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Was having the same issue with 10.2. Just got off the phone with Esri and it appears this is a known issue.
The technician said that the server gets overloaded on reboot and applies security to the System directory.
The fix is easy:
- log in to ArcGIS Server Manager
- Click on System folder. Is the lock icon locked? If so, click on it and make sure it is set to Public and hit SAVE.
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Right now, I'm dealing with symptoms that are common to several threads related to the Publishing Tools service. The problem I was facing is that I could not publish services from ArcMap to an administrative ArcGIS Server connection using port 6080 in ArcGIS for Server 10.2.1. First, here are the ideas I read:
1. You have to make your ArcGIS Server connection in ArcMap using the Web Adaptor URL.
2. You have to enable administrative access through the Web Adaptor.
3. The System folder is locked for some reason and you have to make it public.
However, after lengthy testing, my findings were as follows:
1. You can make a publisher or administrator connection to ArcGIS Server through the Web Adaptor or the GIS Server tier. However, when you try to publish a service, ArcMap needs access to the Publishing Tools service.
2. If the System folder is unlocked (anonymous authentication), you can publish a service no matter how you connect to ArcGIS Server from ArcMap. If the System folder is locked you have to authenticate through the Web Adaptor. This is true if you used roles or any logged in user to set the security on that folder. Your connection to ArcGIS Server does not automatically connect you to the Publishing Tools service. You either have to be anonymous or go through the Web Adaptor.
3. The System folder was locked on our server for some reason. This may have happened automatically when we enabled Web Tier authentication. Maybe it is a bug. No matter what, it got locked, which starts the whole problem. If you're unaware of this, your only chance of publishing a service would be through the Web Adaptor.
5. The following causes the most confusion of all. If you started out using the GIS Server URL, you cannot switch to the Web Adaptor URL unless administrative access is enabled on the Web Adaptor. To make an administrative or publisher connection, ArcMap tries to connect to the Web Adaptor. If administrative access is disabled through the Web Adaptor, ArcMap will revert back to the old GIS Server URL behind your back. The problem is that ArcMap lets you click apply to change the URL, but changes it back after you close the connection dialog. It seems to check the URL after you close it, not when you click apply or right before it closes. That is a design flaw in ArcMap. It should give you an error message that administrative access is disabled through the Web Adaptor. At this point, your only hope would be to enable administrative access through the Web Adaptor and add a role you are a member of to the System folder security settings, all of which you're unlikely to figure out on your own.
6. Thus, if the System folder is unlocked you can connect to ArcGIS Server anyway you want to publish a service. If the System folder is locked, you have to have proper credentials to the System folder, enable administrative access through the Web Adaptor, and connect through the Web Adaptor to publish a service.
7. Apparently, to lock down both the Systems folder and administrative access through the Web Adaptor, you would have to publish your services through ArcGIS Server Manager while connected to the GIS Server tier. Otherwise, to publish through ArcGIS Desktop, you would have to choose between one or the other.