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README.md
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README.md
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# neath: named entity annotation tool
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# neat: named entity annotation tool
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#### version 0.1
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---
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---
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### Table of contents
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[1. Introduction](https://github.com/qurator-spk/neath/blob/master/README.md#1-introduction)
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[1. Introduction](https://github.com/qurator-spk/neat/blob/master/README.md#1-introduction)
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[2. User Guide](https://github.com/qurator-spk/neath/blob/master/README.md#2-user-guide)
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[2. User Guide](https://github.com/qurator-spk/neat/blob/master/README.md#2-user-guide)
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[2.1 Technical requirements](https://github.com/qurator-spk/neath/blob/master/README.md#21-technical-requirements)
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[2.1 Technical requirements](https://github.com/qurator-spk/neat/blob/master/README.md#21-technical-requirements)
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[2.2 Installation](https://github.com/qurator-spk/neath/blob/master/README.md#22-installation)
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[2.2 Installation](https://github.com/qurator-spk/neat/blob/master/README.md#22-installation)
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[2.3 Data format](https://github.com/qurator-spk/neath/blob/master/README.md#23-data-format)
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[2.3 Data format](https://github.com/qurator-spk/neat/blob/master/README.md#23-data-format)
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[2.4 Data preparation](https://github.com/qurator-spk/neath/blob/master/README.md#24-data-preparation)
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[2.4 Data preparation](https://github.com/qurator-spk/neat/blob/master/README.md#24-data-preparation)
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[2.5 Provenance](https://github.com/qurator-spk/neath/blob/master/README.md#25-provenance)
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[2.5 Provenance](https://github.com/qurator-spk/neat/blob/master/README.md#25-provenance)
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[2.6 Keyboard navigation](https://github.com/qurator-spk/neath/blob/master/README.md#26-keyboard-navigation)
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[2.6 Keyboard navigation](https://github.com/qurator-spk/neat/blob/master/README.md#26-keyboard-navigation)
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[2.7 Mouse navigation](https://github.com/qurator-spk/neath/blob/master/README.md#27-mouse-navigation)
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[2.7 Mouse navigation](https://github.com/qurator-spk/neat/blob/master/README.md#27-mouse-navigation)
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[2.8 Image support](https://github.com/qurator-spk/neath/blob/master/README.md#28-image-support)
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[2.8 Image support](https://github.com/qurator-spk/neat/blob/master/README.md#28-image-support)
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[2.9 Saving progress](https://github.com/qurator-spk/neath/blob/master/README.md#29-saving-progress)
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[2.9 Saving progress](https://github.com/qurator-spk/neat/blob/master/README.md#29-saving-progress)
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[3. Annotation Guidelines](https://github.com/qurator-spk/neath/blob/master/README.md#3-annotation-guidelines)
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[3. Annotation Guidelines](https://github.com/qurator-spk/neat/blob/master/README.md#3-annotation-guidelines)
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### 1. Introduction
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[neath](https://github.com/qurator-spk/neath) is a simple, browser-based tool for editing and annotating text with named entities to produce a corpus for training/testing/evaluation. It can be used to add or correct named entity BIO-tags in a TSV file and to correct the token text or tokenization (e.g. due to OCR/segmentation errors).
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[neat](https://github.com/qurator-spk/neat) is a simple, browser-based tool for editing and annotating text with named entities to produce a corpus for training/testing/evaluation. It can be used to add or correct named entity BIO-tags in a TSV file and to correct the token text or tokenization (e.g. due to OCR/segmentation errors).
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[neath](https://github.com/qurator-spk/neath) is developed at the [Berlin State Library](https://staatsbibliothek-berlin.de/) for data annotation in the context of the [SoNAR-IDH](https://sonar.fh-potsdam.de/) project and the [QURATOR](https://qurator.ai/) project.
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[neat](https://github.com/qurator-spk/neat) is developed at the [Berlin State Library](https://staatsbibliothek-berlin.de/) for data annotation in the context of the [SoNAR-IDH](https://sonar.fh-potsdam.de/) project and the [QURATOR](https://qurator.ai/) project.
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### 2. User Guide
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#### 2.1 Technical Requirements
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[neath](https://github.com/qurator-spk/neath) runs locally as a pure HTML+JavaScript webpage in your web browser. No software needs to be installed, but JavaScript has to be enabled in the browser.
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[neat](https://github.com/qurator-spk/neat) runs locally as a pure HTML+JavaScript webpage in your web browser. No software needs to be installed, but JavaScript has to be enabled in the browser.
