WIP: Salad a Schema!

.gitignore

@@ -41,3 +41,4 @@ docs/_build
 
 .venv
 
+java/target

Makefile

@@ -55,7 +55,7 @@ flake8: ## check style using flake8 for current Python (faster than lint)
 	$(IN_VENV) flake8 --max-complexity 11 $(SOURCE_DIR)  $(TEST_DIR)
 
 lint: ## check style using tox and flake8 for Python 2 and Python 3
-	$(IN_VENV) tox -e py27-lint && tox -e py34-lint
+	$(IN_VENV) tox -e py27-lint && tox -e py35-lint
 
 lint-readme: ## check README formatting for PyPI
 	$(IN_VENV) python setup.py check -r -s

build_schema.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+
+set -x
+set -e
+
+PROJECT_DIRECTORY="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+
+
+# Requires schema-salad-doc that recognizes --brandstyle and --brandinverse
+for schema in "v19.09";
+do
+    cd schema/"$schema";
+    python_schema_name=${schema//./_}
+    schema-salad-tool --codegen python workflow.yml > "${PROJECT_DIRECTORY}/gxformat2/schema/${python_schema_name}.py"
+
+    out="../${schema}.html"
+    schema-salad-doc \
+        --brandstyle '<link rel="stylesheet" href="https://jamestaylor.org/galaxy-bootstrap/galaxy_bootstrap.css">' \
+        --brandinverse \
+        --brand '<img src="icon.png" />' \
+        --only "https://galaxyproject.org/gxformat2/${schema}#WorkflowDoc" \
+        --only "https://galaxyproject.org/gxformat2/${schema}#GalaxyWorkflow" \
+        workflow.yml > "$out"
+
+    java_package="${PROJECT_DIRECTORY}/java"
+    schema-salad-tool --codegen java --codegen-target "$java_package" workflow.yml
+    cd "$java_package"
+    mvn test
+    mvn javadoc:javadoc
+    cd "${PROJECT_DIRECTORY}"
+done

dev-requirements.txt

@@ -1,3 +1,6 @@
+# Optional dependencies
+schema-salad
+
 # For testing
 tox
 nose

gxformat2/lint.py

@@ -1,3 +1,4 @@
+import os
 import sys
 
 from gxformat2._yaml import ordered_load
@@ -8,36 +9,60 @@
 EXIT_CODE_FILE_PARSE_FAILED = 3
 
 
-def lint_ga(workflow_dict):
+def lint_ga(workflow_dict, path=None):
     if workflow_dict.get("format-version") != "0.1":
         return EXIT_CODE_FORMAT_ERROR
     if workflow_dict.get("a_galaxy_workflow") != "true":
         return EXIT_CODE_FORMAT_ERROR
 
     native_steps = workflow_dict.get("steps")
+    if not native_steps or not isinstance(native_steps, dict):
+        return EXIT_CODE_FORMAT_ERROR
+
     found_outputs = False
     found_output_without_label = False
 
-    for step in native_steps.values():
+    for order_index_str, step in native_steps.items():
+        if not order_index_str.isdigit():
+            return EXIT_CODE_FORMAT_ERROR
+
         for workflow_output in step.get("workflow_outputs", []):
             found_outputs = True
 
             if not workflow_output.get("label"):
                 found_output_without_label = True
 
+        step_type = step.get("type")
+        if step_type == "subworkflow":
+            subworkflow = step.get("subworkflow")
+            if subworkflow and not isinstance(subworkflow, dict):
+                return EXIT_CODE_FORMAT_ERROR
+            lint_subworkflow_ret = lint_ga(subworkflow)
+            if lint_subworkflow_ret != 0:
+                return lint_subworkflow_ret
+
     if not found_outputs:
         return EXIT_CODE_LINT_FAILED
-    
+
     if found_output_without_label:
         return EXIT_CODE_LINT_FAILED
 
     return EXIT_CODE_SUCCESS
 
 
-def lint_format2(workflow_dict):
+def lint_format2(workflow_dict, path=None):
+    from gxformat2.schema.v19_09 import load_document
+    from schema_salad.exceptions import SchemaSaladException
+    try:
+        load_document("file://" + os.path.normpath(path))
+    except SchemaSaladException as e:
+        print(e)
+        return EXIT_CODE_FORMAT_ERROR
+
     # Lint for outputs...
     if not workflow_dict.get("outputs", None):
         return EXIT_CODE_LINT_FAILED
+
     return EXIT_CODE_SUCCESS
 
 
@@ -49,10 +74,8 @@ def main(argv):
         except Exception:
             return EXIT_CODE_FILE_PARSE_FAILED
     workflow_class = workflow_dict.get("class")
-    if workflow_class == "GalaxyWorkflow":
-        exit_code = lint_format2(workflow_dict)
-    else:
-        exit_code = lint_ga(workflow_dict)
+    lint_func = lint_format2 if workflow_class == "GalaxyWorkflow" else lint_ga
+    exit_code = lint_func(workflow_dict, path=path)
     return exit_code