diff --git a/annotation/.classpath b/annotation/.classpath
index 71a86ecfe6e0f3ee403397c37963606b5852c085..fae1a2b37d5e3386c9651caedb78b9bd107715bd 100644
--- a/annotation/.classpath
+++ b/annotation/.classpath
@@ -30,7 +30,6 @@
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
<attributes>
<attribute name="maven.pomderived" value="true"/>
- <attribute name="org.eclipse.jst.component.nondependency" value=""/>
</attributes>
</classpathentry>
<classpathentry kind="output" path="target/classes"/>
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java
index d02dab68420999703a8bf06da4fb3df3754883a1..95f7c6be70dd753e142dbbfa1108596251446ded 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java
@@ -73,6 +73,14 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
+ " (GENE section in the KEGG enzyme record) should be imported."
+ " Currently ATH (Arabidopsis Thaliana) is supported.");
this.addParameterDefinition(paramDef);
+
+ this.addParameterDefinition(new AnnotatorParamDefinition("test string1", String.class, "test string1 comment"));
+ this.addParameterDefinition(new AnnotatorParamDefinition("test int1", Integer.class, "int1 comment"));
+ this.addParameterDefinition(new AnnotatorParamDefinition("test bool1", Boolean.class, "boolean comment"));
+ this.addParameterDefinition(new AnnotatorParamDefinition("test bool2", Boolean.class, "boolean comment 2"));
+ this.addParameterDefinition(new AnnotatorParamDefinition("test int2", Integer.class, "int2 comment"));
+ this.addParameterDefinition(new AnnotatorParamDefinition("test int3", Integer.class, "int3 comment"));
+ this.addParameterDefinition(new AnnotatorParamDefinition("test string2", String.class, "test string2 comment"));
}
@Override
@@ -112,16 +120,6 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
return status;
}
- //private Boolean resourceInCollection(String resource, Collection<MiriamData> list) {
- //
- // for (MiriamData md: list) {
- // if (md.getResource() == resource) {
- // return true;
- // }
- //
- // }
- // return false;
- //}
@Override
public void annotateElement(BioEntity object) throws AnnotatorException {
diff --git a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
index 322d356fffb6be4bd58920298e40692410da5ed2..b5c8cd956340fb6f24b2118cefc06eb3aa602dd9 100644
--- a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
+++ b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
@@ -57,18 +57,18 @@ ChooseAnnotatorsDialog.prototype.createGui = function () {
self.getElement().appendChild(content);
};
-function onChangeParameterValue(element, user){
- var value = element;
+function onChangeParameterValue(element, user){
var name = $(element).siblings(".minerva-annotator-param-name").text();
var annotatorClassName = $(element).parent().parent().attr('name');
-
+
var data = new UserPreferences();
var annotatorsParams = {};
- annotatorsParams[annotatorClassName] = {name: value};
+ annotatorsParams[annotatorClassName] = {};
+ annotatorsParams[annotatorClassName][name] = element.value;
data.setAnnotatorsParameters(annotatorsParams);
- return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
-
+
+ return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
}
ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
@@ -93,6 +93,7 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
var annotators = configuration.getElementAnnotators(elementType);
var selectedAnnotators = user.getPreferences().getElementAnnotators(elementType.className);
+ var existingAnnotatorsParameters = user.getPreferences().getAnnotatorsParameters();
for (var i = 0; i < annotators.length; i++) {
var annotator = annotators[i];
@@ -103,6 +104,7 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
var paramsDefs = annotator.getParametersDefinitions();
if (paramsDefs.length > 0) {
+
annotatorsParams.appendChild(Functions.createElement({
type: "div",
className: "minerva-annotators-params-header",
@@ -122,7 +124,7 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
}));
for (var k = 0; k < paramsDefs.length; k++) {
- var param = paramsDefs[k];
+ var param = paramsDefs[k];
var paramElement = Functions.createElement({
type: "div",
className: "minerva-annotator-param"
@@ -135,11 +137,20 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
}));
var paramValue;
+
+ var existingParamValue;
+ if (existingAnnotatorsParameters[annotator.getClassName()]) {
+ existingParamValue = existingAnnotatorsParameters[annotator.getClassName()][param.name]
+ }
+
+ console.log('existingParamValue', existingParamValue);
+
if (param.type.indexOf("String") >= 0) {
paramValue = Functions.createElement({
type: "textarea",
onchange: function(){return onChangeParameterValue(this, user);}
});
+ if (existingParamValue) paramValue.value = existingParamValue;
} else if (param.type.indexOf("Integer") >= 0) {
paramValue = Functions.createElement({
type: "input",
@@ -157,7 +168,7 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
}
paramElement.appendChild(paramValue);
- annotatorParams.appendChild(paramElement);
+ annotatorParams.appendChild(paramElement);
}
annotatorsParams.appendChild(annotatorParams);
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java b/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java
index 2e919ca9930498c3eae0de35228e854c58ec84cf..e892d82d38466dbc33b1089f8934921fbe173f71 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java
@@ -91,6 +91,14 @@ public class UserAnnotationSchema implements Serializable {
@OneToMany(mappedBy = "annotationSchema")
@OrderBy("id")
private List<UserClassAnnotators> classAnnotators = new ArrayList<>();
+
+ /**
+ * List of class annotators params.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "annotationSchema")
+ @OrderBy("id")
+ private List<UserAnnotatorsParams> annotatorsParams = new ArrayList<>();
/**
* List of valid annotations for given object type.
