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Batch Processing Article XML Files in JournalMap

Through JournalMap's admin panel articles in NLM 3.0 or JATS formatted XML can be uploaded and geoparsed. This process is available only for users with Editor or Admin rights. The instructions below detail this process.

Batch Processing XML Articles

1. Once logged in, click on the Administration link at the top right of any JournalMap page.

2. From the admin page, click Batches in the navigation menu on the left-hand side of the screen.

3. The batch page presents a blank box toward the top of the page. Drag and drop XML files from your computer onto this box to load them into JournalMap.

Once the XML files are loaded into JournalMap, they will display as a list in the file upload box. Click the Create Batch button to begin batch processing.

4. The batch processing page reports the status of the batch. Because geoparsing of the XML files can take some time, especially for large batches, you should refresh the page until the Article count reaches the number of articles you included in the batch. (Note: occasionally JournalMap's batch processor will ask whether a batch should be run Asynchronously or Synchronously. If this happens, choose Asynchronous). You can approve all articles with locations and without any other errors by clicking the Approve All Pending Articles from this Batch button.

Occasionally article XML will not contain all the required information for an article (or it's not in a readable format). This happens most commonly when articles do not have abstracts or keywords.

If this occurs, click on Needs Fixing from the batch page and address the problems with those articles. Click on an article that needs fixing to open the article details editor. You can correct any problems in this form. If an article does not have an abstract or keywords, check the box that says “No abstract available” or “No keywords available”.

5. Address articles that were not assigned a location by clicking on the Missing Location link to access a list of articles. Click on an article in the list to open the article details editor.

In the batch import process, articles may not be assigned coordinates for two reasons. First, no location was appropriate for that article or the article covered such a broad geographic extent (e.g., global study, entire continent) that a point location is not a meaningful representation of the study's location. In these cases, check the box at the bottom of the article's citation information that says “Article does not have a study area.” Then click the Update Article button to save the change.

The second reason coordinates are not assigned to an article is there was location information in the article that was not readable by the parser (e.g., unknown coordinate format, unexpected character encoding in coordinates, only place names given). In this case locations should be assigned manually. Click on an article from the Missing Location list to open the article details editor and click on the Add Location button at the bottom of the page. Follow the instructions on the Manual Geotagging Articles page.

xml_batch_processing.txt · Last modified: 2015/04/27 23:09 by jkarl


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