Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add methods to delete multiple tables with one API call #63

Merged
merged 5 commits into from
Jun 27, 2023
Merged

Add methods to delete multiple tables with one API call #63

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
65c5bc9
Add methods to delete multiple tables with one API call
Rdornier Jun 19, 2023
33ba484
Use Long array as argument to deleteFiles
ppouchin Jun 27, 2023
17e4fc7
Improve tests
ppouchin Jun 27, 2023
852d2d2
Bump version
ppouchin Jun 27, 2023
7886b53
Weaken deleteTables argument type
ppouchin Jun 27, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@

<groupId>fr.igred</groupId>
<artifactId>simple-omero-client</artifactId>
<version>5.13.1</version>
<version>5.14.0</version>
<packaging>jar</packaging>

<name>Simple OMERO Client</name>
Expand Down
38 changes: 37 additions & 1 deletion src/main/java/fr/igred/omero/Client.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -218,6 +218,24 @@ public void delete(GenericObjectWrapper<?> object)
}


/**
* @param table Table to delete.
*
* @throws ServiceException Cannot connect to OMERO.
* @throws AccessException Cannot access data.
* @throws ExecutionException A Facility can't be retrieved or instantiated.
* @throws IllegalArgumentException ID not defined.
* @throws OMEROServerError Server error.
* @throws InterruptedException If block(long) does not return.
* @deprecated Deletes a table from OMERO.
*/
@Deprecated
public void delete(TableWrapper table)
throws ServiceException, AccessException, ExecutionException, OMEROServerError, InterruptedException {
deleteTable(table);
}


/**
* Deletes a table from OMERO.
*
Expand All @@ -230,12 +248,30 @@ public void delete(GenericObjectWrapper<?> object)
* @throws OMEROServerError Server error.
* @throws InterruptedException If block(long) does not return.
*/
public void delete(TableWrapper table)
public void deleteTable(TableWrapper table)
throws ServiceException, AccessException, ExecutionException, OMEROServerError, InterruptedException {
deleteFile(table.getId());
}


/**
* Deletes tables from OMERO.
*
* @param tables List of tables to delete.
*
* @throws ServiceException Cannot connect to OMERO.
* @throws AccessException Cannot access data.
* @throws ExecutionException A Facility can't be retrieved or instantiated.
* @throws IllegalArgumentException ID not defined.
* @throws OMEROServerError Server error.
* @throws InterruptedException If block(long) does not return.
*/
public void deleteTables(Collection<? extends TableWrapper> tables)
throws ServiceException, AccessException, ExecutionException, OMEROServerError, InterruptedException {
deleteFiles(tables.stream().map(TableWrapper::getId).toArray(Long[]::new));
}


/**
* Returns the user which matches the username.
*
Expand Down
25 changes: 23 additions & 2 deletions src/main/java/fr/igred/omero/GatewayWrapper.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,11 +40,13 @@
import omero.model.FileAnnotationI;
import omero.model.IObject;

import java.util.Arrays;
import java.util.List;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.concurrent.locks.Lock;
import java.util.concurrent.locks.ReentrantLock;
import java.util.stream.Collectors;


/**
Expand Down Expand Up @@ -501,8 +503,27 @@ void delete(List<IObject> objects)
*/
public void deleteFile(Long id)
throws ServiceException, AccessException, ExecutionException, OMEROServerError, InterruptedException {
FileAnnotationI file = new FileAnnotationI(id, false);
delete(file);
deleteFiles(id);
}


/**
* Deletes files from OMERO.
*
* @param ids List of files IDs to delete.
*
* @throws ServiceException Cannot connect to OMERO.
* @throws AccessException Cannot access data.
* @throws ExecutionException A Facility can't be retrieved or instantiated.
* @throws OMEROServerError Server error.
* @throws InterruptedException If block(long) does not return.
*/
public void deleteFiles(Long... ids)
throws ServiceException, AccessException, ExecutionException, OMEROServerError, InterruptedException {
List<IObject> files = Arrays.stream(ids)
.map(id -> new FileAnnotationI(id, false))
.collect(Collectors.toList());
delete(files);
}


