[UI] Revamp Job Details Page with Resources expansion (#239)

Author: Bryan Crampton

api/jobs.yaml

@@ -363,23 +363,26 @@ definitions:
     properties:
       userId:
         type: string
-        description: The user associated with the job
+        description: The user associated with the job.
       statusDetail:
         type: string
         description: Longer text description of the job status.
       logs:
         type: object
-        description: Map of type of log file to its file location
+        description: Map of type of log file to its file location.
       lastUpdate:
         type: string
         format: date-time
-        description: Job last update datetime in ISO8601 format
+        description: Job last update datetime in ISO8601 format.
       envs:
         type: object
-        description: Map of ENV variables associated with the job
+        description: Map of ENV variables key values associated with the job.
+      sourceFile:
+        type: string
+        description: The text of the script executed by this job.
       parentJobId:
         type: string
-        description: The parent job ID for the job
+        description: The parent job ID for the job.
       # TODO: Remove once the diagram is rendered natively.
       timingUrl:
         type: string

servers/cromwell/jobs/__init__.py

@@ -1,3 +0,0 @@
-#!/usr/bin/env python
-
-from __main__ import run

servers/cromwell/jobs/models/extended_fields.py

@@ -13,7 +13,7 @@ class ExtendedFields(Model):
     NOTE: This class is auto generated by the swagger code generator program.
     Do not edit the class manually.
     """
-    def __init__(self, user_id=None, status_detail=None, logs=None, last_update=None, envs=None, parent_job_id=None, timing_url=None, tasks=None):
+    def __init__(self, user_id=None, status_detail=None, logs=None, last_update=None, envs=None, source_file=None, parent_job_id=None, timing_url=None, tasks=None):
         """
         ExtendedFields - a model defined in Swagger
 
@@ -27,6 +27,8 @@ def __init__(self, user_id=None, status_detail=None, logs=None, last_update=None
         :type last_update: datetime
         :param envs: The envs of this ExtendedFields.
         :type envs: object
+        :param source_file: The source_file of this ExtendedFields.
+        :type source_file: str
         :param parent_job_id: The parent_job_id of this ExtendedFields.
         :type parent_job_id: str
         :param timing_url: The timing_url of this ExtendedFields.
@@ -40,6 +42,7 @@ def __init__(self, user_id=None, status_detail=None, logs=None, last_update=None
             'logs': object,
             'last_update': datetime,
             'envs': object,
+            'source_file': str,
             'parent_job_id': str,
             'timing_url': str,
             'tasks': List[TaskMetadata]
@@ -51,6 +54,7 @@ def __init__(self, user_id=None, status_detail=None, logs=None, last_update=None
             'logs': 'logs',
             'last_update': 'lastUpdate',
             'envs': 'envs',
+            'source_file': 'sourceFile',
             'parent_job_id': 'parentJobId',
             'timing_url': 'timingUrl',
             'tasks': 'tasks'
@@ -61,6 +65,7 @@ def __init__(self, user_id=None, status_detail=None, logs=None, last_update=None
         self._logs = logs
         self._last_update = last_update
         self._envs = envs
+        self._source_file = source_file
         self._parent_job_id = parent_job_id
         self._timing_url = timing_url
         self._tasks = tasks
@@ -81,7 +86,7 @@ def from_dict(cls, dikt):
     def user_id(self):
         """
         Gets the user_id of this ExtendedFields.
-        The user associated with the job
+        The user associated with the job.
 
         :return: The user_id of this ExtendedFields.
         :rtype: str
@@ -92,7 +97,7 @@ def user_id(self):
     def user_id(self, user_id):
         """
         Sets the user_id of this ExtendedFields.
-        The user associated with the job
+        The user associated with the job.
 
         :param user_id: The user_id of this ExtendedFields.
         :type user_id: str
@@ -127,7 +132,7 @@ def status_detail(self, status_detail):
     def logs(self):
         """
         Gets the logs of this ExtendedFields.
-        Map of type of log file to its file location
+        Map of type of log file to its file location.
 
         :return: The logs of this ExtendedFields.
         :rtype: object
@@ -138,7 +143,7 @@ def logs(self):
     def logs(self, logs):
         """
         Sets the logs of this ExtendedFields.
-        Map of type of log file to its file location
+        Map of type of log file to its file location.
 
         :param logs: The logs of this ExtendedFields.
         :type logs: object
@@ -150,7 +155,7 @@ def logs(self, logs):
     def last_update(self):
         """
         Gets the last_update of this ExtendedFields.
-        Job last update datetime in ISO8601 format
+        Job last update datetime in ISO8601 format.
 
         :return: The last_update of this ExtendedFields.
         :rtype: datetime
@@ -161,7 +166,7 @@ def last_update(self):
     def last_update(self, last_update):
         """
         Sets the last_update of this ExtendedFields.
-        Job last update datetime in ISO8601 format
+        Job last update datetime in ISO8601 format.
 
