search

metadatacenter / cedar-project

Build project for all CEDAR Java repositories
https://github.com/metadatacenter/cedar-docs/wiki
Other
12 stars 1 forks source link

Template population sometimes unavailable despite write permissions #385

Closed graybeal closed 7 years ago

graybeal commented 7 years ago

i have a created template, which I saved in my folder, but I can't generate an instance from it (Populate is grayed out).

Instance is https://cedar.metadatacenter.net/dashboard?folderId=https:%2F%2Frepo.metadatacenter.net%2Ffolders%2F1d427c28-3d67-44e9-a6a0-bfdedaf3aa89

graybeal commented 7 years ago

I just created another template and populated it, so the problem is not in the folder permissions.

One theory is that something about the included element (which was included long ago) was not done right.

The permissions appear after the code listing below.

graybeal commented 7 years ago

The template is:

{
  "description": "Biocaddie dataset ish element schema autogenerated by the CEDAR Template Editor 1.0.6",
  "title": "Biocaddie dataset ish element schema",
  "type": "object",
  "required": [],
  "additionalProperties": false,
  "properties": {
    "dataType": {
      "@id": "https://repo.metadatacenter.net/template-fields/ce7bd634-c22c-4d4c-9c34-44d97fa60ff1",
      "_valueConstraints": {
        "literals": [
          {
            "label": "Protein Structure"
          },
          {
            "label": "Physiological Signals"
          },
          {
            "label": "Morphology"
          },
          {
            "label": "Nucleotide Sequence"
          },
          {
            "label": "Phenotype"
          },
          {
            "label": "Clinical Trials"
          },
          {
            "label": "Proteomics Data"
          },
          {
            "label": "Gene Expression"
          },
          {
            "label": "Imaging Data"
          },
          {
            "label": "Unspecified"
          }
        ],
        "requiredValue": false
      },
      "description": "Data type field schema autogenerated by the CEDAR Template Editor",
      "title": "Data type field schema",
      "pav:lastUpdatedOn": "2017-04-07T02:09:30-0700",
      "required": [
        "@value"
      ],
      "additionalProperties": false,
      "properties": {
        "@id": {
          "type": [
            "string",
            "null"
          ],
          "format": "uri"
        },
        "@value": {
          "type": [
            "array",
            "null"
          ]
        },
        "pav:createdOn": {
          "type": [
            "string",
            "null"
          ],
          "format": "date-time"
        },
        "pav:createdBy": {
          "type": [
            "string",
            "null"
          ],
          "format": "uri"
        },
        "oslc:modifiedBy": {
          "type": [
            "string",
            "null"
          ],
          "format": "uri"
        },
        "pav:lastUpdatedOn": {
          "type": [
            "string",
            "null"
          ],
          "format": "date-time"
        },
        "@type": {
          "oneOf": [
            {
              "type": "string",
              "format": "uri"
            },
            {
              "minItems": 1,
              "items": {
                "type": "string",
                "format": "uri"
              },
              "uniqueItems": true,
              "type": "array"
            }
          ]
        }
      },
      "pav:createdOn": "2017-04-07T02:09:30-0700",
      "_ui": {
        "inputType": "radio",
        "description": "What kind of data is represented in this dataset?",
        "title": "Data Type"
      },
      "pav:createdBy": "https://metadatacenter.org/users/1adf5ee5-cee0-47d1-9769-efbe00cdebee",
      "oslc:modifiedBy": "https://metadatacenter.org/users/1adf5ee5-cee0-47d1-9769-efbe00cdebee",
      "@context": {
        "oslc": "http://open-services.net/ns/core#",
        "pav": "http://purl.org/pav/",
        "schema": "http://schema.org/"
      },
      "type": "object",
      "@type": "https://schema.metadatacenter.org/core/TemplateField",
      "$schema": "http://json-schema.org/draft-04/schema#"
    },
    "@id": {
      "type": [
        "string",
        "null"
      ],
      "format": "uri"
    },
    "resolvableDatasetID": {
      "@id": "https://repo.metadatacenter.net/template-fields/71507660-0f94-4eca-88c2-7d4469f5f3a1",
      "_valueConstraints": {
        "requiredValue": true
      },
      "description": "Resolvable dataset id field schema autogenerated by the CEDAR Template Editor",
      "title": "Resolvable dataset id field schema",
      "pav:lastUpdatedOn": "2017-04-07T02:09:30-0700",
      "required": [
        "@value"
      ],
      "additionalProperties": false,
