Add option to parse new references from plain text using GROBID service [solving #4826] #5614

NikodemKch · 2019-11-15T11:59:29Z

This PR should solve #4826.
This JabRef extension is developed as part of a software engineering course.
Even though we write this feature mainly for our university course, we are willing to adjust our feature, so that JabRef can benefit from it.

The feature is now ready for review. It reintroduces the possibility to extract references from plain text using a custom GROBID server. This is implemented via a new SearchBasedFetcher.

One could work some more on the GROBID server (See : NikodemKch/grobid@e89810b), but sadly we do not have time for that.

Change in CHANGELOG.md described
Tests created for changes
Manually tested changed features in running JabRef
Screenshots added in PR description (for bigger UI changes)
Ensured that the git commit message is a good one

koppor

Thank you so much for working on this. This is a long awaited feature.

Working on such a huge code base with a community where the developers are working more than five years on the product is hard. Thank you for taking the challenge.

We all had hard discussions within the team on user experience, code design, ... Now you get all these discussions (results) in a shorter time. Please take it as challenge to level-up your coding skills. Both in reading existing code and writing new code.

That said, some general comments:

JabRef 5.0 tries to work with less dialogs. Thus, I propose to remove following dialogs: (Refs MockUp.pdf)

Remove "Diplay Success Dialog". Just do a notificaton. Refs Fix 5555 status popups #5560.
Remove step "Display BibEntry". This is done by the JabRef EntryEditor. Just select the found entries. If you find that uncomfortable, add a feature to add them to the group "new". (I assume that this feature does not yet exist. Should be a one-liner)
Remove "Display Error" --> not able to parse should be logged (maybe popup). Should be automatically handled in the fetcher architecture (?)

Please adapt the use cases accordingly.

I would Add /P50/: There is fetching logic in JabRef. Such as org.jabref.logic.importer.SearchBasedParserFetcher (https://github.com/JabRef/jabref/blob/master/src/main/java/org/jabref/logic/importer/SearchBasedFetcher.java). That should be the interface the functionality builds on. (Especially List<BibEntry> performSearch(String query) throws FetcherException. One can all exception handling is done in the "framework" Example: https://docs.jabref.org/import-export/import-using-online-bibliographic-database/gvk).

Can you add a rendered version of "ProjectPlan.gan" or add a hint to open the "sweng" project? - I am reading it with GitHub at https://github.com/NikodemKch/jabref-1/tree/milestone1/docs/sweng.

There is no need to touch the submodules (just do not commit these changes - or do "git submodule update")

Please update the existing feature:

(Maybe also put a button in the menu bar

)

(Maybe switch the two buttons in the existing implementation - the go-on-button should always be right. And NEVER label "Cancel". Label it "Return to Library" so that the user knows what happens)

Result (opened in the entry editor)

You see, this is not usable. The code at https://github.com/NikodemKch/jabref-1/blob/develop/src/main/java/org/jabref/gui/bibtexextractor/BibtexExtractor.java is wrong. Moreover, it is placed in the wrong module (gui is the wrong package; it should be logic). Think, we overlooked it in the review of #4985 - and the continuation at #5206

These dialogues can be a good start.

My recommendation would be to look at org.jabref.logic.importer.fetcher.DBLPFetcher how a searched-based fetcher is implemented. A team should implement it. Another team should implement test cases.

Side comment: Did you hear about remote mob programming? Maybe, this helps to work on something. We also could do such a session the next days. (Maybe 30 mins).

.idea/runConfigurations/JabRef_Main.xml

build.gradle

docs/sweng/Glossary.md

src/main/java/org/jabref/gui/actions/StandardActions.java

src/main/java/org/jabref/logic/net/HttpPostService.java

src/main/java/org/jabref/logic/plaintextparser/ParserPipeline.java

src/test/java/org/jabref/logic/plaintextparser/ParserPipelineTest.java

koppor · 2019-11-18T05:54:48Z

Note: In #5628 I tried to bring-back the old menu item (as it exists in the 4.x versions of JabRef)

zGatsu · 2019-11-18T11:42:18Z

Quick statement about the points you mentioned:

The documentation you read is not up to date especially in terms of the dialogue-popups. On branch milestone3 we already reused the existing pop-up window and added the entries automatically after parsing. Moreover, since the user might want to add multiple entries at once, we inserted a checkbox, which enables the user to create a new library tab, so that possibly wrong parsed references are not immediately in his (the current) library.
Screenshot:

