backend for scriptbuilder

.travis.yml

@@ -36,6 +36,7 @@ script:
     - npm install
 
     - cd $PROJECT_ROOT
+    - pip install -r requirements.txt
     - echo $(pwd) >> $PATH_FILE
     - cd sandstone_slurm
     - bower install

requirements.txt

@@ -0,0 +1 @@
+jsonschema==2.5.1

sandstone_slurm/handlers.py

@@ -5,6 +5,7 @@
 from sandstone_slurm.mixins.slurm_mixin import SlurmCmdMixin
 from sandstone.lib.handlers.base import BaseHandler
 from sandstone_slurm.config_utils import ConfigLoader
+from sandstone_slurm.script_template_utils import TemplateFinder
 from sandstone import settings
 
 
@@ -56,3 +57,20 @@ def delete(self,jobid):
         # This method should dequeue the job specified
         # by jobid, via scancel.
         pass
+
+class ScriptTemplateHandler(BaseHandler):
+
+    @sandstone.lib.decorators.authenticated
+    def get(self):
+        # get all the templates
+        templates = TemplateFinder.find_all_templates()
+
+        parsed_json = {
+            'templates': []
+        }
+
+        for template in templates:
+            # parse the template
+            parsed_json['templates'].append(template.parse())
+
+        self.write(parsed_json)

sandstone_slurm/script_template_utils.py

@@ -0,0 +1,123 @@
+import re
+import json
+import os
+from sandstone import settings
+from jsonschema import Draft4Validator
+from jsonschema.exceptions import SchemaError
+
+class TemplateFinder(object):
+    """
+    Finds all script templates
+    """
+
+    @staticmethod
+    def find_all_templates():
+        # find all the templates and return
+        all_templates = []
+        base_path = settings.SANDSTONE_TEMPLATES_DIR
+        files = os.listdir(base_path)
+
+        for filename in files:
+            filepath = os.path.join(base_path, filename)
+            if os.path.isfile(filepath):
+                ext = os.path.splitext(filepath)[1]
+                if ext == '.sh':
+                    all_templates.append(BashTemplate(filepath))
+                elif ext == '.json':
+                    json_template = JSONTemplate(filepath)
+                    if json_template.is_valid_schema():
+                        all_templates.append(json_template)
+                    else:
+                        # ignore the template
+                        print 'Template is not valid'
+        return all_templates
+
+class BaseTemplate(object):
+    """
+    Base Script Template
+    """
+
+    def __init__(self, filename):
+        self.filename = filename
+        with open(self.filename) as template_file:
+            self._raw_file_data = template_file.read()
+
+    def parse(self):
+        raise NotImplementedError('Method not implemented')
+
+
+class JSONTemplate(BaseTemplate):
+    """
+    Represents a JSON template
+    """
+
+    def __init__(self, filename):
+        super(JSONTemplate, self).__init__(filename)
+
+    def is_valid_schema(self):
+
+        parsed_json = self.parse()
+
+        if not (parsed_json['title'] and parsed_json['description'] and parsed_json['command']):
+            return False
+
+        variables = parsed_json['variables']
+        try:
+            Draft4Validator.check_schema(variables)
+            return True
+        except SchemaError:
+            return False
+
+    def parse(self):
+        return json.loads(self._raw_file_data)
+
+
+class BashTemplate(BaseTemplate):
+    """
+    Represents a Bash template
+    """
+
+    _template_name = ''
+
+    def __init__(self, filename):
+        super(BashTemplate, self).__init__(filename)
+        self._template_name = filename
+
+    def parse(self):
+        # parsing logic
+        variables = []
+        commands = []
+
+        description = ''
+
+
+        for line in self._raw_file_data.split('\n'):
+            # is sbatch directive or a blank line, continue
+            if line.startswith('#SBATCH') or line == '' or line.startswith('#'):
+                continue
+            elif line.startswith('#SANDSTONE_DESCRIPTION'):
+                # specifies the description
+                description = line.split('=')[1]
+            else:
+                # it is a command
+                # get line till a '#' is seen
+                command = line.split('#')[0].strip()
+                commands.append(command)
+                # get all variables
+                variables.extend([m[0] for m in re.findall(r'(\$SANDSTONE(_(\w){1,}){1,})', command)])
+        parsed_object = {
+            'template_name': self._template_name,
+            'description': description,
+            'command': '\n'.join(commands),
+            'variables': {}
+        }
+
+        for variable in variables:
+            current_variable = {
+                'type': 'string',
+                'description': '',
+                'title': variable
+            }
+            parsed_object['variables'][variable] = current_variable
+
+        return parsed_object

sandstone_slurm/tests/python/test_script_handlers.py

@@ -0,0 +1,26 @@
+import os
+import mock
+import pwd
+import json
+from sandstone.lib.handlers.base import BaseHandler
+from sandstone.lib.test_utils import TestHandlerBase
+from sandstone import settings
+
+EXEC_USER = pwd.getpwuid(os.getuid())[0]
+TEMPLATES_DIR = os.path.join(os.path.dirname(__file__), 'testfiles')
+
+class ScriptTemplateHandlerTestCase(TestHandlerBase):
+
+    @mock.patch.object(BaseHandler, 'get_secure_cookie', return_value=EXEC_USER)
+    def test_get_templates(self, m):
+        settings.SANDSTONE_TEMPLATES_DIR = TEMPLATES_DIR
+        response = self.fetch(
+            '/slurm/a/scripttemplates',
+            method='GET',
+            follow_redirects=False
+        )
+        self.assertEqual(response.code, 200)
+
+        json_response = json.loads(response.body)
+        self.assertIsNotNone(json_response['templates'])
+        self.assertEqual(len(json_response['templates']), 3)

