Initial commit

transfer_example_EMC.json

+{
+  "files": [
+    {
+      "filename": "sample1_R1.fastq.gz", 
+      "md5": "c3875788d22baa678c87c8f903cb2350", 
+      "tags": {
+        "readtype": "forward"
+      }, 
+      "sample_name": "sample5"
+    }, 
+    {
+      "filename": "sample1_R2.fastq.gz", 
+      "md5": "74cedbb88402dd16a6b4f96e5440fdfd", 
+      "tags": {
+        "readtype": "umi"
+      }, 
+      "sample_name": "sample5"
+    }, 
+    {
+      "filename": "sample1_R3.fastq.gz", 
+      "md5": "617e686e88c06ad1d7319f606ebcbfc5", 
+      "tags": {
+        "readtype": "reverse"
+      }, 
+      "sample_name": "sample5"
+    }
+  ], 
+  "run_name": "runname5", 
+  "sample_group": {
+    "samples": [
+      {
+        "sample_name": "sample5", 
+        "tags": {
+          "gender": "V", 
+          "gs_batch": "006", 
+          "gs_sample": "005", 
+          "experimentnr": "1234", 
+          "gs_projectcode": "104785-006", 
+          "sequencer": "Nextseq 500", 
+          "capture_kit": "V7",
+          "verrichting_id": "9049809068123", 
+          "fractienr": "AD8957"
+        }
+      }
+    ], 
+    "group_name": "samplegroup5"
+  }, 
+  "title": "Test for file tags in runs endpoint"
+}

transfer_example_no_tags.json

+{
+    "files": [
+        {
+            "md5": "c3875788d22baa678c87c8f903cb2350",
+            "filename": "sample1_R1.fastq.gz",
+            "sample_name": "sample4",
+            "tags": {
+                "readtype": "forward"
+            }
+        },
+        {
+            "md5": "74cedbb88402dd16a6b4f96e5440fdfd",
+            "filename": "sample1_R2.fastq.gz",
+            "sample_name": "sample4",
+            "tags": {
+                "readtype": "umi"
+            }
+        },
+        {
+            "md5": "617e686e88c06ad1d7319f606ebcbfc5",
+            "filename": "sample1_R3.fastq.gz",
+            "sample_name": "sample4",
+            "tags": {
+                "readtype": "reverse"
+            }
+        }
+    ],
+    "sample_group": {
+        "samples": [
+            {
+            "sample_name": "sample4"
+            }
+        ],
+        "group_name": "samplegroup4"
+    },
+    "run_name": "runname4",
+    "title": "Test for file tags in runs endpoint"
+}

transfer_example_sample_tags.json

+{
+    "files": [
+        {
+            "md5": "c3875788d22baa678c87c8f903cb2350",
+            "filename": "sample1_R1.fastq.gz",
+            "sample_name": "sample5",
+            "tags": {
+                "readtype": "forward"
+            }
+        },
+        {
+            "md5": "74cedbb88402dd16a6b4f96e5440fdfd",
+            "filename": "sample1_R2.fastq.gz",
+            "sample_name": "sample5",
+            "tags": {
+                "readtype": "umi"
+            }
+        },
+        {
+            "md5": "617e686e88c06ad1d7319f606ebcbfc5",
+            "filename": "sample1_R3.fastq.gz",
+            "sample_name": "sample5",
+            "tags": {
+                "readtype": "reverse"
+            }
+        }
+    ],
+    "sample_group": {
+        "samples": [
+            {
+            "sample_name": "sample5",
+            "tags": {
+                "capture_kit": "Cre v2",
+                "experimentnr": "1234",
+                "fractienr": "AD8957",
+                "gender": "V",
+                "gs_batch": "006",
+                "gs_projectcode": "104785-006",
+                "gs_sample": "005",
+                "sequencer": "Nextseq 500",
+                "verrichting_id": "9049809068123"
+            }
+          }
+        ],
+        "group_name": "samplegroup5"
+    },
+    "run_name": "runname5",
+    "title": "Test for file tags in runs endpoint"
+}

