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Fix links to files
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koppor committed Oct 13, 2024
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4 changes: 2 additions & 2 deletions en/advanced/commandline.md
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Expand Up @@ -234,8 +234,8 @@ Show info and error messages in the console.

As developer, you pass arguments to the app using gradle's `--app` switch. Enclose the arguments in quotes. For instance `--args="--debug"` turns on debug mode.

<figure><img src="../.gitbook/assets/image (5).png" alt=""><figcaption></figcaption></figure>
<figure><img src="../.gitbook/assets/image.png" alt=""><figcaption></figcaption></figure>

You can then view the event log in JabRef as follows:

<figure><img src="../.gitbook/assets/image (6).png" alt=""><figcaption></figcaption></figure>
<figure><img src="../.gitbook/assets/image.png" alt=""><figcaption></figcaption></figure>
6 changes: 3 additions & 3 deletions en/advanced/custom-themes.md
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Expand Up @@ -22,11 +22,11 @@ You can find a collection of user contributed themes at [https://themes.jabref.o

## Examples

**Light Theme** ![Light Theme](<../.gitbook/assets/theme-light (1).png>)
**Light Theme** ![Light Theme](<../.gitbook/assets/theme-light.png>)

**Dark Theme** ![Dark Theme](<../.gitbook/assets/theme-dark (1).png>)
**Dark Theme** ![Dark Theme](<../.gitbook/assets/theme-dark.png>)

**Custom Theme** ![Custom Theme](<../.gitbook/assets/theme-custom (1).png>) (based on the Dark Theme)
**Custom Theme** ![Custom Theme](<../.gitbook/assets/theme-custom.png>) (based on the Dark Theme)

## Known bugs

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4 changes: 2 additions & 2 deletions en/advanced/externalfiles.md
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Expand Up @@ -14,10 +14,10 @@ To change the external viewer settings, go to **Options → Preferences → Exte

There are several ways to open an external web page. In the entry editor, click on the icon "open" right of the text field to open the respective DOI or URL.

![Open DOI](<../.gitbook/assets/entryeditor-doi-open (1).png>)
![Open DOI](<../.gitbook/assets/entryeditor-doi-open.png>)

In the entry table you can select an entry and use the menu choice, keyboard shortcut or the right-click menu to open the file or web page. Finally, you can click on a URL or DOI icon.

![Open DOI via popup](<../.gitbook/assets/entrytable-doi-popup (1).png>)
![Open DOI via popup](<../.gitbook/assets/entrytable-doi-popup.png>)

By default the entry table will contain a singly column containing an indicator whether there is a DOI or a URL linked. You can remove the "Link identifiers" column in **Options → Preferences → Entry table**.
4 changes: 2 additions & 2 deletions en/advanced/journalabbreviations.md
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Expand Up @@ -10,7 +10,7 @@ This feature can be configured under **Options → Preferences → Manage journa

JabRef includes a fairly extensive build-in list of journal abbreviations. This list is a merge of all lists available at [https://abbrv.jabref.org](https://abbrv.jabref.org). However, this might still be incomplete (or outdated) for the purposes of some users. Thus, JabRef allows to add abbreviations in the form of a personal list or external lists.

![General view](<../.gitbook/assets/JournalAbbreviations (6).png>)
![General view](<../.gitbook/assets/JournalAbbreviations.png>)

## Using the feature

Expand Down Expand Up @@ -43,7 +43,7 @@ Once you click _Save changes_, if you have selected a file, and the table contai

You can link to a number of external lists. These links can be set up on top of the **Manage journal abbreviations** window. External lists are similar to the personal list. The _Open existing list_ button allows you to select an existing file on your computer.

![External list](<../.gitbook/assets/JournalAbbreviations-ExternalList (2).png>)
![External list](<../.gitbook/assets/JournalAbbreviations-ExternalList.png>)

External lists can be found at [JabRef's repository abbreviation lists](http://abbrv.jabref.org). These data files are in CSV format (using comma as separators):

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8 changes: 4 additions & 4 deletions en/cite/pushtoapplications.md
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Expand Up @@ -14,7 +14,7 @@ To push as citation, first select the entries in your entry table that you would
* Press `CTRL + L`
* Click on the dedicated button in the taskbar (left of the _Generate citation key_ button)

![](<../.gitbook/assets/push-external-button-windows (3).png>)
![](<../.gitbook/assets/push-external-button-windows.png>)

By default the external editor used to push citations is TeXstudio. You can select another application in **Options → Preferences → External programs**. Under the **Push applications** section, click on the **Application to push entries to** field. This will cause a dropdown menu to appear, from which you are then able to select from a list of all the external editors you have configured.