      "properties": {
        "@id": {
          "type": [
            "string",
            "null"
          ],
          "format": "uri"
        },
        "@value": {
          "type": [
            "string",
            "null"
          ]
        },
        "pav:createdOn": {
          "type": [
            "string",
            "null"
          ],
          "format": "date-time"
        },
        "pav:createdBy": {
          "type": [
            "string",
            "null"
          ],
          "format": "uri"
        },
        "oslc:modifiedBy": {
          "type": [
            "string",
            "null"
          ],
          "format": "uri"
        },
        "pav:lastUpdatedOn": {
          "type": [
            "string",
            "null"
          ],
          "format": "date-time"
        },
        "@type": {
          "oneOf": [
            {
              "type": "string",
              "format": "uri"
            },
            {
              "minItems": 1,
              "items": {
                "type": "string",
                "format": "uri"
              },
              "uniqueItems": true,
              "type": "array"
            }
          ]
        }
      },
      "pav:createdOn": "2017-04-07T02:09:30-0700",
      "_ui": {
        "inputType": "textfield",
        "description": "",
        "title": "Resolvable Dataset ID"
      },
      "pav:createdBy": "https://metadatacenter.org/users/1adf5ee5-cee0-47d1-9769-efbe00cdebee",
      "oslc:modifiedBy": "https://metadatacenter.org/users/1adf5ee5-cee0-47d1-9769-efbe00cdebee",
      "@context": {
        "oslc": "http://open-services.net/ns/core#",
        "pav": "http://purl.org/pav/",
        "schema": "http://schema.org/"
      },
      "type": "object",
      "@type": "https://schema.metadatacenter.org/core/TemplateField",
      "$schema": "http://json-schema.org/draft-04/schema#"
    },
    "pav:createdOn": {
      "type": [
        "string",
        "null"
      ],
      "format": "date-time"
    },
    "pav:createdBy": {
      "type": [
        "string",
        "null"
      ],
      "format": "uri"
    },
    "datasetTitle": {
      "@id": "https://repo.metadatacenter.net/template-fields/10860e85-0156-4f6d-9b11-9af58f1692e9",
      "_valueConstraints": {
        "requiredValue": false
      },
      "description": "Dataset title field schema autogenerated by the CEDAR Template Editor",
      "title": "Dataset title field schema",
      "pav:lastUpdatedOn": "2017-04-07T02:09:30-0700",
      "required": [
        "@value"
      ],
      "additionalProperties": false,
      "properties": {
        "@id": {
          "type": [
            "string",
            "null"
          ],
          "format": "uri"
        },
        "@value": {
          "type": [
            "string",
            "null"
          ]
        },
        "pav:createdOn": {
          "type": [
            "string",
            "null"
          ],
          "format": "date-time"
        },
        "pav:createdBy": {
          "type": [
            "string",
            "null"
          ],
          "format": "uri"
        },
        "oslc:modifiedBy": {
          "type": [
            "string",
            "null"
          ],
          "format": "uri"
        },
        "pav:lastUpdatedOn": {
          "type": [
            "string",
            "null"
          ],
          "format": "date-time"
        },
        "@type": {
          "oneOf": [
            {
              "type": "string",
              "format": "uri"
            },
            {
              "minItems": 1,
              "items": {
                "type": "string",
                "format": "uri"
              },
              "uniqueItems": true,
              "type": "array"
            }
          ]
        }
      },
      "pav:createdOn": "2017-04-07T02:09:30-0700",
      "_ui": {
        "inputType": "textfield",
        "description": "Name of the data set",
        "title": "Dataset Title"
      },
      "pav:createdBy": "https://metadatacenter.org/users/1adf5ee5-cee0-47d1-9769-efbe00cdebee",
      "oslc:modifiedBy": "https://metadatacenter.org/users/1adf5ee5-cee0-47d1-9769-efbe00cdebee",
      "@context": {
        "oslc": "http://open-services.net/ns/core#",
        "pav": "http://purl.org/pav/",
        "schema": "http://schema.org/"
      },
      "type": "object",
      "@type": "https://schema.metadatacenter.org/core/TemplateField",
      "$schema": "http://json-schema.org/draft-04/schema#"
    },
    "oslc:modifiedBy": {
      "type": [
        "string",
        "null"
      ],
      "format": "uri"
    },
    "@context": {
      "additionalProperties": false,
      "patternProperties": {
        "^(?!pav)(?!schema)(?!oslc)[a-zA-Z][a-zA-Z0-9]*$": {
          "type": "string",