Expand Down
28 changes: 14 additions & 14 deletions src/test/java/fr/igred/omero/annotations/ImageJTableTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -154,7 +154,7 @@ void testCreateTableWithROIsFromIJResults1() throws Exception {
long roiId = rois.get(0).getId();
Long fileId = table.getFileId();

client.delete(table);
client.deleteTable(table);

assertEquals(1, rowCount);
assertEquals(imageId, ((DataObject) data[0][0]).getId());
Expand Down Expand Up @@ -188,7 +188,7 @@ void testCreateTableWithROIsFromIJResults2() throws Exception {
long roiId = rois.get(0).getId();
Long fileId = table.getFileId();

client.delete(table);
client.deleteTable(table);

assertEquals(1, rowCount);
assertEquals(imageId, ((DataObject) data[0][0]).getId());
Expand Down Expand Up @@ -220,7 +220,7 @@ void testCreateTableWithROIsFromIJResults3() throws Exception {
long roiId = rois.get(0).getId();
Long fileId = table.getFileId();

client.delete(table);
client.deleteTable(table);

assertEquals(1, rowCount);
assertEquals(imageId, ((DataObject) data[0][0]).getId());
Expand Down Expand Up @@ -250,7 +250,7 @@ void testCreateTableWithROIsFromIJResults4() throws Exception {
long roiId = rois.get(0).getId();
Long fileId = table.getFileId();

client.delete(table);
client.deleteTable(table);

assertEquals(1, rowCount);
assertEquals(imageId, ((DataObject) data[0][0]).getId());
Expand Down Expand Up @@ -278,7 +278,7 @@ void testCreateTableFromIJResults() throws Exception {

Object[][] data = tables.get(0).getData();

client.delete(tables.get(0));
client.deleteTable(tables.get(0));
List<TableWrapper> noTables = image.getTables(client);

assertEquals(imageId, ((DataObject) data[0][0]).getId());
Expand Down Expand Up @@ -308,7 +308,7 @@ void testAddRowsFromIJResults() throws Exception {

Object[][] data = tables.get(0).getData();

client.delete(tables.get(0));
client.deleteTables(tables);
List<TableWrapper> noTables = image.getTables(client);

assertEquals(imageId, ((DataObject) data[0][0]).getId());
Expand Down Expand Up @@ -345,7 +345,7 @@ void testAddRowsWithROIsFromIJResults() throws Exception {
long roiId = rois.get(0).getId();
Long fileId = table.getFileId();

client.delete(table);
client.deleteTable(table);

assertEquals(2, rowCount);
assertEquals(imageId, ((DataObject) data[0][0]).getId());
Expand Down Expand Up @@ -385,7 +385,7 @@ void testCreateTableWithLocalROIFromIJResults1() throws Exception {
Object[][] data = table.getData();
Long fileId = table.getFileId();

client.delete(table);
client.deleteTable(table);

assertEquals(2, rowCount);
assertEquals(imageId, ((DataObject) data[0][0]).getId());
Expand Down Expand Up @@ -424,7 +424,7 @@ void testCreateTableWithLocalROIFromIJResults2() throws Exception {
Object[][] data = table.getData();
Long fileId = table.getFileId();

client.delete(table);
client.deleteTable(table);

assertEquals(2, rowCount);
assertEquals(imageId, ((DataObject) data[0][0]).getId());
Expand Down Expand Up @@ -477,7 +477,7 @@ void testCreateTableWithROINamesFromIJResults1() throws Exception {
Object[][] data = table.getData();
Long fileId = table.getFileId();

client.delete(table);
client.deleteTable(table);

assertEquals(2, rowCount);
assertEquals(imageId, ((DataObject) data[0][0]).getId());
Expand Down Expand Up @@ -535,7 +535,7 @@ void testCreateTableWithROINamesFromIJResults2() throws Exception {
Object[][] data = table.getData();
Long fileId = table.getFileId();

client.delete(table);
client.deleteTable(table);

assertEquals(2, rowCount);
assertEquals(imageId, ((DataObject) data[0][0]).getId());
Expand Down Expand Up @@ -596,7 +596,7 @@ void testNumberFormatException() throws Exception {
Object[][] data = table.getData();
Long fileId = table.getFileId();

client.delete(table);
client.deleteTable(table);

assertEquals(1, rowCount);
assertEquals(imageId, ((DataObject) data[0][0]).getId());
Expand Down Expand Up @@ -627,7 +627,7 @@ void testNumericName() throws Exception {
Object[][] data = table.getData();
Long fileId = table.getFileId();

client.delete(table);
client.deleteTable(table);

assertEquals(1, rowCount);
assertEquals(imageId, ((DataObject) data[0][0]).getId());
Expand Down Expand Up @@ -663,7 +663,7 @@ void testAddRowsFromIJResultsInverted() throws Exception {
assertEquals(1, tables.size());
assertEquals(2, tables.get(0).getRowCount());

client.delete(tables.get(0));
client.deleteTables(tables);
List<TableWrapper> noTables = image.getTables(client);

assertEquals(imageId, ((DataObject) data[0][0]).getId());
Expand Down
2 changes: 1 addition & 1 deletion src/test/java/fr/igred/omero/annotations/TableTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@ void testCreateTable() throws Exception {
dataset.addTable(client, table);

List<TableWrapper> tables = dataset.getTables(client);
client.delete(tables.get(0));
client.deleteTables(tables);
List<TableWrapper> noTables = dataset.getTables(client);

assertEquals(1, tables.size());
Expand Down