Question: an error occurred while getting updates from server.
0
gravatar for yychangsd
19 months ago by
yychangsd30
yychangsd30 wrote:

I persistently got this error from my local galaxy instance.

Any idea about it?

thanks so much~~

  {
  "agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/601.7.7 (KHTML, like Gecko) Version/9.1.2 Safari/601.7.7",
  "url": "http://52.34.123.54:8080/api/histories/1cd8e2f6b131e891/contents",
  "data": "",
  "options": {
    "data": {},
    "parse": true,
    "emulateHTTP": false,
    "emulateJSON": false
  },
  "xhr": {
    "readyState": 4,
    "responseText": "{\"traceback\": \"Traceback (most recent call last):\\n  File \\\"/home/oasis/data/galaxy-test/galaxy-dist/lib/galaxy/web/framework/decorators.py\\\", line 258, in decorator\\n    rval = func( self, trans, *args, **kwargs)\\n  File \\\"/home/oasis/data/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/api/history_contents.py\\\", line 70, in index\\n    history = self.history_manager.get_accessible( self.decode_id( history_id ), trans.user, current_history=trans.history )\\n  File \\\"/home/oasis/data/galaxy-test/galaxy-dist/lib/galaxy/managers/secured.py\\\", line 33, in get_accessible\\n    return self.error_unless_accessible( item, user, **kwargs )\\n  File \\\"/home/oasis/data/galaxy-test/galaxy-dist/lib/galaxy/managers/secured.py\\\", line 43, in error_unless_accessible\\n    raise exceptions.ItemAccessibilityException( \\\"%s is not accessible by user\\\" % ( self.model_class.__name__ ) )\\nItemAccessibilityException: History is not accessible by user\\n\", \"err_msg\": \"History is not accessible by user\", \"err_code\": 403002}",
    "responseJSON": {
      "traceback": "Traceback (most recent call last):\n  File \"/home/oasis/data/galaxy-test/galaxy-dist/lib/galaxy/web/framework/decorators.py\", line 258, in decorator\n    rval = func( self, trans, *args, **kwargs)\n  File \"/home/oasis/data/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/api/history_contents.py\", line 70, in index\n    history = self.history_manager.get_accessible( self.decode_id( history_id ), trans.user, current_history=trans.history )\n  File \"/home/oasis/data/galaxy-test/galaxy-dist/lib/galaxy/managers/secured.py\", line 33, in get_accessible\n    return self.error_unless_accessible( item, user, **kwargs )\n  File \"/home/oasis/data/galaxy-test/galaxy-dist/lib/galaxy/managers/secured.py\", line 43, in error_unless_accessible\n    raise exceptions.ItemAccessibilityException( \"%s is not accessible by user\" % ( self.model_class.__name__ ) )\nItemAccessibilityException: History is not accessible by user\n",
      "err_msg": "History is not accessible by user",
      "err_code": 403002
    },
    "status": 403,
    "statusText": "Forbidden",
    "responseHeaders": {
      "Date": "Thu, 15 Sep 2016 18:25:09 GMT\r",
      "Content-Type": "application/json\r",
      "Server": "PasteWSGIServer/0.5 Python/2.7.4\r",
      "Connection": "close\r",
      "X-Frame-Options": "SAMEORIGIN\r",
      "Cache-Control": "max-age=0,no-cache,no-store\r"
    }
  },
  "source": [
    {
      "dataset_id": "f2db41e1fa331b3e",
      "deleted": false,
      "extension": "auto",
      "hid": 1,
      "history_content_type": "dataset",
      "history_id": "1cd8e2f6b131e891",
      "id": "f2db41e1fa331b3e",
      "name": "SP2.fastq",
      "purged": false,
      "state": "running",
      "type": "file",
      "type_id": "dataset-f2db41e1fa331b3e",
      "url": "/api/histories/1cd8e2f6b131e891/contents/f2db41e1fa331b3e",
      "visible": true,
      "accessible": true,
      "data_type": "",
      "file_ext": "",
      "file_size": 0,
      "meta_files": [],
      "misc_blurb": "",
      "misc_info": "",
      "tags": [],
      "model_class": "HistoryDatasetAssociation",
      "urls": {
        "purge": "/datasets/f2db41e1fa331b3e/purge_async",
        "display": "/datasets/f2db41e1fa331b3e/display/?preview=True",
        "edit": "/datasets/f2db41e1fa331b3e/edit",
        "download": "/datasets/f2db41e1fa331b3e/display?to_ext=",