@@ -158,6 +166,21 @@ public class UserAnnotationSchema implements Serializable {
public void setClassAnnotators(List<UserClassAnnotators> classAnnotators) {
this.classAnnotators = classAnnotators;
}
+
+ /**
+ * @return the annotatorsParams
+ */
+ public List<UserAnnotatorsParams> getAnnotatorsParams() {
+ return annotatorsParams;
+ }
+
+ /**
+ * @param annotatorsParams
+ * the annotatorsParams to set
+ */
+ public void setAnnotatorsParams(List<UserAnnotatorsParams> annotatorsParams) {
+ this.annotatorsParams = annotatorsParams;
+ }
/**
* @return the classValidAnnotators
@@ -201,6 +224,42 @@ public class UserAnnotationSchema implements Serializable {
}
ca.setAnnotationSchema(this);
}
+
+ /**
+ * Adds (or updates) {@link UserAnnotatorsParams} information
+ * to {@link #annotatorsParams}.
+ *
+ * @param ap
+ * object to add/update
+ */
+ public void addAnnotatorParam(UserAnnotatorsParams ap) {
+ if (ap.getAnnotatorClassName() == null) {
+ throw new InvalidArgumentException("Class name cannot be null");
+ }
+ if (ap.getParamName() == null) {
+ throw new InvalidArgumentException("Parameter name cannot be null");
+ }
+ if (ap.getParamValue() == null) {
+ throw new InvalidArgumentException("Parameter value cannot be null");
+ }
+
+ for (int i = 0; i < this.annotatorsParams.size(); i++) {
+ UserAnnotatorsParams params = this.annotatorsParams.get(i);
+ if (params.getAnnotatorClassName().equals(ap.getAnnotatorClassName()) &&
+ params.getParamName().equals(ap.getParamName())) {
+ this.annotatorsParams.get(i).setParamValue(ap.getParamValue());
+ } else {
+ ap.setAnnotationSchema(this);
+ this.annotatorsParams.add(ap);
+ }
+ }
+
+ if (this.annotatorsParams.size() == 0) {
+ ap.setAnnotationSchema(this);
+ this.annotatorsParams.add(ap);
+ }
+
+ }
/**
* Adds (or updates) {@link UserClassValidAnnotations valid annotation}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotatorsParams.java b/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotatorsParams.java
new file mode 100644
index 0000000000000000000000000000000000000000..36822aaafc57918c2f5cead97fffdefe634798fc
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotatorsParams.java
@@ -0,0 +1,166 @@
+package lcsb.mapviewer.model.user;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+
+/**
+ * This class defines set of annotators parameters that are used by a user.
+ *
+ * @author David Hoksza
+ *
+ */
+@Entity
+@Table(name = "annotators_params_table")
+public class UserAnnotatorsParams implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private Integer id;
+
+ /**
+ * {@link UserAnnotationSchema} that defines which user is using this set of
+ * annotators.
+ */
+ @ManyToOne
+ private UserAnnotationSchema annotationSchema;
+
+
+ /**
+ * Classname of the annotator {@link #paramName parameter} of which is being set to the {@link #paramValue value}.
+ */
+ @Column(name = "annotator_classname", nullable = false)
+ private Class<?> annotatorClassName;
+
+ /**
+ * Parameter name to be set.
