permissions issue, related to data files

[lukejharmon]

Hi all - I am having a permissions issue running some analyses on arbor.kitware.com. I know you all are working on some of this stuff so forgive me if this is a transient issue.

I have been working on the aceArbor function, which reconstructs ancestral characters on a tree. I can get the function to run just fine on the anolis data.

However, when I try to use new data that I just uploaded and saved to the same collection, I get a permissions issue:

These new data are similar to the anoles and saved in the same collection. I can't see any options to change in girder either.

Thanks!

[zachmullen]

Hi Luke,

When this happens, can you reproduce it with your network tab of your developer console open and capture the request that is failing? I can walk you through how to do that if you need more instructions.

[lukejharmon]

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[lukejharmon]

I am not sure if that is what you wanted - but I tried!

[zachmullen]

Thanks @lukejharmon , that is what I wanted. However, the request you linked actually succeeded:

"response": {
"status": 200,
"statusText": "OK",

Can you capture the one where the 401 response is occurring?

[lukejharmon]

oops. The last thing here I think:

[lukejharmon]

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[zachmullen]

That also has status: 200 (which means the request succeeded)

[lukejharmon]

I don't have a clear idea how to capture the thing then! At the bottom of this you can see the error message:

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[zachmullen]

Ah, I see it now (wasn't showing up for me before). Thanks, that is helpful.

[zachmullen]

I tracked down the job record for the failing job, posting here for posterity:

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               "x":158,
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               "input":"method",
               "input_step":"aceArbor",
               "name":"method"
            },
            {  
               "output":"res",
               "name":"res",
               "output_step":"aceArbor"
            },
            {  
               "output":"treePlot",
               "name":"treePlot",
               "output_step":"aceArbor"
            }
         ],
         "steps":[  
            {  
               "visualization":false,
               "task":{  
                  "inputs":[  
                     {  
                        "format":"r.apetree",
                        "type":"tree",
                        "description":"A Phylogenetic Tree",
                        "name":"tree"
                     },
                     {  
                        "type":"table",
                        "name":"table",
                        "format":"r.dataframe"
                     },
                     {  
                        "default":"island",
                        "domain":{  
                           "input":"table",
                           "format":"column.names"
                        },
                        "type":"string",
                        "name":"column",
                        "format":"text"
                     },
                     {  
                        "default":"discrete",
                        "domain":[  
                           "discrete",
                           "continuous"
                        ],
                        "type":"string",
                        "name":"type",
                        "format":"text"
                     },
                     {  
                        "default":"marginal",
                        "domain":[  
                           "marginal"
                        ],
                        "type":"string",
                        "name":"method",
                        "format":"text"
                     }
                  ],
                  "name":"aceArbor",
                  "script":"library(cardoonTools)\nrequire(aRbor)\n\n\n# Removed this parameter to restore automated use of the analyses from Easy Mode apps\nfont_size <- 1\n\ntd <- make.treedata(tree, table)\ntd1 <- select_(td, column)\noutput <- aceArbor(td1, charType=type, aceType=method)\n\n\nTH <- max(branching.times(td$phy))\n    \n# plot and wrap the result in a PNG for output on the webpage\ntreePlot <- cardoonPlot(expression(plot(output, label.offset=0.05*TH)), width=1000, height=1000, res=100)\ntreePlot <- treePlot$png\n\nres <- output[[1]]    \nnodeLabels<-1:td1$phy$Nnode + length(td1$phy$tip.label)\nres<-cbind(nodeLabels, res)",
                  "outputs":[  
                     {  
                        "type":"table",
                        "name":"res",
                        "format":"r.dataframe"
                     },
                     {  
                        "type":"image",
                        "name":"treePlot",
                        "format":"png.base64"
                     }
                  ],
                  "mode":"r",
                  "description":""
               },
               "name":"aceArbor",
               "modified":"2015-07-10 21:08:13.029000",
               "y":258,
               "girderId":"55a03418d591e49e60b4f40e",
               "x":414
            }
         ],
         "mode":"workflow",
         "name":"ContinuousAncestralStatesWorkflow"
      }
   ],
   "userId":ObjectId("533c616dd591e45cb90d9463"),
   "created":   ISODate("2015-07-14T20:33:26.281   Z"),
   "access":{  
      "users":[  
         {  
            "id":ObjectId("533c616dd591e45cb90d9463"),
            "level":2
         }
      ],
      "groups":[  