        "report_error": "/dataset/errors?id=f2db41e1fa331b3e",
        "rerun": "/tool_runner/rerun?id=f2db41e1fa331b3e",
        "show_params": "/datasets/f2db41e1fa331b3e/show_params",
        "visualization": "/visualization",
        "meta_download": "/dataset/get_metadata_file?hda_id=f2db41e1fa331b3e&metadata_name="
      }
    },
    {
      "dataset_id": "f597429621d6eb2b",
      "deleted": false,
      "extension": "fastq",
      "hid": 2,
      "history_content_type": "dataset",
      "history_id": "1cd8e2f6b131e891",
      "id": "f597429621d6eb2b",
      "name": "Tu1-2.fastq",
      "purged": false,
      "state": "ok",
      "type": "file",
      "type_id": "dataset-f597429621d6eb2b",
      "url": "/api/histories/1cd8e2f6b131e891/contents/f597429621d6eb2b",
      "visible": true,
      "accessible": true,
      "data_type": "",
      "file_ext": "",
      "file_size": 0,
      "meta_files": [],
      "misc_blurb": "",
      "misc_info": "",
      "tags": [],
      "model_class": "HistoryDatasetAssociation",
      "urls": {
        "purge": "/datasets/f597429621d6eb2b/purge_async",
        "display": "/datasets/f597429621d6eb2b/display/?preview=True",
        "edit": "/datasets/f597429621d6eb2b/edit",
        "download": "/datasets/f597429621d6eb2b/display?to_ext=",
        "report_error": "/dataset/errors?id=f597429621d6eb2b",
        "rerun": "/tool_runner/rerun?id=f597429621d6eb2b",
        "show_params": "/datasets/f597429621d6eb2b/show_params",
        "visualization": "/visualization",
        "meta_download": "/dataset/get_metadata_file?hda_id=f597429621d6eb2b&metadata_name="
      }
    },
    {
      "dataset_id": "1cd8e2f6b131e891",
      "deleted": false,
      "extension": "fastq",
      "hid": 3,
      "history_content_type": "dataset",
      "history_id": "1cd8e2f6b131e891",
      "id": "1cd8e2f6b131e891",
      "name": "Tu2-2.fastq",
      "purged": false,
      "state": "ok",
      "type": "file",
      "type_id": "dataset-1cd8e2f6b131e891",
      "url": "/api/histories/1cd8e2f6b131e891/contents/1cd8e2f6b131e891",
      "visible": true,
      "accessible": true,
      "data_type": "",
      "file_ext": "",
      "file_size": 0,
      "meta_files": [],
      "misc_blurb": "",
      "misc_info": "",
      "tags": [],
      "model_class": "HistoryDatasetAssociation",
      "urls": {
        "purge": "/datasets/1cd8e2f6b131e891/purge_async",
        "display": "/datasets/1cd8e2f6b131e891/display/?preview=True",
        "edit": "/datasets/1cd8e2f6b131e891/edit",
        "download": "/datasets/1cd8e2f6b131e891/display?to_ext=",
        "report_error": "/dataset/errors?id=1cd8e2f6b131e891",
        "rerun": "/tool_runner/rerun?id=1cd8e2f6b131e891",
        "show_params": "/datasets/1cd8e2f6b131e891/show_params",
        "visualization": "/visualization",
        "meta_download": "/dataset/get_metadata_file?hda_id=1cd8e2f6b131e891&metadata_name="
      }
    }
  ],
  "user": {
    "username": "test",
    "quota_percent": null,
    "total_disk_usage": 0,
    "nice_total_disk_usage": "0 bytes",
    "email": "test@gmailcom",
    "is_admin": true,
    "tags_used": [],
    "id": "f2db41e1fa331b3e"
  }
}
admin galaxy local permissions • 435 views
ADD COMMENTlink modified 19 months ago by Jennifer Hillman Jackson24k • written 19 months ago by yychangsd30

Hello,

It might be best to get to the root of the issue rather than post each derivative problem separately. There seems to be a problem with Galaxy database itself. Did you attempt the migration from SQLite or did you start over with Postgres? https://biostar.usegalaxy.org/p/19295/

Migration from SQLite is not recommended nor is a method provided. Martin's original suggestion to find an administrator on your side that can help with the more detailed configuration is still a valid option if you want to go forward this way.

Related post (may be merged): https://biostar.usegalaxy.org/p/19531/

Thanks, Jen, Galaxy team

ADD REPLYlink modified 19 months ago • written 19 months ago by Jennifer Hillman Jackson24k
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