+ */
+ @Column(name = "name", nullable = false)
+ private String paramName;
+
+ /**
+ * Parameter value to be set.
+ */
+ @Column(name = "value", nullable = false)
+ private String paramValue;
+
+ /**
+ * Default constructor.
+ */
+ public UserAnnotatorsParams() {
+
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param objectClass
+ * {@link #className}
+ * @param annotators
+ * {@link #annotators}
+ */
+ public UserAnnotatorsParams(Class<?> annotatorClassName, String paramName, String paramValue) {
+ setAnnotatorClassName(annotatorClassName);
+ setParamName(paramName);
+ setParamValue(paramValue);
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public Integer getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(Integer id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the annotationSchema
+ * @see #annotationSchema
+ */
+ public UserAnnotationSchema getAnnotationSchema() {
+ return annotationSchema;
+ }
+
+ /**
+ * @param annotationSchema
+ * the annotationSchema to set
+ * @see #annotationSchema
+ */
+ public void setAnnotationSchema(UserAnnotationSchema annotationSchema) {
+ this.annotationSchema = annotationSchema;
+ }
+
+ /**
+ * @return the className
+ * @see #className
+ */
+ public Class<?> getAnnotatorClassName() {
+ return annotatorClassName;
+ }
+
+ /**
+ * @param className
+ * the className to set
+ * @see #className
+ */
+ public void setAnnotatorClassName(Class<?> annotatorClassName) {
+ this.annotatorClassName = annotatorClassName;
+ }
+
+ /**
+ * @return the parameter name
+ * @see #paramName
+ */
+ public String getParamName() {
+ return paramName;
+ }
+
+ /**
+ * @param paramName
+ * the {@link UserAnnotatorsParams#paramName} to set
+ */
+ public void setParamName(String paramName) {
+ this.paramName = paramName;
+ }
+
+ /**
+ * @return the parameter value
+ * @see #paramValue
+ */
+ public String getParamValue() {
+ return paramValue;
+ }
+
+ /**
+ * @param parameter value
+ * the {@link UserAnnotatorsParams#paramValue} to set
+ */
+ public void setParamValue(String paramValue) {
+ this.paramValue = paramValue;
+ }
+}
diff --git a/persist/src/db/12.0.0/fix_db_20180125.sql b/persist/src/db/12.0.0/fix_db_20180125.sql
index dcc8ee57e39e438781ef7a05e2633d6774345537..9be36abf2fdb54f2a6d8aaea885d9c0af10fa4ee 100644
--- a/persist/src/db/12.0.0/fix_db_20180125.sql
+++ b/persist/src/db/12.0.0/fix_db_20180125.sql
@@ -1,3 +1,5 @@
DELETE FROM cache_type WHERE classname = 'lcsb.mapviewer.annotation.services.annotators.KeggAnnotator';
INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotation.services.annotators.KeggAnnotator');
+UPDATE class_annotator_annotators_table SET annotator_name = 'TAIR' WHERE annotator_name = 'TAIR Locus'
+
diff --git a/persist/src/db/12.0.0/fix_db_20180126.sql b/persist/src/db/12.0.0/fix_db_20180126.sql
new file mode 100644
index 0000000000000000000000000000000000000000..1c227560daf96ef5325474e27cc5007e8b7f1b6d
--- /dev/null
+++ b/persist/src/db/12.0.0/fix_db_20180126.sql
@@ -0,0 +1,19 @@
+CREATE SEQUENCE annotators_params_table_iddb_seq
+ INCREMENT 1
+ MINVALUE 1
+ MAXVALUE 9223372036854775807
+ START 1
+ CACHE 1;
+
+CREATE TABLE annotators_params_table
+(
+ iddb integer NOT NULL DEFAULT nextval('annotators_params_table_iddb_seq'::regclass),
+ annotationschema_iddb integer,
+ annotator_classname character varying(255) NOT NULL,
+ name character varying(255) NOT NULL,
+ value character varying(255) NOT NULL,
+ CONSTRAINT annotators_params_pkey PRIMARY KEY (iddb),
+ CONSTRAINT annotators_params_user_annotation_schema_fk FOREIGN KEY (annotationschema_iddb)
+ REFERENCES user_annotation_schema_table (iddb) MATCH SIMPLE
+ ON UPDATE NO ACTION ON DELETE NO ACTION
+);
\ No newline at end of file