          "format": "uri"
        }
      },
      "required": [
        "resolvableDatasetID",
        "datasetTitle",
        "dataType",
        "uRLForMyDataset",
        "injury"
      ],
      "type": "object",
      "properties": {
        "dataType": {
          "enum": [
            "https://schema.metadatacenter.net/properties/dataType"
          ]
        },
        "datasetTitle": {
          "enum": [
            "https://schema.metadatacenter.net/properties/datasetTitle"
          ]
        },
        "oslc": {
          "enum": [
            "http://open-services.net/ns/core#"
          ],
          "type": "string",
          "format": "uri"
        },
        "pav": {
          "enum": [
            "http://purl.org/pav/"
          ],
          "type": "string",
          "format": "uri"
        },
        "resolvableDatasetID": {
          "enum": [
            "https://schema.metadatacenter.net/properties/resolvableDatasetID"
          ]
        },
        "uRLForMyDataset": {
          "enum": [
            "https://schema.metadatacenter.net/properties/uRLForMyDataset"
          ]
        },
        "injury": {
          "enum": [
            "https://schema.metadatacenter.net/properties/injury"
          ]
        }
      }
    },
    "pav:lastUpdatedOn": {
      "type": [
        "string",
        "null"
      ],
      "format": "date-time"
    },
    "@type": {
      "oneOf": [
        {
          "type": "string",
          "format": "uri"
        },
        {
          "minItems": 1,
          "items": {
            "type": "string",
            "format": "uri"
          },
          "uniqueItems": true,
          "type": "array"
        }
      ]
    },
    "uRLForMyDataset": {
      "@type": "https://schema.metadatacenter.org/core/TemplateField",
      "@context": {
        "xsd": "http://www.w3.org/2001/XMLSchema#",
        "pav": "http://purl.org/pav/",
        "oslc": "http://open-services.net/ns/core#",
        "schema": "http://schema.org/",
        "pav:createdOn": {
          "@type": "xsd:dateTime"
        },
        "pav:createdBy": {
          "@type": "@id"
        },
        "pav:lastUpdatedOn": {
          "@type": "xsd:dateTime"
        },
        "oslc:modifiedBy": {
          "@type": "@id"
        }
      },
      "type": "object",
      "title": "Url for my dataset field schema",
      "description": "Url for my dataset field schema autogenerated by the CEDAR Template Editor ",
      "_ui": {
        "title": "URL for my dataset",
        "description": "",
        "inputType": "textfield"
      },
      "_valueConstraints": {
        "requiredValue": true
      },
      "properties": {
        "@type": {
          "oneOf": [
            {
              "type": "string",
              "format": "uri",
              "enum": [
                "http://data.bioontology.org/ontologies/EDAM/classes/http%3A%2F%2Fedamontology.org%2Fdata_1052"
              ]
            },
            {
              "type": "array",
              "minItems": 1,
              "items": {
                "type": "string",
                "format": "uri",
                "enum": [
                  "http://data.bioontology.org/ontologies/EDAM/classes/http%3A%2F%2Fedamontology.org%2Fdata_1052"
                ]
              },
              "uniqueItems": true
            },
            {
              "enum": [
                "@id"
              ]
            }
          ]
        },
        "@value": {
          "type": [
            "string",
            "null"
          ]
        },
        "_valueLabel": {
          "type": [
            "string",
            "null"
          ]
        },
        "pav:createdOn": {
          "type": [
            "string",
            "null"
          ],
          "format": "date-time"
        },
        "pav:createdBy": {
          "type": [
            "string",
            "null"
          ],
          "format": "uri"
        },
        "pav:lastUpdatedOn": {
          "type": [
            "string",
            "null"
          ],
          "format": "date-time"
        },
        "oslc:modifiedBy": {
          "type": [
            "string",
            "null"
          ],
          "format": "uri"
        }
      },
      "required": [
        "@value"
      ],
      "pav:createdOn": "2017-04-07T02:09:30-0700",
      "pav:createdBy": "https://metadatacenter.org/users/1adf5ee5-cee0-47d1-9769-efbe00cdebee",
      "pav:lastUpdatedOn": "2017-04-07T02:09:30-0700",
      "oslc:modifiedBy": "https://metadatacenter.org/users/1adf5ee5-cee0-47d1-9769-efbe00cdebee",
      "additionalProperties": false,
      "@id": "https://repo.metadatacenter.net/template-fields/8f3828c9-badd-4b75-9185-ce687a92e805",
      "$schema": "http://json-schema.org/draft-04/schema#"
    },
    "injury": {
