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Merged
github-actions merged 4 commits into from
Jul 15, 2020
Merged

Fast-forward for 20.7.0 #43

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1007ea7
Refactor laboratory.workbooks and container listener code to be more …
bbimber Jul 9, 2020
4f19439
Resolve merge conflicts
bbimber Jul 10, 2020
a6e8462
Update LaboratoryContainerListener.java
bbimber Jul 10, 2020
f08774f
Merge pull request #40 from LabKey/fb_merge_discvr-20.3
bbimber Jul 10, 2020
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155 changes: 90 additions & 65 deletions laboratory/src/org/labkey/laboratory/LaboratoryContainerListener.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -68,10 +68,6 @@ public void containerCreated(Container c, User user)
{
_log.warn("Unable to populate default values for laboratory module", e);
}
catch (BatchValidationException e)
{
//ignore, since this may just indicate the table already has these values
}
}
}

Expand Down Expand Up @@ -112,69 +108,11 @@ public void propertyChange(PropertyChangeEvent evt)

if (evt.getPropertyName().equals(ContainerManager.Property.Name.name()))
{
if (evt instanceof ContainerManager.ContainerPropertyChangeEvent)
{
ContainerManager.ContainerPropertyChangeEvent ce = (ContainerManager.ContainerPropertyChangeEvent) evt;
if (ce.container.isWorkbook())
{
TableInfo ti = LaboratorySchema.getInstance().getTable(LaboratorySchema.TABLE_WORKBOOKS);
TableSelector ts = new TableSelector(ti, new SimpleFilter(FieldKey.fromString(LaboratoryWorkbooksTable.WORKBOOK_COL), ce.container.getId()), null);
if (ts.exists())
{
try
{
Integer rowId = Integer.parseInt(ce.container.getName());
WorkbookModel w = ts.getObject(ce.container.getId(), WorkbookModel.class);
w.setWorkbookId(rowId);
Table.update(ce.user, ti, w, ce.container.getId());
}
catch (NumberFormatException e)
{

}
}
}
}
updateWorkbookTableOnNameChange(evt);
}
else if (evt.getPropertyName().equals(ContainerManager.Property.Policy.name()))
else if (evt.getPropertyName().equals(ContainerManager.Property.Modules.name()))
{
if (evt instanceof ContainerManager.ContainerPropertyChangeEvent)
{
ContainerManager.ContainerPropertyChangeEvent ce = (ContainerManager.ContainerPropertyChangeEvent)evt;

User u = ce.user;
if (u == null && HttpView.hasCurrentView())
u = HttpView.currentView().getViewContext().getUser();

if (u == null || !ce.container.hasPermission(u, InsertPermission.class))
return;

if (ce.container.getActiveModules().contains(ModuleLoader.getInstance().getModule(LaboratoryModule.class)))
{
try
{
LaboratoryManager.get().initWorkbooksForContainer(u, ce.container);
}
catch (Exception e)
{
_log.error("Unable to update laboratory workbooks table", e);
}

//attempt to populate default values on load
try
{
LaboratoryManager.get().populateDefaultData(u, ce.container, null);
}
catch (IllegalArgumentException e)
{
_log.error("Unable to populate defaults in laboratory module tables", e);
}
catch (BatchValidationException e)
{
//ignore, since this may just indicate the table already has these values
}
}
}
possiblyInitializeOnActiveModuleChange(evt);
}
}

Expand All @@ -194,4 +132,91 @@ protected void purgeTable(UserSchema userSchema, TableInfo table, Container c)
super.purgeTable(userSchema, table, c);
}
}

/**
* The container name field stores the workbookId as a string. If that name changes (and this should no longer be permitted
* for the most part in LK, we need to update this table
*/
private void updateWorkbookTableOnNameChange(PropertyChangeEvent evt)
{
if (!(evt instanceof ContainerManager.ContainerPropertyChangeEvent))
{
return;
}

ContainerManager.ContainerPropertyChangeEvent ce = (ContainerManager.ContainerPropertyChangeEvent) evt;
if (!ce.container.isWorkbook())
{
return;
}

TableInfo ti = LaboratorySchema.getInstance().getTable(LaboratorySchema.TABLE_WORKBOOKS);
TableSelector ts = new TableSelector(ti, new SimpleFilter(FieldKey.fromString(LaboratoryWorkbooksTable.WORKBOOK_COL), ce.container.getId()), null);
if (ts.exists())
{
try
{
Integer workbookId = Integer.parseInt(ce.container.getName());
WorkbookModel w = ts.getObject(ce.container.getId(), WorkbookModel.class);
w.setWorkbookId(workbookId);
Table.update(ce.user, ti, w, ce.container.getId());
}
catch (NumberFormatException e)
{
_log.error("Non-numeric workbook name: " + ce.container.getName() + " for: " + ce.container.getEntityId());
}
}
}

