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Passing command line arguments using gradle is currently not possible as all arguments \(such as `-Dfile.encoding=windows-1252`\) are passed to the application.
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Passing command line arguments using gradle is currently not possible as all arguments (such as `-Dfile.encoding=windows-1252`) are passed to the application.
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Without jlink, it is not possible to generate a fat jar any more. During development, the capabilities of the IDE has to be used.
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@@ -41,13 +41,12 @@ Diagram showing aspects of groups: [Groups.uml](https://github.com/JabRef/jabref
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[Architectural decisions for JabRef](adr.md) are recorded.
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For new ADRs, please use [template.md](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/template.md) as basis. More information on MADR is available at [https://adr.github.io/madr/](https://adr.github.io/madr/). General information about architectural decision records is available at [https://adr.github.io/](https://adr.github.io/). Add them to the [list of architectural decision records](adr.md).
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For new ADRs, please use [template.md](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/template.md) as basis. More information on MADR is available at [https://adr.github.io/madr/](https://adr.github.io/madr/). General information about architectural decision records is available at [https://adr.github.io/](https://adr.github.io). Add them to the [list of architectural decision records](adr.md).
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## FAQ
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* Q: I get `java: package org.jabref.logic.journals does not exist`.
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*Q: I get `java: package org.jabref.logic.journals does not exist`.
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A: You have to ignore `buildSrc/src/main` as source directory in IntelliJ as indicated in our [setup guide](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace).
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Also filed as IntelliJ issue [IDEA-240250](https://youtrack.jetbrains.com/issue/IDEA-240250).
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A: You have to ignore `buildSrc/src/main` as source directory in IntelliJ as indicated in our [setup guide](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace).
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Also filed as IntelliJ issue [IDEA-240250](https://youtrack.jetbrains.com/issue/IDEA-240250).
Copy file name to clipboardExpand all lines: docs/advanced-reading/fetchers.md
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Fetchers are the implementation of the [search using online services](https://docs.jabref.org/collect/import-using-online-bibliographic-database). Some fetchers require API keys to get them working. To get the fetchers running in a JabRef development setup, the keys need to be placed in the respective environment variable. The following table lists the respective fetchers, where to get the key from and the environment variable where the key has to be placed.
|[Springer Nature](https://docs.jabref.org/collect/import-using-online-bibliographic-database#springer)|[Springer Nature API Portal](https://dev.springernature.com)|`SpringerNatureAPIKey`| 5000 calls/day|
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|[Zentralblatt Math](https://www.zbmath.org)|(none) |(none) | Depending on the current network |
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"Depending on the current network" means that it depends on whether your request is routed through a network having paid access. For instance, some universities have subscriptions to MathSciNet.
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*`EntryBasedFetcher`: Completes an existing bibliographic entry with information retrieved by the fetcher
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*`FulltextFetcher`: Searches for a PDF for an exiting bibliography entry
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*`SearchBasedFetcher`: Searches providers using a given query and returns a set of \(new\) bibliography entry. The user-facing side is implemented in the UI described at [https://docs.jabref.org/collect/import-using-online-bibliographic-database](https://docs.jabref.org/collect/import-using-online-bibliographic-database).
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*`SearchBasedFetcher`: Searches providers using a given query and returns a set of (new) bibliography entry. The user-facing side is implemented in the UI described at [https://docs.jabref.org/collect/import-using-online-bibliographic-database](https://docs.jabref.org/collect/import-using-online-bibliographic-database).
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There are more fetchers supported by JabRef. Investigate the package `org.jabref.logic.importer`. Another possibility is to investigate the inheritance relation of `WebFetcher`\(Ctrl+H in IntelliJ\).
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There are more fetchers supported by JabRef. Investigate the package `org.jabref.logic.importer`. Another possibility is to investigate the inheritance relation of `WebFetcher` (Ctrl+H in IntelliJ).
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## Fulltext Fetchers
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* all fulltext fetchers run in parallel
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* the result with the highest priority wins
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*`InterruptedException`\|`ExecutionException`\|`CancellationException` are ignored
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*`InterruptedException` | `ExecutionException` | `CancellationException` are ignored
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### Trust Levels
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*`SOURCE`\(highest\): definitive URL for a particular paper
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*`SOURCE`(highest): definitive URL for a particular paper
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*`PUBLISHER`: any publisher library
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*`PREPRINT`: any preprint library that might include non final publications of a paper
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*`META_SEARCH`: meta search engines
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*`UNKNOWN`\(lowest\): anything else not fitting the above categories
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*`UNKNOWN`(lowest): anything else not fitting the above categories
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### Current trust levels
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* Springer: Publisher
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* ACS: Publisher
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* IEEE: Publisher
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* Google Scholar: META\_SEARCH, because it is a search engine
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* Google Scholar: META_SEARCH, because it is a search engine
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* Arxiv: PREPRINT, because preprints are published there
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* OpenAccessDOI: META\_SEARCH
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* OpenAccessDOI: META_SEARCH
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Reasoning:
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* A DOI uniquely identifies a paper. Per definition, a DOI leads to the right paper. Everything else is good guessing.
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* We assume the DOI resolution surely points to the correct paper and that publisher fetches may have errors: For instance, a title of a paper may lead to different publications of it. One the conference version, the other the journal version. --> the PDF could be chosen randomly
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* We assume the DOI resolution surely points to the correct paper and that publisher fetches may have errors: For instance, a title of a paper may lead to different publications of it. One the conference version, the other the journal version. --> the PDF could be chosen randomly
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Code was first introduced at [PR\#3882](https://github.com/JabRef/jabref/pull/3882).
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Code was first introduced at [PR#3882](https://github.com/JabRef/jabref/pull/3882).
