ORCID Patch Functionality Missing

[Glenn G]

After applying the ORCID patch, the functionality my users were most interested in is missing.  The ORCID logo does not appear next to the author's name, and the name is not clickable, so a list of the author's publications cannot be retrieved from ORCID as promised.  The ability to search by ORCID number does now appear in the list of search modifiers, but it only works when the entire number is supplied with the "equals" operand.  The patch and functionality are described here:  https://atmire.github.io/expanded-ORCID-support/#/

If you have any idea why the logo and linked name don't appear, please let me know.  We are using the Mirage 2 theme.

Thanks,

Glenn

[Jolien (Atmire)]

Dear Glenn,

First and foremost, thank you for your interest in the patch we created. It is good to hear that it finds resonance in the DSpace user community. 

About the problem you encountered, could you tell us a little more about how you installed the patch and what DSpace version you are using?

Thanks in advance.

Best regards,

Jolien

[Glenn G]

Hello, Jolien,

We are using DSpace 6.3.  To install the patch, I followed the instructions here: https://atmire.github.io/expanded-ORCID-support/#/installation

When I tried to check the patch compatibility in step 2, I received error messages indicating that I was in the wrong directory.  So rather than running the check in the dspace directory as shown in step 1, I changed to the [dspace-src] directory.  The check ran from this location with the following response:

[glenn@rctest dspace-6.3-release]$ git apply --check ./dspace_6x…stable_6x.diff

error: cannot apply binary patch to 'dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/images/orcid_icon.png' without full index line

error: dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/images/orcid_icon.png: patch does not apply

error: dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/xsl/theme.xsl: already exists in working directory

error: cannot apply binary patch to 'dspace/modules/xmlui/src/main/webapp/themes/Mirage/images/orcid_icon.png' without full index line

error: dspace/modules/xmlui/src/main/webapp/themes/Mirage/images/orcid_icon.png: patch does not apply

I wasn't sure the errors were fatal, so I proceeded to apply the patch.  I received this response:

[glenn@rctest dspace-6.3-release]$ git apply --whitespace=nowarn --reject ./dspace_6x…stable_6x.diff

Checking patch dspace/config/dspace.cfg...

Checking patch dspace/config/spring/api/core-services.xml...

Checking patch dspace/config/spring/api/discovery.xml...

Checking patch dspace/config/spring/api/orcid-authority-services.xml...

Checking patch dspace/modules/additions/src/main/java/com/atmire/dspace/authority/OrcidAuthorityValueServiceImpl.java...

Checking patch dspace/modules/additions/src/main/java/com/atmire/dspace/discovery/ORCIDIdIndexingPlugin.java...

Checking patch dspace/modules/additions/src/main/java/org/dspace/authority/AuthorityUtil.java...

Checking patch dspace/modules/additions/src/main/java/org/dspace/authority/AuthorityValueFinder.java...

Checking patch dspace/modules/additions/src/main/java/org/dspace/authority/PersonAuthorityValue.java...

Checking patch dspace/modules/additions/src/main/java/org/dspace/authority/orcid/Orcidv2AuthorityValue.java...

Checking patch dspace/modules/rest/src/main/java/org/dspace/rest/AuthoritiesResource.java...

Checking patch dspace/modules/rest/src/main/java/org/dspace/rest/CollectionsResource.java...

Checking patch dspace/modules/rest/src/main/java/org/dspace/rest/ItemsResource.java...

Checking patch dspace/modules/rest/src/main/java/org/dspace/rest/RestIndex.java...

Checking patch dspace/modules/rest/src/main/java/org/dspace/rest/common/Item.java...

Checking patch dspace/modules/rest/src/main/webapp/WEB-INF/web.xml...

Checking patch dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/images/orcid_icon.png...

error: cannot apply binary patch to 'dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/images/orcid_icon.png' without full index line

error: dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/images/orcid_icon.png: patch does not apply

Checking patch dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/styles/_style.scss...

Checking patch dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/xsl/additions.xsl...

Checking patch dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/xsl/theme.xsl...

error: dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/xsl/theme.xsl: already exists in working directory

Checking patch dspace/modules/xmlui/src/main/java/org/dspace/app/xmlui/cocoon/DSpaceMETSGenerator.java...

Checking patch dspace/modules/xmlui/src/main/java/org/dspace/app/xmlui/objectmanager/AbstractAdapter.java...

