Merge branch 'develop' of github.com:boutiques/boutiques into release…

…0.5.15

README.md

@@ -75,6 +75,18 @@ There are additional custom arguments which can be supplied to this script, such
 no interpretation of output files is attempted by this tool, so your descriptor could certainly be enhanced by addind these and other
 features available through Boutiques, such as tests, tags, error codes, groups, and container images.
 
+Once you've created your descriptor this way you can translate your arguments to a Boutiques-style invocation using the following
+code block on runtime:
+
+    args = myparser.parse_args()
+    invoc = newDescriptor.createInvocation(args)
+
+    # Then, if you want to save them to a file...
+    import json
+    with open('my-inputs.json', 'w') as fhandle:
+        fhandle.write(json.dumps(invoc, indent=4))
+
+
 ### Validation
 
 You just created a Boutiques descriptor (compliant with the [schema](./tools/python/boutiques/schema/descriptor.schema.json), of course)

tools/python/boutiques/creator.py

@@ -29,7 +29,7 @@ def __init__(self, parser=None, **kwargs):
                               kwargs.get('docker_image'),
                               kwargs.get('use_singularity'))
 
-        self.count = 0
+        self.sp_count = 0
         if parser is not None:
             self.parser = parser
             self.descriptor["inputs"] = []
@@ -47,6 +47,11 @@ def save(self, filename):
         with open(filename, "w") as f:
             f.write(json.dumps(self.descriptor, indent=4, sort_keys=True))
 
+    def createInvocation(self, arguments):
+        argdict = vars(arguments)
+        argdict = {k: v for k, v in argdict.items() if v is not None}
+        return argdict
+
     def parse_docker(self, descriptor, docker_image_name, use_singularity):
         cont_image = {}
 
@@ -177,8 +182,13 @@ def parseAction(self, action, **kwargs):
                 print("{0}: Adding".format(actstring))
             actdict = vars(action)
             if action.dest == "==SUPPRESS==":
-                adest = "subparser_{0}".format(self.count)
-                self.count += 1
+                adest = "subparser_{0}".format(self.sp_count)
+                if kwargs.get("verbose"):
+                    print("WARNING: Subparser has no destination set, "
+                          "invocation parsing may not work as expected. This "
+                          "can be fixed by adding \"dest='mysubparser'\" to "
+                          "subparser creation.")
+                self.sp_count += 1
             else:
                 adest = action.dest
 

tools/python/boutiques/invocationSchemaHandler.py

@@ -171,6 +171,7 @@ def validateSchema(s, d=None, **kwargs):
                 try:
                         jsonschema.validate(d, s)
                 except ValidationError as e:
+                        raise e
                         raise InvocationValidationError(e)
                 if kwargs.get("verbose"):
                         print("Invocation Schema validation OK")

tools/python/boutiques/localExec.py

@@ -804,7 +804,10 @@ def escape_string(s):
                             s = str(x)
                             if escape:
                                 s = escape_string(str(x))
-                            s_val += s + " "
+                            if val.index(x) == len(val)-1:
+                                s_val += s
+                            else:
+                                s_val += s + " "
                         val = s_val
                     else:
                         val = str(val)

tools/python/boutiques/schema/examples/no_spaces.json

@@ -1,12 +1,21 @@
 {
-    "command-line": "there[INPUT]shouldnotbeanyspace[INPUT]inhereaftersubstitution", 
+    "command-line": "there[INPUT]shouldnotbeanyspace[INPUT_LIST]inhereaftersubstitution", 
     "description": "A command-line with no space", 
     "inputs": [
         {
             "id": "param", 
             "name": "param", 
             "type": "String", 
             "value-key": "[INPUT]"
+        },
+        {
+            "id": "param2", 
+            "name": "param2", 
+            "type": "String",
+            "list": true, 
+            "min-list-entries": 1,
+            "max-list-entries": 1,
+            "value-key": "[INPUT_LIST]"
         }
     ],
     "name": "nospace", 

tools/python/boutiques/tests/test_creator.py

@@ -7,6 +7,7 @@
 import boutiques.creator as bc
 import subprocess
 import os.path as op
+import json
 import os
 import pytest
 
@@ -50,7 +51,8 @@ def test_success_argparser(self):
                             help="my help 2", type=int)
         parser.add_argument("--myarg3", "-m", action="store",
                             help="my help 3")
-        subparser = parser.add_subparsers(help="the choices you will make")
+        subparser = parser.add_subparsers(help="the choices you will make",
+                                          dest="mysubparser")
         sb1 = subparser.add_parser("option1", help="the first value")
         sb1.add_argument("suboption1", help="the first sub option option")
         sb1.add_argument("suboption2", help="the first sub option option",
@@ -69,6 +71,18 @@ def test_success_argparser(self):
                                          verbose=True,
                                          tags={"purpose": "testing-creator",
                                                "foo": "bar"})
+
         fil = './test-created-argparse-descriptor.json'
         creatorObj.save(fil)
+
+        invof = './test-created-argparse-inputs.json'
+        args = parser.parse_args([['val1', 'val2'], '2', 'option2',
+                                  'subval1', 'subval3',
+                                  '--suboptionflag1', 't1',
+                                  '--suboptionflag2'])
+        invo = creatorObj.createInvocation(args)
+        with open(invof, 'w') as fhandle:
+            fhandle.write(json.dumps(invo, indent=4))
+
         assert bosh(['validate', fil]) is None
+        assert bosh(['invocation', fil, '-i', invof]) is None

tools/python/cleanup_tests.sh

@@ -6,9 +6,9 @@
 #
 
 rm -r temp-*.sh log*.txt config*.txt file.txt creator_output.json \
-      test-created-argparse-descriptor.json .pytest_cache/ bar.dat \
-      baz.txt cwl_inv_out.json cwl_out.json example.conf foo.txt \
-      goodbye.txt hello.js hello.tar stdout.txt
+      test-created-argparse-descriptor.json test-created-argparse-inputs.json \
+      .pytest_cache/ bar.dat baz.txt cwl_inv_out.json cwl_out.json \
+      example.conf foo.txt goodbye.txt hello.js hello.tar stdout.txt
 git checkout boutiques/schema/examples/good.json
 git checkout boutiques/schema/examples/example1/example1_docker.json
 git checkout boutiques/schema/examples/example1/example1_sing.json