Expand All @@ -24,15 +24,15 @@ You can configure the citation command at "Cite command". JabRef intelligently p

Once you have made your selection and click **Save**, the push-to-external application button icon will change to match that of the selected external editor application.

![New Application After Select](<../.gitbook/assets/after-application-selection (4).png>)
![New Application After Select](<../.gitbook/assets/after-application-selection.png>)

When you click on the push-to-external application button, JabRef will export your selected entries to an open LaTeX file in the selected external editor application. As an example, here is what happens when you export one entry to TexStudio.

![Initial Push to External Export](<../.gitbook/assets/initial-push-export (5).png>)
![Initial Push to External Export](<../.gitbook/assets/initial-push-export.png>)

As long as you continue using the same external editor application, clicking on the push-to-external application button for subsequent exports will just add new citations or extend an existing citation with additional entries. Following the example above, here is what happens when you export a second entry to TeXStudio on an existing citation, which is extended to include the new entry in your LaTeX document.

![Subsequent Push to External Export](<../.gitbook/assets/subsequent-push-export (3).png>)
![Subsequent Push to External Export](<../.gitbook/assets/subsequent-push-export.png>)

## Hints on Emacs

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8 changes: 4 additions & 4 deletions en/collaborative-work/sqldatabase/README.md
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Expand Up @@ -16,19 +16,19 @@ Since version 5.0 JabRef supports secure SSL connection to the database. For Pos

After connecting to your shared database, your main window should look like this:

![Screenshot of JabRef with an open shared database](<../../.gitbook/assets/open-shared-databse-screenshot (1).png>)
![Screenshot of JabRef with an open shared database](<../../.gitbook/assets/open-shared-databse-screenshot.png>)

JabRef will automatically detect your changes and push them to the shared side. JabRef will also constantly check if there is a newer version available. If you experience connection issues, you can pull changes from your shared database via the icon in the icon bar. If a newer version is available, JabRef will try to automatically merge the new version and your local copy. If this fails, the **Update refused** dialog will show up. You will then have to manually merge using the **Update refused** dialog. The dialog helps you by pointing out the differences, you then will have to choose if you want to keep your local version or update to the shared version. Confirm your merge by clicking on **Merge entries**.

![Screenshot of Update refused dialog](<../../.gitbook/assets/update-refused-merge-dialog (1).png>)
![Screenshot of Update refused dialog](<../../.gitbook/assets/update-refused-merge-dialog.png>)

The **Update refused** dialog can also take a different form, if the BibEntry you currently work on has been deleted on the shared side. You can choose to keep the BibEntry in the database by clicking **Keep** or update to the shared side and click **Close**.

![Screenshot of Update refused dialog due to a deleted entry](<../../.gitbook/assets/update-refused-deleted-entry-dialog (1).png>)
![Screenshot of Update refused dialog due to a deleted entry](<../../.gitbook/assets/update-refused-deleted-entry-dialog.png>)

If you experience a problem with your connection to your shared database, the **Connection lost** dialog will show up. You can choose to **Reconnect**, **Work offline** or **Close database**. Most of the time simply reconnecting will fix this problem, if that's not the case you will have to choose between **Work offline** or **Close database**. Pick **Work offline** if you want to make sure your changes are saved. If you think there is nothing to save just pick **Close database**. If you choose to work offline, JabRef will convert the shared database to a local .bib database. Since you are no longer working online, but instead on a local database, you will have to import your work via copy and paste into the shared database. However before you import it into the shared database, make sure to check if changes happened during your offline time. Otherwise you might override someone else's work.

![Screenshot of Connection lost dialog](<../../.gitbook/assets/connection-lost-dialog (1).png>)
![Screenshot of Connection lost dialog](<../../.gitbook/assets/connection-lost-dialog.png>)

## Try it out

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2 changes: 1 addition & 1 deletion en/collect/add-entry-manually.md
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Expand Up @@ -8,7 +8,7 @@ A dialog window is displayed. By default, 5 common types of entries are displaye

For other types of entries, click on `Others.` That expands the window and displays the other entry types available:

![Window with all available entry types. Note: the actual content of the "others" menu depends on the database mode (BibTeX or biblatex).](<../.gitbook/assets/jabref-5.3-selectentrytype-expanded (1).png>)
![Window with all available entry types. Note: the actual content of the "others" menu depends on the database mode (BibTeX or biblatex).](<../.gitbook/assets/jabref-5.3-selectentrytype-expanded.png>)

Finally, the [entry editor](../advanced/entryeditor/) opens and let you fill in the various fields.

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8 changes: 4 additions & 4 deletions en/collect/add-entry-using-an-id.md
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Expand Up @@ -38,23 +38,23 @@ First, [eBook.de's](https://www.ebook.de/de/) API is used to fetch bibliographic

ID search is carried out using the [International Standard Book Number](https://en.wikipedia.org/wiki/International\_Standard\_Book\_Number).