Checking patch dspace/modules/xmlui/src/main/java/org/dspace/app/xmlui/objectmanager/ItemAdapter.java...

Checking patch dspace/modules/xmlui/src/main/resources/aspects/Discovery/i18n/messages.xml...

Checking patch dspace/modules/xmlui/src/main/webapp/themes/Mirage/Mirage.xsl...

Checking patch dspace/modules/xmlui/src/main/webapp/themes/Mirage/images/orcid_icon.png...

error: cannot apply binary patch to 'dspace/modules/xmlui/src/main/webapp/themes/Mirage/images/orcid_icon.png' without full index line

error: dspace/modules/xmlui/src/main/webapp/themes/Mirage/images/orcid_icon.png: patch does not apply

Checking patch dspace/modules/xmlui/src/main/webapp/themes/Mirage/lib/css/style.css...

Checking patch dspace/modules/xmlui/src/main/webapp/themes/Mirage/lib/xsl/additions.xsl...

Checking patch dspace/pom.xml...

Checking patch dspace/solr/search/conf/schema.xml...

Applied patch dspace/config/dspace.cfg cleanly.

Applied patch dspace/config/spring/api/core-services.xml cleanly.

Applied patch dspace/config/spring/api/discovery.xml cleanly.

Applied patch dspace/config/spring/api/orcid-authority-services.xml cleanly.

Applied patch dspace/modules/additions/src/main/java/com/atmire/dspace/authority/OrcidAuthorityValueServiceImpl.java cleanly.

Applied patch dspace/modules/additions/src/main/java/com/atmire/dspace/discovery/ORCIDIdIndexingPlugin.java cleanly.

Applied patch dspace/modules/additions/src/main/java/org/dspace/authority/AuthorityUtil.java cleanly.

Applied patch dspace/modules/additions/src/main/java/org/dspace/authority/AuthorityValueFinder.java cleanly.

Applied patch dspace/modules/additions/src/main/java/org/dspace/authority/PersonAuthorityValue.java cleanly.

Applied patch dspace/modules/additions/src/main/java/org/dspace/authority/orcid/Orcidv2AuthorityValue.java cleanly.

Applied patch dspace/modules/rest/src/main/java/org/dspace/rest/AuthoritiesResource.java cleanly.

Applied patch dspace/modules/rest/src/main/java/org/dspace/rest/CollectionsResource.java cleanly.

Applied patch dspace/modules/rest/src/main/java/org/dspace/rest/ItemsResource.java cleanly.

Applied patch dspace/modules/rest/src/main/java/org/dspace/rest/RestIndex.java cleanly.

Applied patch dspace/modules/rest/src/main/java/org/dspace/rest/common/Item.java cleanly.

Applied patch dspace/modules/rest/src/main/webapp/WEB-INF/web.xml cleanly.

Applied patch dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/styles/_style.scss cleanly.

Applied patch dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/xsl/additions.xsl cleanly.

Applied patch dspace/modules/xmlui/src/main/java/org/dspace/app/xmlui/cocoon/DSpaceMETSGenerator.java cleanly.

Applied patch dspace/modules/xmlui/src/main/java/org/dspace/app/xmlui/objectmanager/AbstractAdapter.java cleanly.

Applied patch dspace/modules/xmlui/src/main/java/org/dspace/app/xmlui/objectmanager/ItemAdapter.java cleanly.

Applied patch dspace/modules/xmlui/src/main/resources/aspects/Discovery/i18n/messages.xml cleanly.

Applied patch dspace/modules/xmlui/src/main/webapp/themes/Mirage/Mirage.xsl cleanly.

Applied patch dspace/modules/xmlui/src/main/webapp/themes/Mirage/lib/css/style.css cleanly.

Applied patch dspace/modules/xmlui/src/main/webapp/themes/Mirage/lib/xsl/additions.xsl cleanly.

Applied patch dspace/pom.xml cleanly.

Applied patch dspace/solr/search/conf/schema.xml cleanly.

After applying the patch, I removed existing files in the installer directory and ran Maven:

[glenn@rctest dspace-6.3-release]$ mvn -U clean package -Dmirage2.on=true

...