      ]
   },
   "handler":"romanesco_handler",
   "meta":{  

   },
   "taskId":"80c4683f-aa6a-42d4-8034-a960716f4657",
   "kwargs":"{\"inputs\": {\"column\": {\"type\": \"string\", \"data\": \"svl\", \"format\": \"text\"}, \"table\": {\"_modelType\": \"item\", \"updated\": \"2015-07-13 19:50:20.833000\", \"_id\": \"55a4167cd591e49e60b4f45f\", \"description\": \"\", \"name\": \"phelsuma.csv\", \"created\": \"2015-07-13 19:50:20.833000\", \"url\": \"https://arbor.kitware.com/girder/api/v1/item/55a4167cd591e49e60b4f45f/download\", \"baseParentType\": \"collection\", \"format\": \"csv\", \"collection\": {\"analysisFolder\": \"557705f1d591e49e60b4ef8e\", \"updated\": \"2015-06-09 15:27:45.554000\", \"name\": \"testCollection\", \"saveLocation\": true, \"created\": \"2015-06-09 15:27:45.554000\", \"id\": \"557705f1d591e49e60b4ef8b\", \"description\": \"\", \"public\": false, \"visualizationFolder\": \"557705f1d591e49e60b4ef8f\", \"active\": true, \"_id\": \"557705f1d591e49e60b4ef8b\", \"_modelType\": \"collection\", \"_accessLevel\": 2, \"dataFolder\": \"557705f1d591e49e60b4ef8d\", \"size\": 14957}, \"id\": \"55a4167cd591e49e60b4f45f\", \"headers\": {}, \"baseParentId\": \"557705f1d591e49e60b4ef8b\", \"mode\": \"http\", \"creatorId\": \"533c616dd591e45cb90d9463\", \"folderId\": \"557705f1d591e49e60b4ef8d\", \"type\": \"table\", \"method\": \"GET\", \"size\": 1783}, \"tree\": {\"_modelType\": \"item\", \"updated\": \"2015-07-13 19:50:23.968000\", \"_id\": \"55a4167fd591e49e60b4f463\", \"description\": \"\", \"name\": \"phelsuma.phy\", \"created\": \"2015-07-13 19:50:23.968000\", \"url\": \"https://arbor.kitware.com/girder/api/v1/item/55a4167fd591e49e60b4f463/download\", \"baseParentType\": \"collection\", \"format\": \"newick\", \"collection\": {\"analysisFolder\": \"557705f1d591e49e60b4ef8e\", \"updated\": \"2015-06-09 15:27:45.554000\", \"name\": \"testCollection\", \"saveLocation\": true, \"created\": \"2015-06-09 15:27:45.554000\", \"id\": \"557705f1d591e49e60b4ef8b\", \"description\": \"\", \"public\": false, \"visualizationFolder\": \"557705f1d591e49e60b4ef8f\", \"active\": true, \"_id\": \"557705f1d591e49e60b4ef8b\", \"_modelType\": \"collection\", \"_accessLevel\": 2, \"dataFolder\": \"557705f1d591e49e60b4ef8d\", \"size\": 14957}, \"id\": \"55a4167fd591e49e60b4f463\", \"headers\": {}, \"baseParentId\": \"557705f1d591e49e60b4ef8b\", \"mode\": \"http\", \"creatorId\": \"533c616dd591e45cb90d9463\", \"folderId\": \"557705f1d591e49e60b4ef8d\", \"type\": \"tree\", \"method\": \"GET\", \"size\": 1151}, \"method\": {\"type\": \"string\", \"data\": \"marginal\", \"format\": \"text\"}, \"type\": {\"type\": \"string\", \"data\": \"continuous\", \"format\": \"text\"}}, \"jobInfo\": {\"url\": \"https://arbor.kitware.com/girder/api/v1/job/55a57216d591e4e18e27b953\", \"headers\": {\"Girder-Token\": \"qtw7Zok2XCu3VTrlvIT53TsytV6TQfgG5ROD9mgMtUwszbugfipKkmMk4sIjgfim\"}, \"method\": \"PUT\", \"logPrint\": true}, \"outputs\": {\"res\": {\"type\": \"table\", \"format\": \"rows\"}, \"treePlot\": {\"type\": \"image\", \"format\": \"png.base64\"}}}",
   "progress":null,
   "type":"romanesco_task",
   "public":false
}

