From c60ebc49d23623dc945d499fdf4fc87ec509c5cd Mon Sep 17 00:00:00 2001
From: Ambrus Simon <ambrussimon@invenshure.com>
Date: Fri, 23 Jun 2017 19:33:51 +0200
Subject: [PATCH] POST /api/{cname}/{cid}/analyses working (including job=true)
---
api/api.py | 10 +++----
api/dao/containerstorage.py | 51 ++++++++++++++++++----------------
api/handlers/refererhandler.py | 33 +++++++++++-----------
bin/database.py | 2 +-
4 files changed, 50 insertions(+), 46 deletions(-)
diff --git a/api/api.py b/api/api.py
index c4766f1f..d80ea88c 100644
--- a/api/api.py
+++ b/api/api.py
@@ -248,11 +248,11 @@ endpoints = [
route('/<list_name:files>/<name:{fname}>', FileListHandler, m=['GET', 'DELETE']),
route('/<list_name:files>/<name:{fname}>/info', FileListHandler, h='get_info', m=['GET']),
- route( '/analyses>', AnalysesHandler, m=['POST']),
- prefix('/analyses>', [
- route('/<_id:{cid}>', AnalysesHandler, m=['GET', 'DELETE']),
- route('/<_id:{cid}>/files', AnalysesHandler, h='download', m=['GET']),
- route('/<_id:{cid}>/files/<name:{fname}>', AnalysesHandler, h='download', m=['GET']),
+ route( '/analyses', AnalysesHandler, m=['POST']),
+ prefix('/analyses', [
+ route('/<_id:{cid}>', AnalysesHandler, m=['GET', 'DELETE']),
+ route('/<_id:{cid}>/files', AnalysesHandler, h='download', m=['GET']),
+ route('/<_id:{cid}>/files/<name:{fname}>', AnalysesHandler, h='download', m=['GET']),
]),
route('/<list_name:notes>', NotesListHandler, m=['POST']),
diff --git a/api/dao/containerstorage.py b/api/dao/containerstorage.py
index 3a49b47d..ccd2cb00 100644
--- a/api/dao/containerstorage.py
+++ b/api/dao/containerstorage.py
@@ -461,14 +461,19 @@ class AnalysisStorage(ContainerStorage):
@staticmethod
- def default_analysis(origin):
- analysis_obj = {}
- analysis_obj['_id'] = str(bson.objectid.ObjectId())
- analysis_obj['created'] = datetime.datetime.utcnow()
- analysis_obj['modified'] = datetime.datetime.utcnow()
- analysis_obj['user'] = origin.get('id')
-
- return analysis_obj
+ def fill_values(analysis, cont_name, cid, origin):
+ defaults = {
+ 'parent': {
+ 'type': containerutil.singularize(cont_name),
+ 'id': bson.objectid.ObjectId(cid)
+ },
+ '_id': bson.objectid.ObjectId(),
+ 'created': datetime.datetime.utcnow(),
+ 'modified': datetime.datetime.utcnow(),
+ 'user': origin.get('id'),
+ }
+ defaults.update(analysis)
+ return defaults
def create_job_and_analysis(self, cont_name, cid, analysis, job, origin):
@@ -480,11 +485,7 @@ class AnalysisStorage(ContainerStorage):
from ..jobs.gears import validate_gear_config, get_gear
from ..jobs.jobs import Job
- cid = bson.objectid.ObjectId(cid)
-
- default = self.default_analysis(origin)
- default.update(analysis)
- analysis = default
+ self.fill_values(analysis, cont_name, cid, origin)
# Save inputs to analysis and job
inputs = {} # For Job object (map of FileReferences)
@@ -502,33 +503,35 @@ class AnalysisStorage(ContainerStorage):
files.append(file_)
analysis['files'] = files
- result = self._create_el(cid, analysis, None)
- if result.modified_count != 1:
- raise APIStorageException('Element not added in list analyses of container {} {}'.format(cont_name, cid))
+ result = self.create_el(analysis)
+ if not result.acknowledged:
+ raise APIStorageException('Analysis not created for container {} {}'.format(cont_name, cid))
# Prepare job
tags = job.get('tags', [])
if 'analysis' not in tags:
tags.append('analysis')
- gear_id = job['gear_id']
-
# Config manifest check
- gear = get_gear(gear_id)
+ gear = get_gear(job['gear_id'])
if gear.get('gear', {}).get('custom', {}).get('flywheel', {}).get('invalid', False):
raise APIConflictException('Gear marked as invalid, will not run!')