sandstone_slurm/tests/python/test_script_templates.py

@@ -0,0 +1,47 @@
+import unittest
+import mock
+import json
+import os
+from sandstone import settings
+from sandstone_slurm.script_template_utils import BashTemplate, JSONTemplate, TemplateFinder
+
+TEST_JSON_FILE = os.path.join(os.path.dirname(__file__), 'testfiles/test_json.json')
+TEST_BASH_FILE = os.path.join(os.path.dirname(__file__), 'testfiles/test_script.sh')
+TEST_COMPLEX_BASH_FILE = os.path.join(os.path.dirname(__file__), 'testfiles/test_complex_bash.sh')
+TEMPLATES_DIR = os.path.join(os.path.dirname(__file__), 'testfiles')
+
+class TemplateFinderTestCase(unittest.TestCase):
+    def setUp(self):
+        settings.SANDSTONE_TEMPLATES_DIR = TEMPLATES_DIR
+
+    def test_template_finder(self):
+        all_templates = TemplateFinder.find_all_templates()
+        self.assertEqual(len(all_templates), 3)
+
+
+class JSONTemplateParseTestCase(unittest.TestCase):
+    def setUp(self):
+        self.json_template = JSONTemplate(TEST_JSON_FILE)
+
+    def test_valid_json(self):
+        self.assertTrue(self.json_template.is_valid_schema())
+
+class BashTemplateParseTestCase(unittest.TestCase):
+
+    def test_template_properties(self):
+        self.bash_template = BashTemplate(TEST_BASH_FILE)
+        parsed_object = self.bash_template.parse()
+        self.assertEqual(parsed_object['template_name'], TEST_BASH_FILE)
+        self.assertEqual(parsed_object['description'], "")
+        self.assertEqual(parsed_object['command'], "python $SANDSTONE_FILENAME")
+        self.assertEqual(len(parsed_object['variables'].keys()), 1)
+        self.assertItemsEqual(parsed_object['variables'].keys(), ['$SANDSTONE_FILENAME'])
+
+    def test_complex_template_properties(self):
+        self.bash_template = BashTemplate(TEST_COMPLEX_BASH_FILE)
+        parsed_object = self.bash_template.parse()
+        self.assertEqual(parsed_object['template_name'], TEST_COMPLEX_BASH_FILE)
+        self.assertEqual(parsed_object['description'], "")
+        self.assertEqual(parsed_object['command'], "export OMP_NUM_THREADS=$SANDSTONE_NUM_THREADS\nsrun -n 20 -c 4 $SANDSTONE_SCRIPT_NAME")
+        self.assertEqual(len(parsed_object['variables'].keys()), 2)
+        self.assertItemsEqual(parsed_object['variables'].keys(), ['$SANDSTONE_NUM_THREADS', '$SANDSTONE_SCRIPT_NAME'])

sandstone_slurm/tests/python/testfiles/test_complex_bash.sh

@@ -0,0 +1,11 @@
+#!/bin/bash -l
+
+#SBATCH -p regular
+#SBATCH -N 64
+#SBATCH -t 12:00:00
+#SBATCH -L project
+#SBATCH -C haswell
+
+#to run with pure MPI
+export OMP_NUM_THREADS=$SANDSTONE_NUM_THREADS
+srun -n 20 -c 4 $SANDSTONE_SCRIPT_NAME   # -c is optional since this example is fully packed pure MPI (32 MPI tasks per node)

sandstone_slurm/tests/python/testfiles/test_json.json

@@ -0,0 +1,14 @@
+{
+    "title": "Some JSON template",
+    "description": "Some Description",
+    "command": "ls | grep $SANDSTONE_SEARCH_EXPRESSION",
+    "variables": {
+        "type": "object",
+        "properties": {
+            "$SANDSTONE_SEARCH_EXPRESSION": {
+                "type": "string",
+                "description": "Some Sample description"
+            }
+        }
+    }
+}

sandstone_slurm/tests/python/testfiles/test_script.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+#SBATCH --job-name test-job
+#SBATCH --nodes 2
+#SBATCH --account=crcsupport
+#SBATCH --output output.out
+#python main.py
+
+python $SANDSTONE_FILENAME

sandstone_slurm/urls.py

@@ -1,11 +1,13 @@
 from sandstone_slurm.handlers import FormConfigHandler
 from sandstone_slurm.handlers import JobListHandler
 from sandstone_slurm.handlers import JobHandler
+from sandstone_slurm.handlers import ScriptTemplateHandler
 
 
 
 URL_SCHEMA = [
             (r"/slurm/a/config", FormConfigHandler),
             (r"/slurm/a/jobs", JobListHandler),
             (r"/slurm/a/jobs/(?P<jobid>[0-9]+)?", JobHandler),
+            (r"/slurm/a/scripttemplates", ScriptTemplateHandler),
         ]