#22693

Committed 03 Jul 2024 01:09PM CUT coverage: 20.626% (-0.09%) from 20.716%

Build # #22693

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #10664 from IQSS/develop

merge develop into master for 6.3

Run Details

195 of 1852 new or added lines in 82 files covered. (10.53%)

72 existing lines in 33 files now uncovered.

17335 of 84043 relevant lines covered (20.63%)

0.21 hits per line

Source File
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0.0

/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UpdateDvObjectPIDMetadataCommand.java

package edu.harvard.iq.dataverse.engine.command.impl;

import edu.harvard.iq.dataverse.DataFile;
import edu.harvard.iq.dataverse.Dataset;
import edu.harvard.iq.dataverse.authorization.Permission;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.engine.command.AbstractVoidCommand;
import edu.harvard.iq.dataverse.engine.command.CommandContext;
import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
import edu.harvard.iq.dataverse.engine.command.RequiredPermissions;
import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
import edu.harvard.iq.dataverse.engine.command.exception.PermissionException;
import edu.harvard.iq.dataverse.pidproviders.PidProvider;
import edu.harvard.iq.dataverse.pidproviders.PidUtil;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.BundleUtil;
import java.sql.Timestamp;
import java.util.Collections;
import java.util.Date;

/**
 *
 * @author skraffmi
 * No required permissions because we are enforcing super user status in the execute
 */
@RequiredPermissions({})
public class UpdateDvObjectPIDMetadataCommand extends AbstractVoidCommand {

    private final Dataset target;

    public UpdateDvObjectPIDMetadataCommand(Dataset target, DataverseRequest aRequest) {
        super(aRequest, target);
        this.target = target;
    }

    @Override
    protected void executeImpl(CommandContext ctxt) throws CommandException {


        if (!(getUser() instanceof AuthenticatedUser) || !getUser().isSuperuser()) {
            throw new PermissionException(BundleUtil.getStringFromBundle("datasets.api.updatePIDMetadata.auth.mustBeSuperUser"),
                    this, Collections.singleton(Permission.EditDataset), target);
        }
        if (!this.target.isReleased()){
            //This is for the bulk update version of the api.
            //We don't want to modify drafts, but we want it to keep going
            //the single dataset update api checks for drafts before calling the command
            return;
        }
        PidProvider pidProvider = PidUtil.getPidProvider(target.getGlobalId().getProviderId());
        
        try {
            Boolean doiRetString = pidProvider.updateIdentifier(target);
            if (doiRetString) {
                target.setGlobalIdCreateTime(new Timestamp(new Date().getTime()));
                ctxt.em().merge(target);
                ctxt.em().flush();
                // When updating, we want to traverse through files even if the dataset itself
                // didn't need updating.
                boolean isFilePIDsEnabled = ctxt.systemConfig().isFilePIDsEnabledForCollection(target.getOwner());
                // We will skip trying to update the global identifiers for datafiles if they
                // aren't being used.
                // If they are, we need to assure that there's an existing PID or, as when
                // creating PIDs, that it's possible.
                
                boolean canCreatePidsForFiles = 
                                isFilePIDsEnabled && ctxt.dvObjects().getEffectivePidGenerator(target).canCreatePidsLike(target.getGlobalId());
                
                for (DataFile df : target.getFiles()) {
                    if (isFilePIDsEnabled && // using file PIDs and
                            (!(df.getIdentifier() == null || df.getIdentifier().isEmpty()) || // identifier exists, or
                                     canCreatePidsForFiles) // we can create PIDs for files
                    ) {
                        doiRetString = pidProvider.updateIdentifier(df);
                        if (doiRetString) {
                            df.setGlobalIdCreateTime(new Timestamp(new Date().getTime()));
                            ctxt.em().merge(df);
                            ctxt.em().flush();
                        }
                    }
                }
            } else {
                //do nothing - we'll know it failed because the global id create time won't have been updated.
            }
        } catch (Exception e) {
            //do nothing - item and the problem has been logged
        }
    }