![Screenshot of new entry dialog](<../.gitbook/assets/newentrychoosetype-idgeneratorhighlighted-isbn (3).png>)
![Screenshot of new entry dialog](<../.gitbook/assets/newentrychoosetype-idgeneratorhighlighted-isbn.png>)

### DiVA

[DiVA (Digitala Vetenskapliga Arkivet)](https://info.diva-portal.org/about-diva/) is a database with publications from about [40](https://www.diva-portal.org/smash/aboutdiva.jsf) Swedish universities and research institutions.

ID search is carried out using the DiVA id (diva2).

![Screenshot of new entry dialog](<../.gitbook/assets/newentrychoosetype-idgeneratorhighlighted-diva (1).png>)
![Screenshot of new entry dialog](<../.gitbook/assets/newentrychoosetype-idgeneratorhighlighted-diva.png>)

### DOI

JabRef uses [http://dx.doi.org/](http://dx.doi.org) (provided by [http://crossref.org/](http://crossref.org)) to convert the given DOI to a new entry.

ID search is carried out using the DOI.

![Screenshot of new entry dialog](<../.gitbook/assets/newentrychoosetype-idgeneratorhighlighted (1).png>)
![Screenshot of new entry dialog](<../.gitbook/assets/newentrychoosetype-idgeneratorhighlighted.png>)

{% hint style="warning" %}
If JabRef cannot find the reference of your DOI using this ID type, please, try the same DOI with the ID type "mEDRA". The ID type mEDRA looks for the reference corresponding to a DOI too, but using another registration agency.
Expand Down Expand Up @@ -98,7 +98,7 @@ ID search is carried out using the DOI.

ID search is carried out using the [ADS Bibcode](http://adsabs.github.io/help/actions/bibcode).

![Screenshot of new entry dialog](<../.gitbook/assets/newentrychoosetype-idgeneratorhighlighted-ads (1).png>)
![Screenshot of new entry dialog](<../.gitbook/assets/newentrychoosetype-idgeneratorhighlighted-ads.png>)

### Title

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6 changes: 3 additions & 3 deletions en/collect/add-pdfs-to-an-entry.md
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Expand Up @@ -6,12 +6,12 @@ description: Finding full text documents online

JabRef offers finding full text documents online. Mostly, these are PDFs file. To use this feature, go to "Lookup" and then select "Find full text documents online".

<figure><img src="../.gitbook/assets/image (1).png" alt=""><figcaption><p>Lookup > Search for unlinked local files</p></figcaption></figure>
<figure><img src="../.gitbook/assets/image.png" alt=""><figcaption><p>Lookup > Search for unlinked local files</p></figcaption></figure>

Then, JabRef uses online services to find a PDF. (Implementation details are provided at the [developer's documentation](https://devdocs.jabref.org/code-howtos/fetchers.html).)

<figure><img src="../.gitbook/assets/image (2).png" alt=""><figcaption><p>JabRef looking up full text documents</p></figcaption></figure>
<figure><img src="../.gitbook/assets/image.png" alt=""><figcaption><p>JabRef looking up full text documents</p></figcaption></figure>

Result of the look up:

<figure><img src="../.gitbook/assets/image (4).png" alt=""><figcaption><p>File found</p></figcaption></figure>
<figure><img src="../.gitbook/assets/image.png" alt=""><figcaption><p>File found</p></figcaption></figure>
10 changes: 5 additions & 5 deletions en/collect/findunlinkedfiles.md
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Expand Up @@ -27,10 +27,10 @@ In case you have numerous PDF files and want to convert them into new entries, J
1. Create or open a `.bib` library.
2. Go to **Lookup -> Search for unlinked local files**. (or press `SHIFT + F7`)

![FindUnlinkedFiles - Menu](<../.gitbook/assets/bildschirmfoto-2021-07-05-um-19.19.09 (1).png>) ![FindUnlinkedFiles - Menu](<../.gitbook/assets/findunlinkedfiles-menu-5.2 (6).png>)
![FindUnlinkedFiles - Menu](<../.gitbook/assets/bildschirmfoto-2021-07-05-um-19.19.09.png>) ![FindUnlinkedFiles - Menu](<../.gitbook/assets/findunlinkedfiles-menu-5.2.png>)
3. The "Search for unlinked local files" dialog opens.

<img src="../.gitbook/assets/findunlinkedfiles-window-5.2 (5).png" alt="FindUnlinkedFiles - Initial dialog" data-size="original">
<img src="../.gitbook/assets/findunlinkedfiles-window-5.2.png" alt="FindUnlinkedFiles - Initial dialog" data-size="original">
4. Choose a start directory using the "Browse" button.
5. Click on "Search" / "Scan directory".
6. In "Select files", the files not yet contained in the library are shown.
Expand All @@ -40,9 +40,9 @@ In case you have numerous PDF files and want to convert them into new entries, J
8. Click on `Import`.

