Merge pull request #143 from glatard/develop

Fixed example1 and made minor updates in validator
boutiques · Sep 18, 2017 · 415ce62 · 415ce62
2 parents 52d1246 + 5bff791
commit 415ce62
Show file tree

Hide file tree

Showing 6 changed files with 122 additions and 85 deletions.
diff --git a/examples/example1/Dockerfile b/examples/example1/Dockerfile
@@ -0,0 +1,2 @@
+FROM centos:latest
+ADD exampleTool1 /bin
diff --git a/examples/example1/example1.json b/examples/example1/example1.json
@@ -1,82 +1,107 @@
 {
-    "name" : "Example Boutiques Tool",
-    "tool-version" : "0.0.1",
-    "description" : "This property describes the tool or application",
-    "command-line" : "exampleTool1 [STRING_INPUT] [FILE_INPUT] [ENUM_INPUT] | exampleTool2 [FLAG_INPUT] [NUMBER_INPUT] >> [LOG]",
+    "tool-version": "0.0.1", 
+    "name": "Example Boutiques Tool", 
+    "command-line": "exampleTool1 [STRING_INPUT] [FILE_INPUT] [FLAG_INPUT] [NUMBER_INPUT] [ENUM_INPUT]  &> [LOG]", 
+    "inputs": [
+        {
+            "command-line-flag": "-i", 
+            "description": "Describe the use and meaning of the parameter", 
+            "default-value": "aStringValue", 
+            "value-key": "[STRING_INPUT]", 
+            "type": "String", 
+            "list": true, 
+            "max-list-entries": 3, 
+            "optional": false, 
+            "id": "str_input", 
+            "min-list-entries": 1, 
+            "name": "A string input"
+        }, 
+        {
+            "command-line-flag": "-n", 
+            "name": "A number input", 
+            "value-key": "[NUMBER_INPUT]", 
+            "type": "Number", 
+            "exclusive-maximum": false, 
+            "maximum": 1, 
+            "minimum": 0, 
+            "command-line-flag-separator": "=", 
+            "integer": false, 
+            "exclusive-minimum": true, 
+            "optional": true, 
+            "id": "num_input"
+        }, 
+        {
+            "value-key": "[FILE_INPUT]", 
+            "optional": true, 
+            "type": "File", 
+            "id": "file_input", 
+            "name": "A file input"
+        }, 
+        {
+            "name": "An enum input", 
+            "value-key": "[ENUM_INPUT]", 
+            "optional": true, 
+            "value-choices": [
+                "val1", 
+                "val2", 
+                "val3"
+            ], 
+            "type": "String", 
+            "id": "enum_input"
+        }, 
+        {
+            "command-line-flag": "-f", 
+            "name": "A flag input", 
+            "value-key": "[FLAG_INPUT]", 
+            "optional": true, 
+            "requires-inputs": [
+                "file_input"
+            ], 
+            "disables-inputs": [
+                "num_input"
+            ], 
+            "type": "Flag", 
+            "id": "flag_input"
+        }
+    ], 
     "container-image": {
-        "type": "docker",
-        "image": "boutiques/examples"
-    },
-    "schema-version" : "0.4",
-    "inputs" : [{
-        "id" : "str_input",
-        "name" : "A string input",
-        "type" : "String",
-        "description" : "Describe the use and meaning of the parameter",
-        "optional" : false,
-        "command-line-flag" : "-i",
-        "value-key" : "[STRING_INPUT]",
-        "list" : true, 
-        "min-list-entries" : 1,
-        "max-list-entries" : 3,
-        "default-value" : "aStringValue"
-    }, {
-        "id" : "num_input",
-        "name" : "A number input",
-        "type" : "Number",
-        "value-key" : "[NUMBER_INPUT]",
-        "optional" : true, 
-        "command-line-flag" : "-n",
-        "command-line-separator" : "=",
-        "minimum" : 0,
-        "maximum" : 1,
-        "exclusive-minimum" : true,
-        "exclusive-maximum" : false,
-        "integer" : false
-    }, {
-        "id" : "file_input",
-        "name" : "A file input",
-        "type" : "File",
-        "optional" : true,
-        "value-key" : "[FILE_INPUT]"
-    }, {
-        "id" : "enum_input",
-        "name" : "An enum input",
-        "type" : "Enum",
-        "enum-value-choices" : ["val1","val2","val3"],
-        "value-key" : "[ENUM_INPUT]",
-        "optional": true
-    }, {
-        "id" : "flag_input",
-        "name" : "A flag input",
-        "type" : "Flag",
-        "command-line-flag" : "-f",
-        "value-key" : "[FLAG_INPUT]",
-        "requires-inputs" : ["file_input"],
-        "disables-inputs" : ["num_input"],
-        "optional": true
-    }],
-    "output-files" : [{
-        "id" : "logfile",
-        "name" : "Log file",
-        "description" : "The output log file from the example tool",
-        "path-template" : "log-[STRING_INPUT].txt",
-        "value-key" : "[LOG]",
-        "path-template-stripped-extensions" : [".txt", ".csv"],
-        "optional" : false
-    }, {
-        "id" : "output_files",
-        "name" : "outfiles",
-        "list" : true,
-        "path-template" : "output/*_exampleOutputTag.resultType",
-        "optional" : true
-    }],
-    "groups" : [{
-        "id" : "an_example_group",
-        "name" : "Example group 1",
-        "description" : "This group forces us to choose exactly one of the file or the enum input to use.",
-        "members" : ["file_input", "enum_input"],
-        "mutually-exclusive" : true,
-        "one-is-required" : true
-    }]
+        "image": "boutiques/examples", 
+        "type": "docker"
+    }, 
+    "schema-version": "0.5", 
+    "groups": [
+        {
+            "description": "This group forces us to choose exactly one of the file or the enum input to use.", 
+            "one-is-required": true, 
+            "mutually-exclusive": true, 
+            "members": [
+                "file_input", 
+                "enum_input"
+            ], 
+            "id": "an_example_group", 
+            "name": "Example group 1"
+        }
+    ], 
+    "output-files": [
+        {
+            "description": "The output log file from the example tool", 
+            "value-key": "[LOG]", 
+            "id": "logfile", 
+            "optional": false, 
+            "path-template": "log-[STRING_INPUT].txt", 
+            "path-template-stripped-extensions": [
+                ".txt", 
+                ".csv"
+            ], 
+            "name": "Log file"
+        }, 
+        {
+            "path-template": "output/*_exampleOutputTag.resultType", 
+            "optional": true, 
+            "list": true, 
+            "id": "output_files", 
+            "name": "outfiles"
+        }
+    ], 
+    "description": "This property describes the tool or application"
 }
diff --git a/examples/example1/exampleTool1 b/examples/example1/exampleTool1
@@ -1,3 +1,8 @@
 #!/bin/bash
 