transfer_schema.json

+{
+    "definitions": {
+        "Name": {
+            "description": "Valid name that is unlikely to break parsing, spaces are not allowed",
+            "type": "string",
+            "pattern": "^([A-Za-z0-9]+[A-Za-z0-9-_.]*[A-Za-z0-9]+)$|^([A-Za-z0-9])$"
+        },
+        "Description": {
+            "description": "Valid description for objects, no restrictions",
+            "type": "string"
+        },
+        "FileTag": {
+            "description": "FileTag object, required for Files",
+            "type": "object",
+            "required": [
+                "readtype"
+            ],
+            "properties": {
+                "readtype": {
+                    "type": "string",
+                    "enum": [
+                        "forward",
+                        "reverse",
+                        "umi"
+                    ]
+                }
+            }
+        },
+        "File": {
+            "description": "Minimum required properties for a file",
+            "type": "object",
+            "required": [
+                "md5",
+                "filename",
+                "sample_name",
+                "tags"
+            ],
+            "additionalProperties": false,
+            "properties": {
+                "md5": {
+                    "description": "MD5 checksum of the content of the file",
+                    "type": "string",
+                    "pattern": "^[a-f0-9]{32}$"
+                },
+                "filename": {
+                    "description": "Name of the file",
+                    "$ref": "#/definitions/Name"
+                },
+                "sample_name": {
+                    "description": "The associated sample of this file",
+                    "$ref": "#/definitions/Name"
+                },
+                "tags": {
+                    "description": "The tags that belong to this file",
+                    "$ref": "#/definitions/FileTag"
+                }
+            }
+        },
+        "SampleGroup": {
+            "description": "Minimum required properties for a sample group",
+            "type": "object",
+            "required": [
+                "group_name",
+                "samples"
+            ],
+            "properties": {
+                "group_name": {
+                    "description": "Name of the sample group",
+                    "$ref": "#definitions/Name"
+                },
+                "samples": {
+                    "description": "An array of one or more Samples",
+                    "type": "array",
+                    "minItems": 1,
+                    "uniqueItems": true,
+                    "items": {
+                        "$ref": "#/definitions/Sample"
+                    }
+                }
+            }
+        },
+        "Sample": {
+            "description": "Minimum required properties for a sample",
+            "type": "object",
+            "required": [
+                "sample_name"
+            ],
+            "additionalProperties": false,
+            "properties": {
+                "sample_name": {
+                    "description": "Name of the sample",
+                    "type": "string",
+                    "$ref": "#/definitions/Name"
+                }
+            }
+        },
+        "EMC_Sample": {
+            "description": "Minimum required properties for an EMC sample",
+            "type": "object",
+            "required": [
+                "sample_name",
+                "tags"
+            ],
+            "additionalProperties": false,
+            "properties": {
+                "sample_name": {
+                    "description": "Name of the sample",
+                    "type": "string",
+                    "$ref": "#/definitions/Name"
+                },
+                "tags": {
+                    "$ref": "#/definitions/EMC_Tags"
+                }
+            }
+        },
+        "EMC_Tag": {
+            "description": "Minimum required properties for EMC Sample tags",
+            "type": "object",
+            "required": [
+                "gender",
+                "gs_batch",
+                "gs_sample",
+                "gs_projectcode",
+                "sequencer",
+                "capture_kit",
+                "verrichting_id",
+                "fractienr"
+            ],
+            "additionalProperties": false,
+            "properties": {
+                "gender": {
+                    "$ref": "#/definitions/Name"
+                },
+                "gs_batch": {
+                    "$ref": "#/definitions/Name"
+                },
+                "gs_sample": {
+                    "$ref": "#/definitions/Name"
+                },
+                "experimentnr": {
+                    "$ref": "#/definitions/Name"
+                },
+                "gs_projectcode": {
+                    "$ref": "#/definitions/Name"
+                },
+                "sequencer": {
+                    "$ref": "#/definitions/Description"
+                },
+                "capture_kit": {
+                    "$ref": "#/definitions/Description"
+                },
+                "verrichtingen_id": {
+                    "$ref": "#/definitions/Name"
+                },
+                "fractienr": {
+                    "$ref": "#/definitions/Name"
+                }
+            }
+        }
+    },
+    "title": "Minimal transfer metadata",
+    "description": "Transfer schema for Illumina data. With or without UMI",
+    "type": "object",
+    "required": [
+        "title",
+        "sample_group",
+        "run_name",
+        "files"
+    ],
+    "additionalProperties": false,
+    "properties": {
+        "files": {
+            "description": "An array of one or more Files",
+            "type": "array",
+            "minItems": 1,
+            "uniqueItems": true,
+            "items": {
+                "$ref": "#/definitions/File"
+            }
+        },
+        "sample_group": {
+            "description": "Sample group information for this transfer",
+            "$ref": "#/definitions/SampleGroup"
+        },
+        "run_name": {
+            "description": "Run name for this transfer",
+            "$ref": "#/definitions/Name"
+        },
+        "title": {
+            "description": "Title of this transfer, this will be used in the notification email",
+            "$ref": "#/definitions/Description"
+        }
+    }
+}