}

1	package edu.harvard.iq.dataverse.engine.command.impl;
2
3	import edu.harvard.iq.dataverse.DataFile;
4	import edu.harvard.iq.dataverse.Dataset;
5	import edu.harvard.iq.dataverse.authorization.Permission;
6	import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
7	import edu.harvard.iq.dataverse.engine.command.AbstractVoidCommand;
8	import edu.harvard.iq.dataverse.engine.command.CommandContext;
9	import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
10	import edu.harvard.iq.dataverse.engine.command.RequiredPermissions;
11	import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
12	import edu.harvard.iq.dataverse.engine.command.exception.PermissionException;
13	import edu.harvard.iq.dataverse.pidproviders.PidProvider;
14	import edu.harvard.iq.dataverse.pidproviders.PidUtil;
15	import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
16	import edu.harvard.iq.dataverse.util.BundleUtil;
17	import java.sql.Timestamp;
18	import java.util.Collections;
19	import java.util.Date;
20
21	/**
22	*
23	* @author skraffmi
24	* No required permissions because we are enforcing super user status in the execute
25	*/
26	@RequiredPermissions({})
27	public class UpdateDvObjectPIDMetadataCommand extends AbstractVoidCommand {
28
29	private final Dataset target;
30
31	public UpdateDvObjectPIDMetadataCommand(Dataset target, DataverseRequest aRequest) {
32	super(aRequest, target);	×
33	this.target = target;	×
34	}	×
35
36	@Override
37	protected void executeImpl(CommandContext ctxt) throws CommandException {
38
39
40	if (!(getUser() instanceof AuthenticatedUser) \|\| !getUser().isSuperuser()) {	×
41	throw new PermissionException(BundleUtil.getStringFromBundle("datasets.api.updatePIDMetadata.auth.mustBeSuperUser"),	×
42	this, Collections.singleton(Permission.EditDataset), target);	×
43	}
44	if (!this.target.isReleased()){	×
45	//This is for the bulk update version of the api.
46	//We don't want to modify drafts, but we want it to keep going
47	//the single dataset update api checks for drafts before calling the command
48	return;	×
49	}
50	PidProvider pidProvider = PidUtil.getPidProvider(target.getGlobalId().getProviderId());	×
51
52	try {
NEW 53	Boolean doiRetString = pidProvider.updateIdentifier(target);	×
54	if (doiRetString) {	×
55	target.setGlobalIdCreateTime(new Timestamp(new Date().getTime()));	×
56	ctxt.em().merge(target);	×
57	ctxt.em().flush();	×
58	// When updating, we want to traverse through files even if the dataset itself
59	// didn't need updating.
60	boolean isFilePIDsEnabled = ctxt.systemConfig().isFilePIDsEnabledForCollection(target.getOwner());	×
61	// We will skip trying to update the global identifiers for datafiles if they
62	// aren't being used.
63	// If they are, we need to assure that there's an existing PID or, as when
64	// creating PIDs, that it's possible.
65
66	boolean canCreatePidsForFiles =	×
67	isFilePIDsEnabled && ctxt.dvObjects().getEffectivePidGenerator(target).canCreatePidsLike(target.getGlobalId());	×
68
69	for (DataFile df : target.getFiles()) {	×
70	if (isFilePIDsEnabled && // using file PIDs and	×
71	(!(df.getIdentifier() == null \|\| df.getIdentifier().isEmpty()) \|\| // identifier exists, or	×
72	canCreatePidsForFiles) // we can create PIDs for files
73	) {
NEW 74	doiRetString = pidProvider.updateIdentifier(df);	×
75	if (doiRetString) {	×
76	df.setGlobalIdCreateTime(new Timestamp(new Date().getTime()));	×
77	ctxt.em().merge(df);	×
78	ctxt.em().flush();	×
79	}
80	}
81	}	×
82	} else {
83	//do nothing - we'll know it failed because the global id create time won't have been updated.
84	}
85	} catch (Exception e) {	×
86	//do nothing - item and the problem has been logged
87	}	×
88	}	×
89
90	}

IQSS / dataverse / #22693

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