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Is there a way to prepare a project on QGIS with many layers and to publish it under WMS service on GeoServer?

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Yes. There is the plugin "geoserver explorer" which communicate with geoserver through the REST API. You can publish layer and styles. Haven't tested it the last two years but last time i used it it was pretty useful.

https://plugins.qgis.org/plugins/geoserverexplorer/

  • Unfortunately this plugin is no longer maintained and does not work with the latest version of QGIS. – mike.bronner Mar 13 at 17:54
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If you have many layers to upload, you should look at the geoserver rest API - see here

You can also use the opengeo plugin - see information

However using shapefiles with geoserver isn't the best bet, it would be faster to use a DB (PostGis for instance) - here is why !

  • I think this answer would become useful by including some summary information from each of the links that it contains. I'm also not clear how your last link to "The Top Nine Reasons to Use a File Geodatabase" relates to the question, and the remainder of your answer. – PolyGeo Jul 21 '16 at 2:31

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