[zachmullen]

And the kwargs after unescaping shows the source of the bug:

{  
   "inputs":{  
      "column":{  
         "type":"string",
         "data":"svl",
         "format":"text"
      },
      "table":{  
         "_modelType":"item",
         "updated":"2015-07-13 19:50:20.833000",
         "_id":"55a4167cd591e49e60b4f45f",
         "description":"",
         "name":"phelsuma.csv",
         "created":"2015-07-13 19:50:20.833000",
         "url":"https://arbor.kitware.com/girder/api/v1/item/55a4167cd591e49e60b4f45f/download",
         "baseParentType":"collection",
         "format":"csv",
         "collection":{  
            "analysisFolder":"557705f1d591e49e60b4ef8e",
            "updated":"2015-06-09 15:27:45.554000",
            "name":"testCollection",
            "saveLocation":true,
            "created":"2015-06-09 15:27:45.554000",
            "id":"557705f1d591e49e60b4ef8b",
            "description":"",
            "public":false,
            "visualizationFolder":"557705f1d591e49e60b4ef8f",
            "active":true,
            "_id":"557705f1d591e49e60b4ef8b",
            "_modelType":"collection",
            "_accessLevel":2,
            "dataFolder":"557705f1d591e49e60b4ef8d",
            "size":14957
         },
         "id":"55a4167cd591e49e60b4f45f",
         "headers":{  

         },
         "baseParentId":"557705f1d591e49e60b4ef8b",
         "mode":"http",
         "creatorId":"533c616dd591e45cb90d9463",
         "folderId":"557705f1d591e49e60b4ef8d",
         "type":"table",
         "method":"GET",
         "size":1783
      },
      "tree":{  
         "_modelType":"item",
         "updated":"2015-07-13 19:50:23.968000",
         "_id":"55a4167fd591e49e60b4f463",
         "description":"",
         "name":"phelsuma.phy",
         "created":"2015-07-13 19:50:23.968000",
         "url":"https://arbor.kitware.com/girder/api/v1/item/55a4167fd591e49e60b4f463/download",
         "baseParentType":"collection",
         "format":"newick",
         "collection":{  
            "analysisFolder":"557705f1d591e49e60b4ef8e",
            "updated":"2015-06-09 15:27:45.554000",
            "name":"testCollection",
            "saveLocation":true,
            "created":"2015-06-09 15:27:45.554000",
            "id":"557705f1d591e49e60b4ef8b",
            "description":"",
            "public":false,
            "visualizationFolder":"557705f1d591e49e60b4ef8f",
            "active":true,
            "_id":"557705f1d591e49e60b4ef8b",
            "_modelType":"collection",
            "_accessLevel":2,
            "dataFolder":"557705f1d591e49e60b4ef8d",
            "size":14957
         },
         "id":"55a4167fd591e49e60b4f463",
         "headers":{  

         },
         "baseParentId":"557705f1d591e49e60b4ef8b",
         "mode":"http",
         "creatorId":"533c616dd591e45cb90d9463",
         "folderId":"557705f1d591e49e60b4ef8d",
         "type":"tree",
         "method":"GET",
         "size":1151
      },
      "method":{  
         "type":"string",
         "data":"marginal",
         "format":"text"
      },
      "type":{  
         "type":"string",
         "data":"continuous",
         "format":"text"
      }
   },
   "jobInfo":{  
      "url":"https://arbor.kitware.com/girder/api/v1/job/55a57216d591e4e18e27b953",
      "headers":{  
         "Girder-Token":"qtw7Zok2XCu3VTrlvIT53TsytV6TQfgG5ROD9mgMtUwszbugfipKkmMk4sIjgfim"
      },
      "method":"PUT",
      "logPrint":true
   },
   "outputs":{  
      "res":{  
         "type":"table",
         "format":"rows"
      },
      "treePlot":{  
         "type":"image",
         "format":"png.base64"
      }
   }
}

Note that the headers list is empty -- it should contain the current user's token. I will investigate why this is happening.