxPanel comboBox = (VocabularyTermsComboBoxPanel) formField;
- if(propertyValue.getClass().isArray()){
+ if(propertyValue != null && propertyValue.getClass().isArray()){
Serializable[] values = (Serializable[]) propertyValue;
for(Serializable val : values) {
setVocabToComboBox(comboBox, (String) val);