(We will change the buttons soon).
We changed our mind and do not intend to implement the conversion function (.tei to .bib) by ourselves anymore. (After seeing this method and this method.)
The reference text is parsed by the grobid server which already has the needed function. We just change the function to return the processed citation in bibtex format rather than tei format. (Here) That's why we need a custom GROBID server. (We will link this server in this PR)
We already implemented a checkbox to use a custom grobid server ip( preferences -> advanced tab), if unchecked the default value is selected. Probably we should set that to http://cloud.science-miner.com/grobid/ , but the problem is, that this server seems to be constantly overwhelmed by the number of incoming requests. That's why we hosted the server on localhost for testing purposes. You can find a manual how to start that server here. (It uses gradle.)
Screenshot:
We will try to change our package structure, button placing as well as used dependencies according to your suggestions this week. We will also try to update the documentation.

tobiasdiez · 2019-11-18T11:51:35Z

Concerning:

(Maybe switch the two buttons in the existing implementation - the go-on-button should always be right. And NEVER label "Cancel". Label it "Return to Library" so that the user knows what happens)

That depends on the OS. You can add the correct type and then JavaFX will put them in the right order automatically. (And "Cancel" is pretty ok)

koppor · 2019-11-18T13:14:59Z

Please merge #5628 into your branch. Then I will close that PR.

koppor · 2019-11-18T13:16:44Z

👍 - I would make the checkbox an additional button.

"Insert into current library" and "Insert into new library"

NikodemKch · 2019-11-18T22:46:03Z

Here is the link to the custom GROBID server: https://github.com/NikodemKch/grobid

tobiasdiez · 2019-11-19T11:54:22Z

@koppor do we have the resources to host the grobid server? I don't think many people have the knowledge to install and setup gropid on localhost...

koppor · 2019-11-19T20:26:34Z

@tobiasdiez There are options. Maybe, we "just" limit the request rates, "just" limit the requests per user per hour or simply charge for it.

src/main/java/org/jabref/logic/importer/fetcher/GrobidCitationFetcher.java

koppor · 2019-11-22T15:09:02Z

We will check options how to host and maybe host some public service in beta.

guenesaydin · 2019-11-22T16:12:57Z

We finished our work for this week. (except unit-test and documentation)
We added a new button in the toolbar:

After pressing this button (or the corresponding context menu button) this window appears:

While waiting for the server response, the following dialog is displayed:

After successfully parsing, the entries are created and one of them is displayed inside the EntryEditor:

When Grobid fails to parse a String, the following message is displayed: (This is also the case, when some entries are parsed successfully and some are not.)

The user must separate the entries with double semicolon (;;) (we had no better idea).

The still open to do's are:

Write the unit tests
Update the documentation
Add localization entries
Work on the GROBID server

Also we intergrated our code better into the existing code base. It would be nice to get some feedback on that.

NOTE: The GROBID server does not work right with Java 13. We used Java 11 for the server but recommended is Java 8 (As stated here)(The server had some NullPointer exceptions for no reason sometimes).

obsluk00 · 2019-11-25T11:13:04Z

Unit tests have now been implemented.
The documentation was updated to match the current development status and to track changes in our timeline and planning.

LinusDietz · 2019-11-26T10:13:47Z

Hey @NikodemKch, @obsluk00, @marcelluethi!
We want to help you by deploying a grobid server. I hope you understand that it is important that the server is maintained by the @JabRef/developers team. I've already set up the default grobid server, but what I read is that you want to customize the server? Can you point me to a repo from which I can deploy you custom server?

NikodemKch · 2019-11-26T10:38:39Z

Hey @LinusDietz
The repo is here.
The only difference to the original server is the following: NikodemKch/grobid@e89810b
We still have to look at the requested changes.
Thank you for deploying the server.

LinusDietz · 2019-12-04T13:23:34Z

Hey @LinusDietz
The repo is here.
The only difference to the original server is the following: NikodemKch/grobid@e89810b
We still have to look at the requested changes.
Thank you for deploying the server.

So, I do have the server running. It might be a bit slow, but feel free to test it and report your findings to me. (potentially via Slack, I've invited @NikodemKch )

http://grobid.cm.in.tum.de:8070/

tobiasdiez · 2019-12-04T19:06:51Z

What's the current status here? Is this already ready for review, or do you need input on certain parts?

NikodemKch · 2019-12-05T10:05:28Z

Today we will fix the requested changes and try to fix the Travis pipeline. Then, we will open the PR for review. Sadly, we will probably not find the time to change the GROBID server as requested, as the examination phase is kicking in (First exam on December 20th)...

NikodemKch · 2019-12-06T10:01:05Z

This PR is now ready for review. Sadly the provided server (http://grobid.cm.in.tum.de:8070/) seems to not work properly (I cant access the page even in a browser, it says the server took too long to respond). The feature was tested with a locally hosted server.

LinusDietz · 2019-12-06T11:45:50Z

Sadly the provided server (http://grobid.cm.in.tum.de:8070/) seems to not work properly (I cant access the page even in a browser, it says the server took too long to respond).

