Added email argument, removed all references to config file.

chipathlon/workflow.py

@@ -60,13 +60,14 @@ class Workflow(object):
     def __init__(self, job_home, run_file, param_file, properties_file,
                 chip_bin, idr_bin, execute_site="local", output_site="local",
                 host="localhost", username=None, password=None, save_db=True,
-                rewrite=False, debug=False):
+                email=None, rewrite=False, debug=False):
         # debug mode, print out additional information
         self.debug = debug
         # Job site information
         self.execute_site = execute_site
         self.output_site = output_site
         self.save_db = save_db
+        self.email = email
 
         # DB information
         self.username = username
@@ -84,6 +85,11 @@ class Workflow(object):
         self.run_file = os.path.abspath(run_file)
         self.param_file = os.path.abspath(param_file)
         self.properties_file = os.path.abspath(properties_file)
+        # Validate the existance of but not the contents of the
+        # pegasus properties file
+        if not os.path.isfile(self.properties_file):
+            self.errors.append("Provided pegasus properties file '%s' does not exist." % (self.properties_file,))
+
         self.chip_bin = chip_bin
         self.idr_bin = idr_bin
 
@@ -162,28 +168,6 @@ class Workflow(object):
         self.dax.addFile(gen_file_obj["file"])
         return
 
-    def _load_config(self):
-        # Validate input config.yaml file
-        # required & optional keys can be found in conf.py
-        try:
-            with open(self.config_file, "r") as rh:
-                self.config = yaml.load(rh)
-            for key in chipathlon.conf.config_file["required_keys"]:
-                if key not in self.config:
-                    self.errors.append("Config file '%s' does not have required key '%s'." % (config_file, key))
-            all_keys = chipathlon.conf.config_file["optional_keys"] + chipathlon.conf.config_file["required_keys"]
-            for key in self.config:
-                if key not in all_keys:
-                    self.errors.append("Config file '%s' has invalid key '%s' specified, should be one of: %s." % (config_file, key, all_keys))
-        except yaml.YAMLError as ye:
-            self.errors.append("Error reading config file '%s': %s" % (config_file, ye))
-
-        # Validate the existance of but not the contents of the
-        # pegasus properties file
-        if not os.path.isfile(self.properties_file):
-            self.errors.append("Provided pegasus properties file '%s' does not exist." % (self.properties_file,))
-        return
-
     def _add_executable(self, name, path, os_type="linux", arch="x86_64", site="local", installed=True):
         self.executables[name] = Executable(name=name, os=os_type.lower(), arch=arch, installed=installed)
         self.executables[name].addPFN(PFN(os.path.join("file://", path), site))
@@ -199,8 +183,8 @@ class Workflow(object):
                 executable,
                 os.path.join(self.idr_bin if executable == "idr" else self.chip_bin, executable),
                 site=self.execute_site,
-                arch=self.config.get("arch", "x86_64"),
-                os_type=self.config.get("os", "linux")
+                arch=arch,
+                os_type=os_type
             )
         # Load actual scripts
         for root, dirs, files in os.walk("%s/%s" % (os.path.dirname(os.path.realpath(__file__)), chipathlon.conf.job_scripts)):
@@ -210,8 +194,8 @@ class Workflow(object):
                         f,
                         os.path.join(self.chip_bin, f),
                         site=self.execute_site,
-                        arch=self.config.get("arch", "x86_64"),
-                        os_type=self.config.get("os", "linux")
+                        arch=arch,
+                        os_type=os_type,
                     )
             break
         # Handle necessary installed scripts
@@ -220,8 +204,8 @@ class Workflow(object):
                 cmd,
                 os.path.join(chipathlon.conf.system_path, cmd),
                 site=self.execute_site,
-                arch=self.config.get("arch", "x86_64"),
-                os_type=self.config.get("os", "linux")
+                arch=arch,
+                os_type=os_type
 	    )
         return
 
@@ -344,15 +328,16 @@ class Workflow(object):
         """
         Add the script to email when the workflow is finished.
         """
-        notify_path = os.path.join(self.base_path, "input/notify.sh")
-        with open(notify_path, "w") as wh:
-            notify = textwrap.dedent("""\
-                    #!/bin/bash
-                    pegasus-email -t %s --report=pegasus-analyzer
-            """ % (self.config["email"],))
-            wh.write(notify)
-            os.chmod(notify_path, 0755)
-        self.dax.invoke(When.AT_END, notify_path)
+        if self.email is not None:
+            notify_path = os.path.join(self.base_path, "input/notify.sh")
+            with open(notify_path, "w") as wh:
+                notify = textwrap.dedent("""\
+                        #!/bin/bash
+                        pegasus-email -t %s --report=pegasus-analyzer
+                """ % (self.email,))
+                wh.write(notify)
+                os.chmod(notify_path, 0755)
+            self.dax.invoke(When.AT_END, notify_path)
         return
 
     def _create_pegasus_files(self):

doc/source/scripts/chip-gen

@@ -16,6 +16,7 @@ parser.add_argument("--output-site", dest="output_site", required=True, default=
 parser.add_argument("--chip-bin", dest="chip_bin", required=True, help="Path to chipathlon conda environment bin.")
 parser.add_argumnet("--idr-bin", dest="idr_bin", required=True, help="Path to idr conda enviornment bin.")
 
+parser.add_argument("--email", dest="email", help="An email address to notify when the workflow is finished.")
 parser.add_argument("--no-save-db", dest="save_db", default=True, action="store_false", help="Whether or not to save results to the database.  Default: True")
 parser.add_argument("--rewrite", dest="rewrite", default=False, action="store_true", help="If specified, don't load from the database, rewrite files.")
 parser.add_argument("--debug", dest="debug", default=False, action="store_true", help="Print out more information while generating.")

scripts/chip-gen

@@ -16,6 +16,7 @@ parser.add_argument("--output-site", dest="output_site", required=True, default=
 parser.add_argument("--chip-bin", dest="chip_bin", required=True, help="Path to chipathlon conda environment bin.")
 parser.add_argumnet("--idr-bin", dest="idr_bin", required=True, help="Path to idr conda enviornment bin.")
 
+parser.add_argument("--email", dest="email", help="An email address to notify when the workflow is finished.")
 parser.add_argument("--no-save-db", dest="save_db", default=True, action="store_false", help="Whether or not to save results to the database.  Default: True")
 parser.add_argument("--rewrite", dest="rewrite", default=False, action="store_true", help="If specified, don't load from the database, rewrite files.")
 parser.add_argument("--debug", dest="debug", default=False, action="store_true", help="Print out more information while generating.")
@@ -33,6 +34,7 @@ workflow = Workflow(
     password=args.password,
     execute_site=args.execute_site,
     output_site=args.output_site,
+    email=email,
     save_db=args.save_db,
     rewrite=args.rewrite,
     debug=args.debug