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#### 2.2. Installation
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Simply clone the repo using ``git clone https://github.com/qurator-spk/neath.git`` or download the [ZIP](https://github.com/qurator-spk/neath/archive/master.zip). Make sure you have at minimum ``neath.html`` and ``neath.js`` residing in a local directory, then it is sufficient to just open ``neath.html`` in a browser. Any fairly recent browser should work, but only Chrome and Firefox are tested.
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Simply clone the repo using ``git clone https://github.com/qurator-spk/neat.git`` or download the [ZIP](https://github.com/qurator-spk/neat/archive/master.zip). Make sure you have at minimum ``neat.html`` and ``neat.js`` residing in a local directory, then it is sufficient to just open ``neat.html`` in a browser. Any fairly recent browser should work, but only Chrome and Firefox are tested.
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#### 2.3 Data format
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The data format is based on the format used in the [GermEval2014 Named Entity Recognition Shared Task](https://sites.google.com/site/germeval2014ner/data). Text is encoded as one token per line, with name spans encoded in the BIO-scheme, provided as tab-separated values:
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@ -77,7 +77,7 @@ No. TOKEN NE-TAG NE-EMB
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For our purposes we extend this format by adding
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* a fifth column for an ``ID`` for the outer ``NE-TAG`` from an authority file (in this case, the [GND](https://www.dnb.de/EN/Professionell/Standardisierung/GND/gnd_node.html) is used)
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* column six for use as a variable ``url_id`` (see [Image Support](https://github.com/qurator-spk/neath/blob/master/README.md#28-image-support) for further details)
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* column six for use as a variable ``url_id`` (see [Image Support](https://github.com/qurator-spk/neat/blob/master/README.md#28-image-support) for further details)
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* finally, columns 7+ are used for storing ``left,right,top,bottom`` pixel coordinates for facsimile snippets
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Example (full):
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@ -105,7 +105,7 @@ No. TOKEN NE-TAG NE-EMB GND-ID url_id left,right,top,bottom
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```
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#### 2.4 Data preparation
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The source data that is used for annotation are OCR results in [PAGE-XML](https://github.com/PRImA-Research-Lab/PAGE-XML) format. We provide a [Python tool](https://github.com/qurator-spk/page2tsv) that supports the transformation of [PAGE-XML](https://github.com/PRImA-Research-Lab/PAGE-XML) OCR files into the [TSV format](https://github.com/qurator-spk/neath/blob/master/README.md#23-data-format) required for use with [neath](https://github.com/qurator-spk/neath).
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The source data that is used for annotation are OCR results in [PAGE-XML](https://github.com/PRImA-Research-Lab/PAGE-XML) format. We provide a [Python tool](https://github.com/qurator-spk/page2tsv) that supports the transformation of [PAGE-XML](https://github.com/PRImA-Research-Lab/PAGE-XML) OCR files into the [TSV format](https://github.com/qurator-spk/neat/blob/master/README.md#23-data-format) required for use with [neat](https://github.com/qurator-spk/neat).
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#### 2.5 Provenance
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The processing pipeline applied at the Berlin State Library comprises the follows steps:
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@ -115,7 +115,7 @@ Layout Analysis & Textline Extraction @[sbb_textline_detector](https://github.co
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2. OCR & Word Segmentation
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OCR is based on [OCR-D](https://github.com/OCR-D)'s [ocrd_tesserocr](https://github.com/OCR-D/ocrd_tesserocr) which requires [Tesseract](https://github.com/tesseract-ocr/tesseract) **>= 4.1.0**. The [GT4HistOCR_2000000](https://ub-backup.bib.uni-mannheim.de/~stweil/ocrd-train/data/GT4HistOCR_2000000.traineddata) model, which is [trained](https://github.com/tesseract-ocr/tesstrain/wiki/GT4HistOCR) on the [GT4HistOCR](https://zenodo.org/record/1344132) corpus, is used. Further details are available in the [paper](https://arxiv.org/abs/1809.05501).
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3. TSV Transformation
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A simple [Python tool](https://github.com/qurator-spk/page2tsv) is used for the transformation of the OCR results in [PAGE-XML](https://github.com/PRImA-Research-Lab/PAGE-XML) to [TSV](https://github.com/qurator-spk/neath/blob/master/docs/README.md#23-data-format).
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A simple [Python tool](https://github.com/qurator-spk/page2tsv) is used for the transformation of the OCR results in [PAGE-XML](https://github.com/PRImA-Research-Lab/PAGE-XML) to [TSV](https://github.com/qurator-spk/neat/blob/master/docs/README.md#23-data-format).
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4. Tokenization
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For tokenization, [SoMaJo](https://github.com/tsproisl/SoMaJo) is used.