[INFO] Copying files to /ebs/dspace-source/dspace-6.3-release/dspace/target/dspace-installer

[INFO] ------------------------------------------------------------------------

[INFO] Reactor Summary:

[INFO]

[INFO] DSpace Addon Modules ............................... SUCCESS [  1.105 s]

[INFO] DSpace Kernel :: Additions and Local Customizations  SUCCESS [ 12.330 s]

[INFO] DSpace XML-UI Mirage2 Theme :: Local Customisations  SUCCESS [02:04 min]

[INFO] DSpace XML-UI (Manakin) :: Local Customizations .... SUCCESS [ 25.179 s]

[INFO] DSpace JSP-UI :: Local Customizations .............. SUCCESS [  6.990 s]

[INFO] DSpace RDF :: Local Customizations ................. SUCCESS [  7.367 s]

[INFO] DSpace REST :: Local Customizations ................ SUCCESS [ 13.744 s]

[INFO] DSpace SWORD :: Local Customizations ............... SUCCESS [  5.532 s]

[INFO] DSpace SWORD v2 :: Local Customizations ............ SUCCESS [  5.744 s]

[INFO] DSpace SOLR :: Local Customizations ................ SUCCESS [  8.435 s]

[INFO] DSpace OAI-PMH :: Local Customizations ............. SUCCESS [  8.241 s]

[INFO] DSpace Assembly and Configuration 6.3 .............. SUCCESS [01:03 min]

[INFO] ------------------------------------------------------------------------

[INFO] BUILD SUCCESS

I added orcid.connector.url = https://orcid.org/ to local.cfg in [dspace-source]/dspace-6.3-release/dspace/target/dspace-installer/config/local.cfg.

Then I ran "ant update" and restarted Tomcat.

Hope you can tell me where I went wrong.

Thanks,

Glenn

[Jolien (Atmire)]

Hello again Glenn,

Thank you for the details and sorry for the late reply! To follow-up on your problem, could you maybe check if the following file exists within the install-directory:

webapps/xmlui/themes/Mirage2/images/orcid_icon.png

Thanks!

Best regards,

Jolien

On Tuesday, December 3, 2019 at 12:10:42 AM UTC+1, Glenn G wrote:

[Glenn G]

Hello, Jolien,

No, the file does not exist in that location.

Thanks,

Glenn

[Alex Fletcher]

That file is not contained in the patch released by atmire.

That section of the patch file itself is simply:

diff --git a/dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/images/orcid_icon.png b/dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/images/orcid_icon.png
new file mode 100644
index 0000000..ef10914
Binary files /dev/null and b/dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/images/orcid_icon.png differ

The "orcid_icon.png" is not actually included.

We encountered the same issue when trying to implement this patch.

Alex

[Jolien (Atmire)]

In fact, the file should be contained in the patch. You can see that here (for the DSpace 6 version): https://github.com/atmire/expanded-ORCID-support/blob/stable_6x/dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/images/orcid_icon.png. For some reason, it looks like it is not accessed correctly when you do the installation. 

What could be happening is that in your DSpace installation, the path dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2 does not exist or exists under a different name. Could you check that? 

On Tuesday, December 3, 2019 at 12:10:42 AM UTC+1, Glenn G wrote:

[Glenn G]

Jolien,

Our DSpace installation does not have the path you mentioned.  The Mirage2 directory is located here:

[dspace]/webapps/xmlui/themes/Mirage2

Our [dspace] directory is not literally "dspace".  It has the format, id-dspace.  Also, our modules directory is located here:

[dspace]/config/modules

There are various possible reasons why our installation is different from that anticipated by the patch:

- It has been upgraded multiple times.

- It was moved to a standalone server after being hosted on a server with several other DSpace installations.

- It was originally upgraded to 6.3 using the binary install.  I added the [dspace-source] later in order to install patches.

Nonetheless, Alex indicates the patch could be installed if I do one or both of the following beforehand:

- Put a copy of orcid_icon.png in [dspace]/webapps/xmlui/themes/Mirage2

- Create a directory, [dspace]/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2 and put orcid_icon.png there.

Does either approach seem reasonable?

Thanks,

Glenn

[Glenn G]

Oh, now it occurs to me that you meant [dspace-source]/dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2.  Yes, we have that directory, and no, orcid_icon.png does not exist there.  Should I copy it there before applying the patch?

Thanks,

Glenn

[Alex Fletcher]

Glenn:

I downloaded the orcid_icon.png file that Jolene mentioned earlier and put it here:

- [dspace]/webapps/xmlui/themes/Mirage2/images

That seemed to do the trick for us.

