From e070b045506f1d2775c6a4bf5d9478332f2aade9 Mon Sep 17 00:00:00 2001
From: Philippe Rocca-Serra <philippe.rocca-serra@oerc.ox.ac.uk>
Date: Thu, 8 Jun 2017 12:19:26 +0100
Subject: [PATCH] update to json file

---
 isatools/create/isa-possible-workflows.json | 203 +++++++++++++-------
 1 file changed, 131 insertions(+), 72 deletions(-)

diff --git a/isatools/create/isa-possible-workflows.json b/isatools/create/isa-possible-workflows.json
index 8209d901..862c2939 100644
--- a/isatools/create/isa-possible-workflows.json
+++ b/isatools/create/isa-possible-workflows.json
@@ -2,86 +2,145 @@
   "assay_type": {
     "name": "mass spectrometry",
     "abbreviation": "MS",
-    "uri" : "",
-    "sample_injection_type": {
-        "name": "direct infusion assay",
-        "abbreviation" : "DIA",
-        "polarity_mode": ["positive_mode","negative mode"],
-        "number_of_injection": ""
-      },
+    "uri": "",
     "sample_injection_type": {
-        "name": "liquid chromatography assay",
-        "abbreviation" : "LC",
-        "polarity_mode": ["positive_mode","negative mode"],
-        "number_of_injection": ""
-      },
-    "sample_injection_type": {
-        "name": "gas chromatography assay",
-        "abbreviation" : "GC",
-        "polarity_mode": ["positive_mode","negative mode"],
-        "number_of_injection": ""
-      }
+      "name": "direct infusion assay",
+      "abbreviation": "DIA",
+      "polarity_mode": [
+        "positive_mode",
+        "negative mode"
+      ],
+      "number_of_injection": ""
     },
-  "name": "nmr spectroscopy",
-    "abbreviation": "NMR",
-    "uri" : "",
     "sample_injection_type": {
-        "name": "liquid chromatography assay",
-        "abbreviation" : "LC",
-        "acquisition": {
-            "dimension": {
-              "name": "1 dimension NMR",
-              "abbreviation" : "1D",
-              "nucleus": ["1H","13C"],
-              "pulse_sequence" : ["CPMG","NOESY","J-RES"]
-            }
-          },
+      "name": "liquid chromatography assay",
+      "abbreviation": "LC",
+      "polarity_mode": [
+        "positive_mode",
+        "negative mode"
+      ],
       "number_of_injection": ""
-      },
-      "sample_injection_type": {
-        "name": "liquid chromatography assay",
-        "abbreviation" : "LC",
-        "acquisition": {
-            "dimension": {
-              "name": "2 dimension NMR",
-              "abbreviation" : "2D",
-              "nucleus": ["1H-1H","1H-13C","13C-13C"],
-              "pulse_sequence" : ["HSQC","TOCSY","TOESY","other"]
-            }
-          },
-      "number_of_injection": ""
-      },
+    },
     "sample_injection_type": {
       "name": "gas chromatography assay",
       "abbreviation": "GC",
-      "acquisition": {
-        "dimension": {
-          "name": "1 dimension NMR",
-          "abbreviation": "1D",
-          "nucleus": [
-            "1H",
-            "13C"
-          ],
-          "pulse_sequence": [
-            "CPMG",
-            "NOESY",
-            "J-RES"
-          ]
-        }
-      },
+      "polarity_mode": [
+        "positive_mode",
+        "negative mode"
+      ],
       "number_of_injection": ""
+    }
+  },
+  "assay_type": {
+  "name": "nmr spectroscopy",
+  "abbreviation": "NMR",
+  "uri": "",
+  "sample_injection_type": {
+    "name": "liquid chromatography assay",
+    "abbreviation": "LC",
+    "acquisition": {
+      "dimension": {
+        "name": "1 dimension NMR",
+        "abbreviation": "1D",
+        "nuclei": [
+          "1H",
+          "13C"
+        ],
+        "pulse_sequence": [
+          "CPMG",
+          "NOESY",
+          "J-RES"
+        ]
+      }
     },
-    "sample_injection_type": {
-        "name": "gas chromatography assay",
-        "abbreviation" : "GC",
-        "acquisition": {
-            "dimension": {
-              "name": "2 dimension NMR",
-              "abbreviation" : "2D",
-              "nucleus": ["1H-1H","1H-13C","13C-13C"],
-              "pulse_sequence" : ["HSQC","TOCSY","TOESY","other"]
-            }
-          },
-      "number_of_injection": ""
+    "number_of_injection": ""
+  },
+  "sample_injection_type": {
+    "name": "liquid chromatography assay",
+    "abbreviation": "LC",
+    "acquisition": {
+      "dimension": {
+        "name": "2 dimension NMR",
+        "abbreviation": "2D",
+        "nuclei": [
+          "1H-1H",
+          "1H-13C",
+          "13C-13C"
+        ],
+        "pulse_sequence": [
+          "HSQC",
+          "TOCSY",
+          "TOESY",
+          "other"
+        ]
+      }
+    },
+    "number_of_injection": ""
+  },
+  "sample_injection_type": {
+    "name": "gas chromatography assay",
+    "abbreviation": "GC",
+    "acquisition": {
+      "dimension": {
+        "name": "1 dimension NMR",
+        "abbreviation": "1D",
+        "nuclei": [
+          "1H",
+          "13C"
+        ],
+        "pulse_sequence": [
+          "CPMG",
+          "NOESY",
+          "J-RES"
+        ]
       }
+    },
+    "number_of_injection": ""
+  },
+  "sample_injection_type": {
+    "name": "gas chromatography assay",
+    "abbreviation": "GC",
+    "acquisition": {
+      "dimension": {
+        "name": "2 dimension NMR",
+        "abbreviation": "2D",
+        "nuclei": [
+          "1H-1H",
+          "1H-13C",
+          "13C-13C"
+        ],
+        "pulse_sequence": [
+          "HSQC",
+          "TOCSY",
+          "TOESY",
+          "other"
+        ]
+      }
+    },
+    "number_of_injection": ""
+  }
+},
+  "assay_type": {
+    "name" : "dna microarray",
+    "abbreviation" : "genechip",
+    "uri" : "",
+    "array_designs" : {
+      "name" : "",
+      "uri" : ""
+    },
+    "acquisition" : {
+      "channels" : ["1","2","3"]
+    },
+    "number_of_techrep": ""
+  },
+  "assay_type" : {
+    "name" : "dna sequencing",
+    "abbreviation" : "NGS",
+    "uri" : "",
+    "number_of_libraries":"",
+    "acquisition" :{
+      "multiplex_identifier":["",""]
+    },
+    "number_of_techrep": ""
+  }
 }