Sorry! Indeed the server is running, but the port in question is unreachable from the internet. I'll have a look.

…ed message

NikodemKch · 2020-02-16T22:21:09Z

Thanks a lot for the very good revision. I've only a couple of minor remarks left before we can merge. Would be awesome if you could address them in a timely manner so that your PR still makes it into the 5.0 release in two weeks.

@koppor is it possible to create the domain grobid.jabref.org as an alias for @LinusDietz grobid server? In this way we can change the server in the future without changing the url and thus without the need of a new release.

I have resolved all these issues and am re-requesting your review.

koppor

Small code nitpicks. Is it possible to fix it soon?

src/main/java/org/jabref/logic/importer/fetcher/GrobidCitationFetcher.java

koppor · 2020-02-19T14:53:53Z

src/main/java/org/jabref/logic/importer/util/GrobidService.java

+ * Implements an API to a GROBID server, as described at
+ * https://grobid.readthedocs.io/en/latest/Grobid-service/#grobid-web-services
+ * <p>
+ * Note: Currently a custom GROBID server is used...


Please ensure that you send an Accept header here (can be done in a follow-up pull request)

src/test/java/org/jabref/logic/importer/util/GrobidServiceTest.java

koppor · 2020-02-19T16:19:09Z

Pasting

Kolb, S., Wirtz G.: Towards Application Portability in Platform as a Service
Proceedings of the 8th IEEE International Symposium on Service-Oriented System Engineering (SOSE), Oxford, United Kingdom, April 7 - 10, 2014.

from https://www.uni-bamberg.de/pi/team/kolb-stefan/

Result:

@Misc{Kolb,
  author = {S Kolb and G Wirtz},
  title  = {Towards Application Portability in Platform as a Service},
}

Result is so, so. However, user experience is OK. The only thing is the textbox. Can it be soft-wrapped?

koppor · 2020-02-19T16:25:48Z

src/main/java/org/jabref/logic/importer/fetcher/GrobidCitationFetcher.java

+public class GrobidCitationFetcher implements SearchBasedFetcher {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(GrobidCitationFetcher.class);
+    private static final String GROBID_URL = "http://grobid.cm.in.tum.de:8070";


Please change to http://grobid.jabref.org:8070

This address is not working for some reason...

obsluk00 · 2020-02-19T17:48:22Z

Pasting
Kolb, S., Wirtz G.: Towards Application Portability in Platform as a Service
Proceedings of the 8th IEEE International Symposium on Service-Oriented System Engineering (SOSE), Oxford, United Kingdom, April 7 - 10, 2014.
from https://www.uni-bamberg.de/pi/team/kolb-stefan/

Result:
@Misc{Kolb,
  author = {S Kolb and G Wirtz},
  title  = {Towards Application Portability in Platform as a Service},
}
Result is so, so. However, user experience is OK. The only thing is the textbox. Can it be soft-wrapped?

We made the conscious design choice to go without softwrapping user input to improve quality of user experience when passing multiple entries.
But changing it isn't a problem and we should be able implement softwrapping together with the other requested changes until the weekend.

NikodemKch · 2020-02-19T17:59:33Z

I see the problem. We decided to split entries at line breaks (regex: "[\\r\\n]+")
Without the line break you copied over from the website, the result is quite better:

@Article{KolbJune27July22015,
  author    = {S Kolb and J Lenhard and G Wirtz},
  year      = {June 27 - July 2, 2015},
  address   = {New York, NY, USA},
  booktitle = {Application Migration Effort in the Cloud - The Case of Cloud Platforms Proceedings of the 8th IEEE International Conference on Cloud Computing (CLOUD)},
}

Softwrap makes sense, since it (mentally) prevents the user from adding more breaks after he pasted his references.

We thought using line breaks would be most convenient, but we can easily change this to double line breaks or even something else, so what do you think? @koppor

tobiasdiez · 2020-02-19T20:16:31Z

As the example shows it would be indeed good to change the item separation to two lines (so that one empty line needs to be between the entries). Could you also add this as a short comment in the prompt text "Please enter the plain text references ..." to make it easier for users to discover the feature. Thanks

Co-Authored-By: obsluk00 <obsluk00@users.noreply.github.com>

Some minor imrovements and switch to softwrap Co-Authored-By: obsluk0…

NikodemKch · 2020-02-19T22:00:54Z

Ready for review again.
See comments in open issues above.

Also the feature now separates at double empty lines only.
And this is displayed to the user. (Since the commit below)

tobiasdiez

Perfect! Thanks a lot for the quick follow-up!

koppor · 2020-02-20T12:44:35Z

Think, we are good to go.

For a follow up, the Accept header should be set. I created a follow-up issue at koppor#406.