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5. Named Entity Recognition
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@ -180,13 +180,13 @@ For Named Entity Recognition, a [BERT-Base](https://github.com/google-research/b
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* left-click the `POSITION` of a row and select `start-sentence` from the drop-down menu to start a new sentence
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#### 2.8 Image Support
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Provided facsimile images are available online via the [iiif.io](https://iiif.io/) Image API, [neath](https://github.com/qurator-spk/neath) supports the embedding of facsimile snippets into its interface to help with data annotation and correction.
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Provided facsimile images are available online via the [iiif.io](https://iiif.io/) Image API, [neat](https://github.com/qurator-spk/neat) supports the embedding of facsimile snippets into its interface to help with data annotation and correction.
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This further requires that OCR with word segmentation is applied to the image to determine bounding boxes for tokens.
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The iiif-image-url contained in the source ``#`` can then be used as a replacement for ``url_id`` in combination with the token bounding boxes as ``left,right,top,bottom`` to obtain the facsimile snippet url and display the image in the leftmost column. Clicking on the facsimile snippet opens up a new tab with a larger context.
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#### 2.9 Saving progress
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[neath](https://github.com/qurator-spk/neath) runs fully locally in the browser. Therefore it can not automatically save any changes you made to disk. You have to use the `Save Changes` button in order to so manually from time to time. If your browser automatically saves all downloads to your `Downloads` folder, you might want to configure it so that it instead prompts you where to save.
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[neat](https://github.com/qurator-spk/neat) runs fully locally in the browser. Therefore it can not automatically save any changes you made to disk. You have to use the `Save Changes` button in order to so manually from time to time. If your browser automatically saves all downloads to your `Downloads` folder, you might want to configure it so that it instead prompts you where to save.
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### 3. Annotation Guidelines
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The most recent version of the [Annotation Guidelines](https://github.com/qurator-spk/neath/blob/master/Annotation_Guidelines.pdf) is included in this repository.
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The most recent version of the [Annotation Guidelines](https://github.com/qurator-spk/neat/blob/master/Annotation_Guidelines.pdf) is included in this repository.
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@ -2,8 +2,8 @@
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<html>
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<head>
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<meta charset="UTF-8">
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<title>neath</title>
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<base href="neath.html" target="_blank">
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<title>neat</title>
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<base href="neat.html" target="_blank">
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<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css"
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integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">
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<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/PapaParse/5.1.0/papaparse.min.js"></script>
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<div class="col-9">
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<div class="row">
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<div class="col text-center">
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<h3><a href="https://github.com/qurator-spk/neath" target="_blank" tabindex="-1">neath</a>: named entity annotation tool</h3>
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<a href="https://github.com/qurator-spk/neath/blob/master/README.md#2-user-guide" target="_blank" tabindex="-1">User Guide</a> | <a href="https://github.com/qurator-spk/neath/blob/master/Annotation_Guidelines.pdf" target="_blank" tabindex="-1">Annotation Guidelines</a> | <a href="https://github.com/qurator-spk/neath/issues" target="_blank" tabindex="-1">Issues</a><hr>
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<h3><a href="https://github.com/qurator-spk/neat" target="_blank" tabindex="-1">neat</a>: named entity annotation tool</h3>
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<a href="https://github.com/qurator-spk/neat/blob/master/README.md#2-user-guide" target="_blank" tabindex="-1">User Guide</a> | <a href="https://github.com/qurator-spk/neat/blob/master/Annotation_Guidelines.pdf" target="_blank" tabindex="-1">Annotation Guidelines</a> | <a href="https://github.com/qurator-spk/neat/issues" target="_blank" tabindex="-1">Issues</a><hr>
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</div>
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</div>
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</div>
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</a>
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</div>
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<div class="col-8 text-center" id="tableregion">
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Please upload a TSV<sup>(<a href="https://github.com/qurator-spk/neath/blob/master/User_Guide.md#22-data-format">i</a>)</sup> file:
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Please upload a TSV<sup>(<a href="https://github.com/qurator-spk/neat/blob/master/User_Guide.md#22-data-format">i</a>)</sup> file:
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<br><br>
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<input type="file" id="tsv-file" name="files"/>
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</div>
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</div>
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<script src="neath.js"></script>
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<script src="neat.js"></script>
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</body>
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</html>
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loadFile ( evt,
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function(results, file, urls) {
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let neath = setupInterface(results, file, urls);
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let neat = setupInterface(results, file, urls);
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$(window).bind("beforeunload",
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function() {
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console.log(neath.hasChanges());
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console.log(neat.hasChanges());
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if (neath.hasChanges())
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if (neat.hasChanges())
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return confirm("You have unsaved changes. Do you want to save them before leaving?");
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}
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);
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