validate_gear_config(gear, job.get('config'))
- destination = containerutil.create_containerreference_from_dictionary({'type': 'analysis', 'id': analysis['_id']})
+ destination = containerutil.create_containerreference_from_dictionary(
+ {'type': 'analysis', 'id': str(analysis['_id'])})
- job = Job(gear_id, inputs, destination=destination, tags=tags, config_=job.get('config'), origin=origin)
+ job = Job(job['gear_id'], inputs,
+ destination=destination, tags=tags, config_=job.get('config'), origin=origin)
job_id = job.insert()
if not job_id:
- raise APIStorageException(500, 'Job not created for analysis {} of container {} {}'.format(analysis['_id'], cont_name, cid))
+ # NOTE #775 remove unusable analysis - until jobs have a 'hold' state
+ self.delete_el(analysis['_id'])
+ raise APIStorageException(500, 'Job not created for analysis of container {} {}'.format(cont_name, cid))
- result = self._update_el(cid, {'_id': analysis['_id']}, {'job': job_id}, None)
- return { 'analysis': analysis, 'job_id':job_id, 'job': job}
+ result = self.update_el(analysis['_id'], {'job': job_id}, None)
+ return {'analysis': analysis, 'job_id': job_id, 'job': job}
@staticmethod
diff --git a/api/handlers/refererhandler.py b/api/handlers/refererhandler.py
index eeff1063..d1675f8f 100644
--- a/api/handlers/refererhandler.py
+++ b/api/handlers/refererhandler.py
@@ -50,7 +50,8 @@ class RefererHandler(base.RequestHandler):
elif self.public_request:
return containerauth.public_request(self, container=parent_container)
else:
- return self.permchecker(self, parent_container=parent_container)
+ # NOTE The handler (self) is passed implicitly
+ return self.permchecker(parent_container=parent_container)
class AnalysesHandler(RefererHandler):
@@ -69,26 +70,26 @@ class AnalysesHandler(RefererHandler):
analyses are only allowed at the session level.
"""
parent = self.storage.get_parent(cont_name, cid)
- permchecker = self._get_permchecker(parent)
+ permchecker = self.get_permchecker(parent)
permchecker(noop)('POST')
if self.is_true('job'):
- if cont_name == 'sessions':
- payload = self.request.json_body
- self.input_validator(payload.get('analysis', {}), 'POST')
- analysis = payload.get('analysis')
- job = payload.get('job')
- if job is None or analysis is None:
- self.abort(400, 'JSON body must contain map for "analysis" and "job"')
- result = self.storage.create_job_and_analysis(cont_name, cid, analysis, job, self.origin)
- return {'_id': result['analysis']['_id']}
- else:
+ if cont_name != 'sessions':
self.abort(400, 'Analysis created via a job must be at the session level')
- payload = upload.process_upload(self.request, upload.Strategy.analysis, origin=self.origin)
- analysis = self.storage.default_analysis(self.origin)
- analysis.update(payload)
- result = self.storage.exec_op('POST', payload=analysis)
+ payload = self.request.json_body
+ analysis = payload.get('analysis')
+ job = payload.get('job')
+ if not analysis or not job:
+ self.abort(400, 'JSON body must contain map for "analysis" and "job"')
+ self.input_validator(analysis, 'POST')
+ result = self.storage.create_job_and_analysis(cont_name, cid, analysis, job, self.origin)
+ return {'_id': result['analysis']['_id']}
+
+ analysis = upload.process_upload(self.request, upload.Strategy.analysis, origin=self.origin)
+ self.storage.fill_values(analysis, cont_name, cid, self.origin)
+ self.input_validator(analysis, 'POST')
+ result = self.storage.create_el(analysis)
if result.acknowledged:
return {'_id': result.inserted_id}
diff --git a/bin/database.py b/bin/database.py
index c912fcc0..30e7005b 100755
--- a/bin/database.py
+++ b/bin/database.py
@@ -20,7 +20,7 @@ from api.jobs.jobs import Job
from api.jobs import gears
from api.types import Origin
-CURRENT_DATABASE_VERSION = 31 # An int that is bumped when a new schema change is made
+CURRENT_DATABASE_VERSION = 32 # An int that is bumped when a new schema change is made
def get_db_version():
--
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