transfer_schema_EMC.json

+{
+    "definitions": {
+        "Name": {
+            "description": "Valid name that is unlikely to break parsing, spaces are not allowed",
+            "type": "string",
+            "pattern": "^([A-Za-z0-9]+[A-Za-z0-9-_.]*[A-Za-z0-9]+)$|^([A-Za-z0-9])$"
+        },
+        "Description": {
+            "description": "Valid description for objects, no restrictions",
+            "type": "string"
+        },
+        "FileTag": {
+            "description": "FileTag object, required for Files",
+            "type": "object",
+            "required": [
+                "readtype"
+            ],
+            "properties": {
+                "readtype": {
+                    "type": "string",
+                    "enum": [
+                        "forward",
+                        "reverse",
+                        "umi"
+                    ]
+                }
+            }
+        },
+        "File": {
+            "description": "Minimum required properties for a file",
+            "type": "object",
+            "required": [
+                "md5",
+                "filename",
+                "sample_name",
+                "tags"
+            ],
+            "additionalProperties": false,
+            "properties": {
+                "md5": {
+                    "description": "MD5 checksum of the content of the file",
+                    "type": "string",
+                    "pattern": "^[a-f0-9]{32}$"
+                },
+                "filename": {
+                    "description": "Name of the file",
+                    "$ref": "#/definitions/Name"
+                },
+                "sample_name": {
+                    "description": "The associated sample of this file",
+                    "$ref": "#/definitions/Name"
+                },
+                "tags": {
+                    "description": "The tags that belong to this file",
+                    "$ref": "#/definitions/FileTag"
+                }
+            }
+        },
+        "SampleGroup": {
+            "description": "Minimum required properties for a sample group",
+            "type": "object",
+            "required": [
+                "group_name",
+                "samples"
+            ],
+            "properties": {
+                "group_name": {
+                    "description": "Name of the sample group",
+                    "$ref": "#definitions/Name"
+                },
+                "samples": {
+                    "description": "An array of one or more Samples",
+                    "type": "array",
+                    "minItems": 1,
+                    "uniqueItems": true,
+                    "items": {
+                        "$ref": "#/definitions/Sample"
+                    }
+                }
+            }
+        },
+        "Sample": {
+            "description": "Minimum required properties for an EMC sample",
+            "type": "object",
+            "required": [
+                "sample_name",
+                "tags"
+            ],
+            "additionalProperties": false,
+            "properties": {
+                "sample_name": {
+                    "description": "Name of the sample",
+                    "type": "string",
+                    "$ref": "#/definitions/Name"
+                },
+                "tags": {
+                    "$ref": "#/definitions/SampleTag"
+                }
+            }
+        },
+        "SampleTag": {
+            "description": "Minimum required properties for EMC Sample tags",
+            "type": "object",
+            "required": [
+                "gender",
+                "gs_batch",
+                "gs_sample",
+                "gs_projectcode",
+                "sequencer",
+                "capture_kit",
+                "verrichting_id",
+                "fractienr"
+            ],
+            "additionalProperties": false,
+            "properties": {
+                "gender": {
+                    "enum": [
+                        "V",
+                        "M",
+                        "O"
+                    ]
+                },
+                "gs_batch": {
+                    "$ref": "#/definitions/Name"
+                },
+                "gs_sample": {
+                    "$ref": "#/definitions/Name"
+                },
+                "experimentnr": {
+                    "$ref": "#/definitions/Name"
+                },
+                "gs_projectcode": {
+                    "$ref": "#/definitions/Name"
+                },
+                "sequencer": {
+                    "$ref": "#/definitions/Description"
+                },
+                "capture_kit": {
+                    "enum": [
+                        "Cardio",
+                        "Cre v2",
+                        "V7_CNV",
+                        "Human all exon V7"
+                    ]
+                },
+                "verrichting_id": {
+                    "$ref": "#/definitions/Name"
+                },
+                "fractienr": {
+                    "$ref": "#/definitions/Name"
+                }
+            }
+        }
+    },
+    "title": "Minimal transfer metadata",
+    "description": "Transfer schema for Illumina data. With or without UMI",
+    "type": "object",
+    "required": [
+        "title",
+        "sample_group",
+        "run_name",
+        "files"
+    ],
+    "additionalProperties": false,
+    "properties": {
+        "files": {
+            "description": "An array of one or more Files",
+            "type": "array",
+            "minItems": 1,
+            "uniqueItems": true,
+            "items": {
+                "$ref": "#/definitions/File"
+            }
+        },
+        "sample_group": {
+            "description": "Sample group information for this transfer",
+            "$ref": "#/definitions/SampleGroup"
+        },
+        "run_name": {
+            "description": "Run name for this transfer",
+            "$ref": "#/definitions/Name"
+        },
+        "title": {
+            "description": "Title of this transfer, this will be used in the notification email",
+            "$ref": "#/definitions/Description"
+        }
+    }
+}