      "@type": "https://schema.metadatacenter.org/core/TemplateField",
      "@context": {
        "xsd": "http://www.w3.org/2001/XMLSchema#",
        "pav": "http://purl.org/pav/",
        "oslc": "http://open-services.net/ns/core#",
        "schema": "http://schema.org/",
        "pav:createdOn": {
          "@type": "xsd:dateTime"
        },
        "pav:createdBy": {
          "@type": "@id"
        },
        "pav:lastUpdatedOn": {
          "@type": "xsd:dateTime"
        },
        "oslc:modifiedBy": {
          "@type": "@id"
        }
      },
      "type": "object",
      "title": "Injury field schema",
      "description": "Injury field schema autogenerated by the CEDAR Template Editor ",
      "_ui": {
        "title": "Injury",
        "description": "",
        "inputType": "textfield"
      },
      "_valueConstraints": {
        "requiredValue": false,
        "ontologies": [],
        "valueSets": [],
        "classes": [],
        "branches": [
          {
            "source": "National Cancer Institute Thesaurus (NCIT)",
            "acronym": "NCIT",
            "uri": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3671",
            "name": "Injury",
            "maxDepth": 0
          }
        ],
        "multipleChoice": false
      },
      "properties": {
        "@type": {
          "oneOf": [
            {
              "type": "string",
              "format": "uri",
              "enum": [
                "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C3671"
              ]
            },
            {
              "type": "array",
              "minItems": 1,
              "items": {
                "type": "string",
                "format": "uri",
                "enum": [
                  "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C3671"
                ]
              },
              "uniqueItems": true
            },
            {
              "enum": [
                "@id"
              ]
            }
          ]
        },
        "_valueLabel": {
          "type": [
            "string",
            "null"
          ]
        },
        "pav:createdOn": {
          "type": [
            "string",
            "null"
          ],
          "format": "date-time"
        },
        "pav:createdBy": {
          "type": [
            "string",
            "null"
          ],
          "format": "uri"
        },
        "pav:lastUpdatedOn": {
          "type": [
            "string",
            "null"
          ],
          "format": "date-time"
        },
        "oslc:modifiedBy": {
          "type": [
            "string",
            "null"
          ],
          "format": "uri"
        },
        "@id": {
          "type": [
            "string",
            "null"
          ],
          "format": "uri"
        }
      },
      "required": [
        "@id"
      ],
      "pav:createdOn": "2017-04-07T02:09:30-0700",
      "pav:createdBy": "https://metadatacenter.org/users/1adf5ee5-cee0-47d1-9769-efbe00cdebee",
      "pav:lastUpdatedOn": "2017-04-07T02:09:30-0700",
      "oslc:modifiedBy": "https://metadatacenter.org/users/1adf5ee5-cee0-47d1-9769-efbe00cdebee",
      "additionalProperties": false,
      "@id": "https://repo.metadatacenter.net/template-fields/3a84526e-5dbf-4bcc-b3e9-edb60a1f43fd",
      "$schema": "http://json-schema.org/draft-04/schema#"
    }
  },
  "pav:createdOn": "2016-09-14T15:50:15-0700",
  "_ui": {
    "order": [
      "resolvableDatasetID",
      "datasetTitle",
      "dataType",
      "uRLForMyDataset",
      "injury"
    ],
    "description": "Dataset components used by BioCADDIE",
    "title": "BioCADDIE Dataset Ish",
    "propertyLabels": {}
  },
  "pav:createdBy": "https://repo.metadatacenter.net/users/1adf5ee5-cee0-47d1-9769-efbe00cdebee",
  "oslc:modifiedBy": "https://metadatacenter.org/users/1adf5ee5-cee0-47d1-9769-efbe00cdebee",
  "@context": {
    "oslc": "http://open-services.net/ns/core#",
    "pav": "http://purl.org/pav/"
  },
  "pav:lastUpdatedOn": "2017-04-07T02:09:30-0700",
  "@id": "https://repo.metadatacenter.net/template-elements/2ddd6ffe-3db9-482c-aeb8-796767e9b0a1",
  "@type": "https://schema.metadatacenter.org/core/TemplateElement",
  "$schema": "http://json-schema.org/draft-04/schema#"
}
graybeal commented 7 years ago

Permissions are:

Type element
Location /Users/John Graybeal/BioCADDIE Elements/BioCADDIE Dataset Ish
Owner John Graybeal
Modified 4/7/17 11:09 AM by John Graybeal
Created 9/15/16 12:50 AM by John Graybeal
Can read true
Can write true
Can change owner true
Dataset components used by BioCADDIE
martinjoconnor commented 7 years ago

Can't reproduce for moment.

willrett commented 7 years ago

If you were using the toolbar rather than the context menu to select the populate menu item, then this issue will be with issue #413.