/**
* The intent of this is to initialize the laboratory folder if the set of active modules
* changes to include Laboratory. This should only occur on the parent folder, not individual workbooks.
*/
private void possiblyInitializeOnActiveModuleChange(PropertyChangeEvent evt)
{
if (!(evt instanceof ContainerManager.ContainerPropertyChangeEvent))
{
return;
}

ContainerManager.ContainerPropertyChangeEvent ce = (ContainerManager.ContainerPropertyChangeEvent)evt;

//Only make these changes from the parent container for performance reasons
if (ce.container.isWorkbook())
{
return;
}

User u = ce.user;
if (u == null && HttpView.hasCurrentView())
{
u = HttpView.currentView().getViewContext().getUser();
}

if (u == null || !ce.container.hasPermission(u, InsertPermission.class))
{
return;
}

if (ce.container.getActiveModules().contains(ModuleLoader.getInstance().getModule(LaboratoryModule.class)))
{
try
{
LaboratoryManager.get().recursivelyInitWorkbooksForContainer(u, ce.container);
}
catch (Exception e)
{
_log.error("Unable to update laboratory workbooks table", e);
}

try
{
LaboratoryManager.get().populateDefaultData(u, ce.container, null);
}
catch (Exception e)
{
_log.error("Unable to populate defaults in laboratory module tables", e);
}
}
}
}
76 changes: 4 additions & 72 deletions laboratory/src/org/labkey/laboratory/LaboratoryController.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -471,7 +471,7 @@ public boolean handlePost(Object form, BindException errors) throws Exception
{
try
{
LaboratoryManager.get().initWorkbooksForContainer(getUser(), getContainer());
LaboratoryManager.get().recursivelyInitWorkbooksForContainer(getUser(), getContainer());

return true;
}
Expand Down Expand Up @@ -747,7 +747,7 @@ public ApiResponse execute(UpdateWorkbookForm form, BindException errors) throws
return null;
}

WorkbookModel model = LaboratoryManager.get().getWorkbookModel(getContainer());
WorkbookModel model = LaboratoryManager.get().getWorkbookModel(getContainer(), true);
if (model == null)
{
errors.reject(ERROR_MSG, "Unable to find workbook record for this folder");
Expand All @@ -759,11 +759,11 @@ public ApiResponse execute(UpdateWorkbookForm form, BindException errors) throws
model.setResults(form.getResults());
model.setDescription(form.getDescription(), getUser());

LaboratoryManager.get().updateWorkbook(getUser(), model);
LaboratoryManager.get().createOrUpdateWorkbook(getUser(), model);

if (form.isForceTagUpdate() || form.getTags() != null)
{
LaboratoryManager.get().updateWorkbookTags(getUser(), getContainer(), (form.getTags() == null ? (Collection)Collections.emptyList() : Arrays.asList(form.getTags())));
LaboratoryManager.get().updateWorkbookTags(getUser(), getContainer(), (form.getTags() == null ? Collections.emptyList() : Arrays.asList(form.getTags())));
}

results.put("success", true);
Expand Down Expand Up @@ -2295,74 +2295,6 @@ public void setProtocol(Integer protocol)
}
}

@RequiresPermission(AdminPermission.class)
public class MigrateWorkbooksAction extends MutatingApiAction<MigrateWorkbooksForm>
{
@Override
public ApiResponse execute(MigrateWorkbooksForm form, BindException errors) throws Exception
{
if (getContainer().isWorkbook())
{
errors.reject(ERROR_MSG, "Cannot be run on workbooks");
return null;
}

//find current workbook #


//find all workbooks where workbookId doesnt match LK ID
TreeMap<Integer, Container> toFix = new TreeMap<>();
for (Container c : ContainerManager.getChildren(getContainer()))
{
if (c.isWorkbook())
{
WorkbookModel w = LaboratoryManager.get().getWorkbookModel(c);
if (w != null)
{
_log.warn("workbook model not found for: " + c.getName());
}
else if (!c.getName().equals(w.getWorkbookId().toString()))
{
toFix.put(w.getWorkbookId(), c);
}
}
}

_log.info("workbooks to migrate: " + toFix.size());
Set<Integer> list = form.getReverseOrder() == true ? toFix.keySet() : toFix.descendingKeySet();
for (Integer id : list)
{
Container wb = toFix.get(id);
Container target = ContainerManager.getChild(wb.getParent(), id.toString());
if (target != null)
{
_log.warn("target workbook exists, skipping: " + id);
}
else
{
ContainerManager.rename(wb, getUser(), id.toString());
}
}

return new ApiSimpleResponse("success", true);
}
}

public static class MigrateWorkbooksForm
{
private Boolean reverseOrder = false;

public Boolean getReverseOrder()
{
return reverseOrder;
}

public void setReverseOrder(Boolean reverseOrder)
{
this.reverseOrder = reverseOrder;
}
}

@RequiresPermission(ReadPermission.class)
public class DataBrowserAction extends SimpleViewAction<Object>
{
Expand Down
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