+set -e
+set -u
+
+test -f $3 || echo "$3 does not exist"
+
 echo $*
diff --git a/examples/example1/exampleTool2 b/examples/example1/exampleTool2
diff --git a/examples/example1/invocation.json b/examples/example1/invocation.json
@@ -0,0 +1,9 @@
+{
+  "inputs" : [
+    { "str_input" : "foo" },
+    { "num_input" : 4 },
+    { "file_input" : "test.txt" },
+      { "enum_input" : "val1" }
+  ]
+}
+
diff --git a/tools/python/boutiques/validator.py b/tools/python/boutiques/validator.py
@@ -53,6 +53,7 @@ def validate_json(json_file):
         validate(descriptor, schema)
     except ValidationError as e:
         print("JSON Validation error (Rigorous Boutiques validation not yet performed)")
+        print(str(e))
         raise ValidationError(e)
 
     # Helper get-function
@@ -122,7 +123,7 @@ def validate_json(json_file):
             msg_template = " InputError: \"{}\" must have a command-line flag"
             errors += [msg_template.format(inp["id"])] if "command-line-flag" not in inp.keys() else []
 
-            msg_template = " InputError: \"{}\" should not be required"
+            msg_template = " InputError: \"{}\" is of type Flag, it has to be optional"
             errors += [msg_template.format(inp["id"])] if inp["optional"] is False else []
 
         # Verify number-type inputs min/max are sensible