diff --git a/persist/src/main/resources/applicationContext-persist.xml b/persist/src/main/resources/applicationContext-persist.xml
index 718f752f950dbf2dd1f2886e95842d24a54e4b5c..a4c758484060b50253fa9d42cfbed876dcacb874 100644
--- a/persist/src/main/resources/applicationContext-persist.xml
+++ b/persist/src/main/resources/applicationContext-persist.xml
@@ -85,8 +85,9 @@
<value>lcsb.mapviewer.model.user.Configuration</value>
<value>lcsb.mapviewer.model.user.ObjectPrivilege</value>
<value>lcsb.mapviewer.model.user.User</value>
+ <value>lcsb.mapviewer.model.user.UserAnnotatorsParams</value>
<value>lcsb.mapviewer.model.user.UserAnnotationSchema</value>
- <value>lcsb.mapviewer.model.user.UserClassAnnotators</value>
+ <value>lcsb.mapviewer.model.user.UserClassAnnotators</value>
<value>lcsb.mapviewer.model.user.UserClassValidAnnotations</value>
<value>lcsb.mapviewer.model.user.UserClassRequiredAnnotations</value>
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
index 0dd97ad5f6c08a59e50694a418a6e7c4630bc6b6..c105de496996c1cc7beb497a6120d635e745d5b8 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
@@ -23,6 +23,7 @@ import lcsb.mapviewer.model.user.ObjectPrivilege;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.model.user.UserAnnotationSchema;
+import lcsb.mapviewer.model.user.UserAnnotatorsParams;
import lcsb.mapviewer.model.user.UserClassAnnotators;
import lcsb.mapviewer.model.user.UserClassRequiredAnnotations;
import lcsb.mapviewer.model.user.UserClassValidAnnotations;
@@ -133,8 +134,29 @@ public class UserRestImpl extends BaseRestImpl {
result.put("element-annotators", prepareElementAnnotators(schema.getClassAnnotators()));
result.put("element-required-annotations", prepareRequiredAnnotations(schema.getClassRequiredAnnotators()));
result.put("element-valid-annotations", prepareValidAnnotations(schema.getClassValidAnnotators()));
+ result.put("annotators-parameters", prepareAnnotatorsParams(schema.getAnnotatorsParams()));
return result;
}
+
+ /**
+ * Prepares annotator parameters in the form of a map having annotators
+ * class names as keys and map of name:value pairs of given annotator as values.
+ * @param annotatorsParams
+ * @return
+ */
+ private Map<String, Object> prepareAnnotatorsParams(List<UserAnnotatorsParams> annotatorsParams) {
+ Map<String, Object> result = new HashMap<>();
+ for (UserAnnotatorsParams param : annotatorsParams) {
+ String className = param.getAnnotatorClassName().getName();
+ Map<String, String> annotatorParams = (Map<String, String>)result.get(className);
+ if (annotatorParams == null) {
+ annotatorParams = new HashMap<>();
+ result.put(className, annotatorParams);
+ }
+ annotatorParams.put(param.getParamName(), param.getParamValue());
+ }
+ return result;
+ }
private Map<String, Object> prepareValidAnnotations(List<UserClassValidAnnotations> classValidAnnotators) {
Map<String, Object> result = new HashMap<>();
@@ -164,8 +186,19 @@ public class UserRestImpl extends BaseRestImpl {
}
}
- private void updateAnnotatorsParams(UserAnnotationSchema schema, Map<String, Object> data) {
-
+ private void updateAnnotatorsParams(UserAnnotationSchema schema, Map<String, Object> data) throws QueryException {
+ for (String annotatorClassname : data.keySet()) {
+ Map<String, Object> nameValueS = (Map<String, Object>)data.get(annotatorClassname);
+ for (String name: nameValueS.keySet()) {
+ String value = (String)nameValueS.get(name);
+ try {
+ UserAnnotatorsParams param = new UserAnnotatorsParams(Class.forName(annotatorClassname), name, value);
+ schema.addAnnotatorParam(param);
+ } catch (ClassNotFoundException e) {
+ throw new QueryException("Unknown annotator class name: " + annotatorClassname);
+ }
+ }
+ }
}
private Map<String, Object> prepareRequiredAnnotations(List<UserClassRequiredAnnotations> classRequiredAnnotators) {