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## Background on embedding the keys in JabRef
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The keys are placed into the `build.properties` file.
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```text
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```
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springerNatureAPIKey=${springerNatureAPIKey}
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```
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```
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When executing `./gradlew run`, gradle executes `processResources` and populates `build/build.properties` accordingly. However, when working directly in the IDE, Eclipse keeps reading `build.properties` from `src/main/resources`. In IntelliJ, the task `JabRef Main` is executing `./gradlew processResources` before running JabRef from the IDE to ensure the `build.properties` is properly populated.
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We welcome contributions to JabRef and encourage you to follow the GitHub workflow specified below. If you are not familiar with this type of workflow, take a look at GitHub's excellent overview on the [GitHub flow](https://guides.github.com/introduction/flow/index.html) and the explanation of [Feature Branch Workflow](https://atlassian.com/git/tutorials/comparing-workflows#feature-branch-workflow) for the idea behind this kind of development.
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1. Get the JabRef code on your local machine. Detailed instructions about this step can be found in our [guidelines for setting up a local workspace](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace).
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1. Get the JabRef code on your local machine. Detailed instructions about this step can be found in our [guidelines for setting up a local workspace](getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md).
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1. Fork the JabRef into your GitHub account.
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2. Clone your forked repository on your local machine.
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2.**Create a new branch**\(such as `fix-for-issue-121`\). Be sure to create a **separate branch** for each improvement you implement.
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2.**Create a new branch** (such as `fix-for-issue-121`). Be sure to create a **separate branch** for each improvement you implement.
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3. Do your work on the **new branch — not the master branch.** Refer to our [code how-tos](https://devdocs.jabref.org/getting-into-the-code/code-howtos) if you have questions about your implementation.
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4. Create a pull request. For an overview of pull requests, take a look at GitHub's [pull request help documentation](https://help.github.com/articles/about-pull-requests/).
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5. In case your pull request is not yet complete or not yet ready for review, consider creating a [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/) instead.
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You should edit the [`CHANGELOG.md`](https://github.com/JabRef/jabref/blob/master/CHANGELOG.md#changelog) file located in the root directory of the JabRef source. Add a line with your changes in the appropriate section.
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If you did internal refactorings or improvements not visible to the user \(e.g., UI, .bib file\), then you don't need to put an entry there.
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If you did internal refactorings or improvements not visible to the user (e.g., UI, .bib file), then you don't need to put an entry there.
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#### **Format of keyboard shortcuts**
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Example:
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```text
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```
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java.lang.AssertionError: DETECTED LANGUAGE KEYS WHICH ARE NOT IN THE ENGLISH LANGUAGE FILE
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PASTE THESE INTO THE ENGLISH LANGUAGE FILE
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#### When adding a library
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Please try to use a version available at JCenter and add it to `build.gradle`. In any case, describe the library at [`external-libraries.md`](https://github.com/JabRef/jabref/blob/master/external-libraries.md#external-libraries). We need that information for our package maintainers \(e.g., those of the [debian package](https://tracker.debian.org/pkg/jabref)\). Also add a txt file stating the license in `libraries/`. It is used at `gradlew processResources` to generate the About.html files. You can see the result in `build\resources\main\help\en\About.html` or when clicking Help -> About.
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Please try to use a version available at JCenter and add it to `build.gradle`. In any case, describe the library at [`external-libraries.md`](https://github.com/JabRef/jabref/blob/master/external-libraries.md#external-libraries). We need that information for our package maintainers (e.g., those of the [debian package](https://tracker.debian.org/pkg/jabref)). Also add a txt file stating the license in `libraries/`. It is used at `gradlew processResources` to generate the About.html files. You can see the result in `build\resources\main\help\en\About.html` or when clicking Help -> About.
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#### When making an architectural decision
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In case you add a library or do major code rewrites, we ask you to document your decision. Recommended reading: [https://adr.github.io/](https://adr.github.io/).
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In case you add a library or do major code rewrites, we ask you to document your decision. Recommended reading: [https://adr.github.io/](https://adr.github.io).
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We simply ask to create a new markdown file in `docs/adr` following the template presented at [https://adr.github.io/madr/](https://adr.github.io/madr/).
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In case you want to directly add a comment to a class, simply use the following template \(based on [sustainable architectural decisions](https://www.infoq.com/articles/sustainable-architectural-design-decisions)\):
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In case you want to directly add a comment to a class, simply use the following template (based on [sustainable architectural decisions](https://www.infoq.com/articles/sustainable-architectural-design-decisions)):
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```text
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```
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In the context of <use case/user story u>,
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facing <concern c>
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we decided for <option o>
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Create a pull request on GitHub following GitHub's guide "[Creating a pull request from a fork](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request-from-a-fork)". For text inspirations, consider [How to write the perfect pull request](https://github.com/blog/1943-how-to-write-the-perfect-pull-request).
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If you want to indicate that a pull request is not yet complete **before** creating the pull request, you may consider creating a [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/). Alternatively, once the PR has been created, you can add the prefix `[WIP]`\(which stands for "Work in Progress"\) to indicate that the pull request is not yet complete, but you want to discuss something or inform about the current state of affairs.
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If you want to indicate that a pull request is not yet complete **before** creating the pull request, you may consider creating a [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/). Alternatively, once the PR has been created, you can add the prefix `[WIP]` (which stands for "Work in Progress") to indicate that the pull request is not yet complete, but you want to discuss something or inform about the current state of affairs.
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## How to improve the developer's documentation
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3.`gitbook serve`
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Then, you can see a near-to-reality rendering of the development documentation at [http://localhost:4000](http://localhost:4000).
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