Alex

[Jolien (Atmire)]

Hi Glenn and Alex,

Thanks for checking. The orcid_icon.png file should have been added into the right folder automatically when you installed the patch, hence my question about the path. I'll try to do the installation on a vanilla DSpace again to see if it renders the same problem for me. If so, we'll make sure to get this fixed. 

To already fix the issue on your DSpace right now, you can indeed just download the file and add it to [dspace]/webapps/xmlui/themes/Mirage2/images as Alex already suggested. If that does not work, let me know. 

Best,

Jolien

[Glenn G]

Jolien and Alex,

Thanks for the information!  I will give it another shot as soon as I get my test server rebuilt.

Glen

[Glenn G]

Hello, Jolien,

I applied the patch to my restored test system today, but unfortunately the results are the same, even with the orcid_icon.png file in place before and after running the patch.  When I submit a test document, I can select an author with an ORCID ID and add her to the item submission.  When I click the button to submit the item, it takes more than 90 seconds to acknowledge the submission.  After the item is submitted, no ORCID icon appears by the author's name and the name is not clickable.

Thanks for any help.

Glenn

[Jolien (Atmire)]

Hi again Glenn,

Sorry to hear it didn’t work. We’ll try to reproduce your problem on a fresh instal, that may help to trouble shoot further. I’ll keep you informed!

Best,

Jolien

[Jolien (Atmire)]

Dear Glenn,

We were able to reproduce your problem by creating the patch through the GitHub UI compare. The problem is that it comes through as straight text this way, whereas we would need a .patch file if we want the file with the ORCID badge to be included as well. 

To mitigate the issue, we have created the relevant patch files for both DSpace 5 and 6. We have also updated the download link in the patch documentation so that it links to those patches instead of the compare view. For reference, here is the link for the DSpace 6 version: https://github.com/atmire/expanded-ORCID-support/blob/master/patches/dspace_6x.patch. In case you would like to create the patch yourself, you can find the instructions on how to do this here: https://atmire.github.io/expanded-ORCID-support/#/prerequisites?id=download-patch.

If you try to apply the patch with the .patch file, the ORCID badge file should be added correctly. Please do let me know if this does not work. 

Best wishes,

Jolien

[Goodspeed, Glenn]

Hello, Jolien,

 

Thanks for the update.  I downloaded, or more correctly, copied and pasted the patch text to a file on my test server.  I ran “git apply --check <patch>” as instructed, and I get the following error messages.  Is this also your experience?  I wait to apply the patch until I hear from you.

 

Thanks,

Glenn

 

[root@rctest dspace-6.3-release]# git apply --check ./dspace_6x_orcid.patch                                                                    error: missing binary patch data for 'dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/images/orcid_icon.png'

error: binary patch does not apply to 'dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/images/orcid_icon.png'

error: dspace/modules/xmlui-mirage2/src/main/webapp/themes/Mirage2/images/orcid_icon.png: patch does not apply

error: missing binary patch data for 'dspace/modules/xmlui/src/main/webapp/themes/Mirage/images/orcid_icon.png'

error: binary patch does not apply to 'dspace/modules/xmlui/src/main/webapp/themes/Mirage/images/orcid_icon.png'

error: dspace/modules/xmlui/src/main/webapp/themes/Mirage/images/orcid_icon.png: patch does not apply

 

 

 

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[Jolien (Atmire)]

Hi Glenn,

No, when we applied this to a vanilla DSpace, we did not get an error. Did you make sure that when you saved the file, it was saved under the patch format? I did notice that, when you copy and paste, the default selected format is plain text. If you start from this page: https://github.com/atmire/expanded-ORCID-support/tree/master/patches, click right on the patch version you need and then select "save link as", the default selected format should be the patch one. The documentation has been adjusted to reflect that approach.

Best wishes,

Jolien

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[Goodspeed, Glenn]

Jolien,

 

I saved the patch file as you suggested, but now when I run “git apply --check ./dspace_6x.patch”, the response is “error: unrecognized input”.

 

Thanks again for your help.

 

Glenn

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[Tuan Nguyen]

I applied the patch, got the same error. The item display did not show hyperlink for author or the ORCID icon. 

Here is what I did to get it to work.

1. Copied the image as suggested by Alex.

2. Run /dspace/bin/dspace index-authority

3. Run /dspace/bin/dspace index-discovery

Now the search and display of the ORCID and related items are showing when clicking on the author name.

Hope it helps you!