         :param last_update: The last_update of this ExtendedFields.
         :type last_update: datetime
@@ -173,7 +178,7 @@ def last_update(self, last_update):
     def envs(self):
         """
         Gets the envs of this ExtendedFields.
-        Map of ENV variables associated with the job
+        Map of ENV variables key values associated with the job.
 
         :return: The envs of this ExtendedFields.
         :rtype: object
@@ -184,19 +189,42 @@ def envs(self):
     def envs(self, envs):
         """
         Sets the envs of this ExtendedFields.
-        Map of ENV variables associated with the job
+        Map of ENV variables key values associated with the job.
 
         :param envs: The envs of this ExtendedFields.
         :type envs: object
         """
 
         self._envs = envs
 
+    @property
+    def source_file(self):
+        """
+        Gets the source_file of this ExtendedFields.
+        The text of the script executed by this job.
+
+        :return: The source_file of this ExtendedFields.
+        :rtype: str
+        """
+        return self._source_file
+
+    @source_file.setter
+    def source_file(self, source_file):
+        """
+        Sets the source_file of this ExtendedFields.
+        The text of the script executed by this job.
+
+        :param source_file: The source_file of this ExtendedFields.
+        :type source_file: str
+        """
+
+        self._source_file = source_file
+
     @property
     def parent_job_id(self):
         """
         Gets the parent_job_id of this ExtendedFields.
-        The parent job ID for the job
+        The parent job ID for the job.
 
         :return: The parent_job_id of this ExtendedFields.
         :rtype: str
@@ -207,7 +235,7 @@ def parent_job_id(self):
     def parent_job_id(self, parent_job_id):
         """
         Sets the parent_job_id of this ExtendedFields.
-        The parent job ID for the job
+        The parent job ID for the job.
 
         :param parent_job_id: The parent_job_id of this ExtendedFields.
         :type parent_job_id: str

servers/cromwell/jobs/swagger/swagger.yaml

@@ -371,25 +371,28 @@ definitions:
     properties:
       userId:
         type: "string"
-        description: "The user associated with the job"
+        description: "The user associated with the job."
       statusDetail:
         type: "string"
         description: "Longer text description of the job status."
       logs:
         type: "object"
-        description: "Map of type of log file to its file location"
+        description: "Map of type of log file to its file location."
         properties: {}
       lastUpdate:
         type: "string"
         format: "date-time"
-        description: "Job last update datetime in ISO8601 format"
+        description: "Job last update datetime in ISO8601 format."
       envs:
         type: "object"
-        description: "Map of ENV variables associated with the job"
+        description: "Map of ENV variables key values associated with the job."
         properties: {}
+      sourceFile:
+        type: "string"
+        description: "The text of the script executed by this job."
       parentJobId:
         type: "string"
-        description: "The parent job ID for the job"
+        description: "The parent job ID for the job."
       timingUrl:
         type: "string"
         description: "URL for tasks timing diagram."

servers/dsub/jobs/controllers/capabilities_controller.py

@@ -31,7 +31,8 @@ def get_capabilities():
             is_required=True,
             scopes=[
                 'https://www.googleapis.com/auth/genomics',
-                'https://www.googleapis.com/auth/cloudplatformprojects.readonly'
+                'https://www.googleapis.com/auth/cloudplatformprojects.readonly',
+                'https://www.googleapis.com/auth/devstorage.read_only',
             ])
 
     return capabilities

servers/dsub/jobs/controllers/utils/extensions.py

@@ -11,9 +11,16 @@ def get_extensions(job):
         Returns:
             ExtendedFields: Populated extensions on the job
     """
+    envs = job['envs']
+    script = None
+    if envs and envs['_SCRIPT']:
+        script = envs['_SCRIPT']
+        del envs['_SCRIPT']
+
     return ExtendedFields(
         user_id=job['user-id'],
         status_detail=job.get('status-detail'),
         logs=logs.dsub_to_api(job),
         last_update=job.get('last-update'),
-        envs=job['envs'])
+        envs=job['envs'],
+        source_file=script)

servers/dsub/jobs/controllers/utils/logs.py

@@ -11,8 +11,8 @@ def dsub_to_api(job):
     if job['logging'] and job['logging'].endswith('.log'):
         base_log_path = job['logging'][:-4]
         return {
-            'controller-log': '{}.log'.format(base_log_path),
-            'stderr': '{}-stderr.log'.format(base_log_path),
-            'stdout': '{}-stdout.log'.format(base_log_path),
+            'Controller Log': '{}.log'.format(base_log_path),
+            'Output Log': '{}-stderr.log'.format(base_log_path),
+            'Error Log': '{}-stdout.log'.format(base_log_path),
         }
     return None