The windows close and the entry table now contains the newly-imported entries.
9. The entry editor with the last imported entry is shown ![FindUnlinkedFiles - 08 - entry editor](<../.gitbook/assets/findunlinkedfiles-08-entry-editor (1).png>)
9. The entry editor with the last imported entry is shown ![FindUnlinkedFiles - 08 - entry editor](<../.gitbook/assets/findunlinkedfiles-08-entry-editor.png>)
10. You can now save the file and are finished.
11. Optional: Click on "General" to see the linked file ![FindUnlinkedFiles - 09 - entry editor - General](<../.gitbook/assets/findunlinkedfiles-09-entry-editor-general (5).png>)
11. Optional: Click on "General" to see the linked file ![FindUnlinkedFiles - 09 - entry editor - General](<../.gitbook/assets/findunlinkedfiles-09-entry-editor-general.png>)
12. Optional: Click on "BibTeX source" to see the BibTeX source ![FindUnlinkedFiles - 10 - entry editor - BibTeX source](../.gitbook/assets/findunlinkedfiles-10-entry-editor-bibtex-source.png)
13. Optional: You have to shrink it to see the entry in the entry table, enlarge the JabRef window and use the mouse at the upper border of the entry editor ![FindUnlinkedFiles - 11 - entry editor - shrunk](../.gitbook/assets/findunlinkedfiles-11-entry-editor-shrunk.png)
14. Optional: Press Esc to show the entry preview ![FindUnlinkedFiles - 12 - entry preview](../.gitbook/assets/findunlinkedfiles-12-entry-preview.png)
Expand All @@ -65,7 +65,7 @@ We are also [thinking about](https://github.com/koppor/jabref/issues/169) replac

JabRef also offers to change the filenames. You can adapt the pattern at Preferences -> Import ![Preferences - Import](../.gitbook/assets/preferences-import.png)

Select "Choose pattern" and choose "bibtexkey - title" ![Preferences - Import - Choose pattern](<../.gitbook/assets/preferences-import-choose-pattern (4).png>) This results in the setting `\bibtexkey\begin{title} - \format[RemoveBrackets]{\title}\end{title}`.
Select "Choose pattern" and choose "bibtexkey - title" ![Preferences - Import - Choose pattern](<../.gitbook/assets/preferences-import-choose-pattern.png>) This results in the setting `\bibtexkey\begin{title} - \format[RemoveBrackets]{\title}\end{title}`.

This makes the filenames start with the bibtey key followed by the full title. In the concrete case, `\bibtexkey` only may be the better option as the described bibtey key already contains the title.

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2 changes: 1 addition & 1 deletion en/collect/import/importinspectiondialog.md
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Expand Up @@ -10,7 +10,7 @@ Entries are first shown in the inspection window. Note that, if this takes too l

Once the entries displayed in the inspection window, none of them have been added to one of your databases yet.

![Screenshot of the inspection window](<../../.gitbook/assets/inspectionwindow (2).png>)
![Screenshot of the inspection window](<../../.gitbook/assets/inspectionwindow.png>)

By default, all the entries are selected for importation, as shown by the checked boxes in the _Keep_ column. You can select/unselect an entry by clicking on these checkboxes. On the left panel, buttons allow you to **Select all** the entries for importation, or to **Deselect all** the entries.

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6 changes: 3 additions & 3 deletions en/collect/newentryfromplaintext.md
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Expand Up @@ -15,11 +15,11 @@ O. Kopp, A. Armbruster, und O. Zimmermann, "Markdown Architectural Decision Reco
<img src="../.gitbook/assets/new-entry-from-plain-text-step-1.png" alt="New entry from plain text" data-size="original">
2. The "Plain Reference Parser" window opens

<img src="../.gitbook/assets/new-entry-from-plain-text-step-2 (1).png" alt="Plain Reference Parser" data-size="original">
<img src="../.gitbook/assets/new-entry-from-plain-text-step-2.png" alt="Plain Reference Parser" data-size="original">
3. Paste the reference text:

<img src="../.gitbook/assets/new-entry-from-plain-text-step-3 (1).png" alt="Paste" data-size="original">
<img src="../.gitbook/assets/new-entry-from-plain-text-step-3.png" alt="Paste" data-size="original">
4. Click "Add to current library"
5. The result is selected in the entry table:

<img src="../.gitbook/assets/new-entry-from-plain-text-step-4 (1).png" alt="Result of Grobid Parsing" data-size="original">
<img src="../.gitbook/assets/new-entry-from-plain-text-step-4.png" alt="Result of Grobid Parsing" data-size="original">
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