Thank you so much for working on this issue and keeping up the work after the exam phase! 🎉

tobiasdiez · 2020-02-20T12:48:04Z

@koppor The address is still pointing to tum and your alias is not working: https://github.com/JabRef/jabref/pull/5614/files#r381558452. Would be nice to fix this before the release.

zGatsu · 2020-02-20T15:33:54Z

We also want to thank you very much! It was a great experience for the whole team to participate on your project. It was very helpful that you mentioned so many import details that we didn't see. That helped us improving our skills to become a good software engineer! :-) 🎉

koppor · 2020-02-20T15:37:35Z

@tobiasdiez Added it to koppor#406

tobiasdiez · 2020-02-20T20:27:43Z

@koppor good, but can we also fix that before we release this weekend?!

NikodemKch · 2020-02-25T08:45:20Z

Thank you for your support and feedback during the development of this feature!

I got response for my feature request at Grobid, asking for a service call that can process multiple requests at once. kermitt2/grobid#540 (comment)

Indeed, the second use case is not what we are looking for.
As I understand, I as caller would have the choice between sending everything in one request with little slower processing, or creating and collecting multiple async. threads but slightly faster processing.

So what do you think @koppor @tobiasdiez ?

* upstream/master: Add option to parse new references from plain text using GROBID… (#5614) update jlink plugin and gradle to 6.2 (#5964) Remove background command line window (#5965)

3b00357 Update urad-rs-za-makroekonomske-analize-in-razvoj.csl (#5639) fcf6625 updated styles (#5638) 0df0633 Update universite-du-quebec-a-montreal-etudes-litteraires-et-semiolog… (#5614) eaddf8e Human Molecular Genetics (#5635) 0afd7fb Update harvard-cardiff-university.csl (#5623) f424672 Switch ISQ to Chicago author-date ccb7184 Update chicago-author-date.csl (#5605) a408957 SBL: implementation of book reviews (#5613) fbbe7b3 Update harvard-swinburne-university-of-technology.csl to meet published spec (#5627) 8d7a0d8 Add UNESCO IIEP style (#5631) git-subtree-dir: buildres/csl/csl-styles git-subtree-split: 3b00357

koppor requested changes Nov 15, 2019

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tobiasdiez mentioned this pull request Nov 18, 2019

Rename "Extract BibTeX from plain text" to (pre-existing) "New entry from plain text" #5628

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NikodemKch pushed a commit to NikodemKch/jabref-1 that referenced this pull request Nov 18, 2019

Merged JabRef#5628 into JabRef#5614

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NikodemKch force-pushed the develop branch from 0f15e34 to 0eef0f1 Compare November 18, 2019 22:11

NikodemKch pushed a commit to NikodemKch/jabref-1 that referenced this pull request Nov 18, 2019

Merged JabRef#5628 into JabRef#5614

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NikodemKch force-pushed the develop branch from 0eef0f1 to eed4fb5 Compare November 18, 2019 22:13

tobiasdiez added the status: devcall label Nov 19, 2019

koppor mentioned this pull request Nov 21, 2019

Integrate anystyle koppor/jabref#315

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Siedlerchr requested changes Nov 22, 2019

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koppor removed the status: devcall label Nov 22, 2019

NikodemKch marked this pull request as ready for review December 6, 2019 09:57

NikodemKch changed the title ~~[WIP][solving #4826] Add option to parse new references from plain text using GROBID service~~ [solving #4826] Add option to parse new references from plain text using GROBID service Dec 6, 2019

Make GROBIDCitationFetcherTest more independent and clarified display…

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NikodemKch mentioned this pull request Feb 16, 2020

Add possibility to process multiple raw references by http request kermitt2/grobid#540

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NikodemKch requested a review from tobiasdiez February 16, 2020 22:21

Merge branch 'master' into develop

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NikodemKch and others added 3 commits February 19, 2020 21:34

minor improvements and switch to softwrap

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Co-Authored-By: obsluk00 <obsluk00@users.noreply.github.com>

Resolved open issues

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Merge pull request #21 from NikodemKch/newsoftwrap

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Some minor imrovements and switch to softwrap Co-Authored-By: obsluk0…

NikodemKch added 2 commits February 19, 2020 23:05

feature is exposed to user

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hotfix fetchertest

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koppor mentioned this pull request Feb 20, 2020

Ensure correct Accept header for Grobid koppor/jabref#406

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koppor merged commit 5fa1dcf into JabRef:master Feb 20, 2020

koppor deleted the develop branch February 20, 2020 12:45

koppor mentioned this pull request Jul 7, 2020

Confused plain text citation to entry #6672

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Add option to parse new references from plain text using GROBID service [solving #4826] #5614

Add option to parse new references from plain text using GROBID service [solving #4826] #5614

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