Enable automated cross library search using a cross library query lan…

[DominikVoigt]

This PR adds the capabilities to perform certain aspects of literature studies.
Fixes JabRef#369

It adds the capabilities to:
- Create studies and share the result with others using git
- Define certain aspects of the study, such as search terms and used E-Libraries
- Automatically crawl the specified E-Libraries and import their results to JabRef,
and merge the results of all E-Libraries into one result BibDatabase.
- Create diffs to inform the user of newly found publications since the last crawl.
- To filter the results of the crawling systematically.

• Change in CHANGELOG.md described (if applicable)
• Tests created for changes (if applicable)
• Manually tested changed features in running JabRef (always required)
• Screenshots added in PR description (for UI changes)
• Checked documentation: Is the information available and up to date? If not created an issue at https://github.com/JabRef/user-documentation/issues or, even better, submitted a pull request to the documentation repository.

[Siedlerchr]

I cannot say anything about the functionality, but I have some suggestions/improvements for the code

[koppor]

Besides comments by @Siedlerchr LGTM

[tobiasdiez]

Two general questions:

• Why did you decided to implement the study format as a bib file? That is highly counter-intuitive (from a user as well as developer standpoint). Yml or json would have been a more logical choice.
• Why do you require that the study file has to be in a git repository? Doesn't this reduce possible use cases? Moreover, what happens if the user want's to see the new papers, without pushing the repo? I would leave git management to the user.

Moreover, we should think about how to improve the experience for users trying out the feature the first time. Right now they are confronted with a file selection dialog, without any explanation of what they should actually select etc.

[DominikVoigt]

Thanks for the feedback :)!

Regarding the first bullet point:
One reason was that JabRef already knew how to parse such a file, making the implementation fairly easy. Additionally, the entries can easily be modified directly in JabRef. Therefore it was a straightforward choice. This certainly is not the most user-friendly variant, but this can and will be addressed by offering a GUI for the creation of this file in the future.

Regarding the second bullet point:
The reason for this is that this allows easy versioning of search sessions allowing to track new entries without reevaluating old entries. I do not see how this could reduce the number of use cases? Furthermore, if the user does not want to create a remote repository for pushing a local one will suffice. In case a remote repository is configured I do not see any use case where a search should not be documented?

I agree that the UX is currently poor, however with the GUI implementation and the existing documentation for the feature it should suffice :).

[tobiasdiez]

One reason was that JabRef already knew how to parse such a file, making the implementation fairly easy.

I agree, and think it's a good short term solution. However, in the long term, I would strongly favor a solution based on a different file format. There are also parsers that can be reused easily.

The reason for this is that this allows easy versioning of search sessions allowing to track new entries without reevaluating old entries.

That also works if the user manages the git repo on its own, right? Then one can also manually remove false-positives etc before commit.

I do not see how this could reduce the number of use cases?

Many users don't even know what a git repository is.

[koppor]

One reason was that JabRef already knew how to parse such a file, making the implementation fairly easy.

I agree, and think it's a good short term solution. However, in the long term, I would strongly favor a solution based on a different file format. There are also parsers that can be reused easily.

Sure. The idea was as follows:

• The project had a time-constraint of 6 month with fixed costs. Thus, we had to adjust the content. (See Stakeholdererwartungen)
• We wanted a GUI at the end of the thesis.
• JabRef offers a GUI. Editing .bib files.
• Thus, the currently delivered feature can be used with JabRef as UI.

The reason for this is that this allows easy versioning of search sessions allowing to track new entries without reevaluating old entries.

That also works if the user manages the git repo on its own, right? Then one can also manually remove false-positives etc before commit.

The user creates a separate branch (e.g., jabref-slr-search). The SLR functionality prepends new entry. Thus, there won't be any git merge conflicts when mergin the survey results into the own branch. This merging has to be done manually.

In other words: the SLR feature maintaines the branch jabref-slr-search. The user maintains the other branches. When a user wants to remove search results, he does it in his branch. With a commit message indicating why he removed the search result. Thus, another person can trace what happened in the search:

• What did the crawler find?
• What did the user remove?

Future work: SLR feature switches to branch slr-search, searches, commits, and switches back to the branch before. Thus, the user can choose an arbitrary branch name (such as main).

I do not see how this could reduce the number of use cases?

Many users don't even know what a git repository is.

With the upcoming GUI support, JabRef will create the git repository magically. No external dependencies required. The connection to an upstream repository is depatable. Maybe the thought-of target group is not that large as thought. Maybe a discussion with @xJREB could help here. Maybe, we should really do not do any git magic (push/pull), but leave that to the user.

Nevertheless, I would keep the "branch switchting magic". The SLR feature only works at the branch jabref-slr-search.

[tobiasdiez]

The project had a time-constraint of 6 month with fixed costs. Thus, we had to adjust the content.

That I fully understand. And I'm impressed by what Dominik accomplished in such a short time period.
I just wanted to point out that for the integration in JabRef one needs to rethink a few of these decisions. For example, once we release a version that uses bib files as the study definition, it's way harder do later change it to say yaml, because you have to think about migration etc.

For the git support, it would maybe be good if you could outline what the goal and the workflow looks like. What are the use cases?
For example,

With the upcoming GUI support, JabRef will create the git repository magically.
Why would I want to have this as a user?

By skimming the code, I couldn't see how JabRef only maintains only the branch jabref-slr-search. It looked like it operates on the currently selected branch, and mostly commits everything (staged) - so even unrelated files in other directories. That might be undesired/unexpected from a user perspective.