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Create a path to directly download the spreadsheet file (and avoid the weird dance on the front end of making an API call to get file data.)

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Fixing pagination.  Seems the front end uses a page_index that is 0 based, and sqlAlchemy prefers to start at 1.
This commit is contained in:
Dan 2022-03-12 16:19:07 -05:00
parent a536a79e87
commit 2fc4b44ef3
6 changed files with 60 additions and 15 deletions
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9
crc/api.yml
View File

@ -293,14 +293,21 @@ paths:
schema:
type: integer
format: int32
- name : auth_token
in : query
required : true
description : User Auth Toeken
schema:
type: string
get:
operationId: crc.api.study.download_logs_for_study
summary: Returns a csv file of logged events that occured within a study
security: [] # Will verify manually with provided Auth Token.
tags:
- Studies
responses:
'200':
description: Returns the csv file of logged events
description: Returns the spreadsheet file of logged events
content:
application/octet-stream:
schema:

9
crc/api/study.py
View File

@ -2,7 +2,6 @@ from datetime import datetime
from flask import g, send_file
from sqlalchemy.exc import IntegrityError
from crc import session
from crc.api.common import ApiError, ApiErrorSchema
from crc.models.study import Study, StudyEventType, StudyModel, StudySchema, StudyForUpdateSchema, \
@ -15,6 +14,7 @@ from crc.services.user_service import UserService
from crc.services.workflow_processor import WorkflowProcessor
from crc.services.workflow_service import WorkflowService
from crc.services.workflow_spec_service import WorkflowSpecService
from crc.api.user import verify_token
import io
@ -117,11 +117,16 @@ def get_study_associates(study_id):
def get_logs_for_study(study_id, body):
task_log_query = TaskLogQuery(**body)
task_log_query.study_id = study_id # Force the study id
return TaskLogQuerySchema().dump(
TaskLoggingService.get_logs_for_study_paginated(study_id, task_log_query))
def download_logs_for_study(study_id):
def download_logs_for_study(study_id, auth_token):
# Download links incorporate an auth token in the request for direct download
if not verify_token(auth_token):
raise ApiError('not_authenticated', 'You need to include an authorization token in the URL with this')
title = f'Study {study_id}'
logs, headers = TaskLoggingService.get_log_data_for_download(study_id)
spreadsheet = SpreadsheetService.create_spreadsheet(logs, headers, title)

29
crc/models/task_log.py
View File

@ -1,6 +1,10 @@
import enum
import urllib
import flask
import marshmallow
from flask import url_for
from marshmallow.fields import Method
from crc import db, ma
from crc.models.study import StudyModel
@ -62,9 +66,10 @@ class TaskLogModelSchema(ma.Schema):
class TaskLogQuery:
"""Encapsulates the paginated queries and results when retrieving and filtering task logs over the
API"""
def __init__(self, code="", level="", user="", page=1, per_page=10,
def __init__(self, study_id=None, code="", level="", user="", page=0, per_page=10,
sort_column=None, sort_reverse=False, items=None,
pages=0, total=0, has_next=False, has_prev=False):
pages=0, total=0, has_next=False, has_prev=False, download_url=None):
self.study_id = study_id # Filter on Study.
self.code = code # Filter on code.
self.level = level # Filter on level.
self.user = user # Filter on user.
@ -77,11 +82,12 @@ class TaskLogQuery:
self.pages = pages
self.has_next = False
self.has_prev = False
self.download_url = None
def update_from_sqlalchemy_paginator(self, paginator):
"""Updates this with results that are returned from the paginator"""
self.items = paginator.items
self.page = paginator.page
self.page = paginator.page - 1
self.per_page = paginator.per_page
self.pages = paginator.pages
self.has_next = paginator.has_next
@ -94,5 +100,18 @@ class TaskLogQuerySchema(ma.Schema):
model = TaskLogModel
fields = ["code", "level", "user",
"page", "per_page", "sort_column", "sort_reverse", "items", "pages", "total",
"has_next", "has_prev"]
items = marshmallow.fields.List(marshmallow.fields.Nested(TaskLogModelSchema))
"has_next", "has_prev", "download_url"]
items = marshmallow.fields.List(marshmallow.fields.Nested(TaskLogModelSchema))
download_url = Method("get_url")
def get_url(self, obj):
token = 'not_available'
if hasattr(obj, 'study_id') and obj.study_id is not None:
file_url = url_for("/v1_0.crc_api_study_download_logs_for_study", study_id=obj.study_id, _external=True)
if hasattr(flask.g, 'user'):
token = flask.g.user.encode_auth_token()
url = file_url + '?auth_token=' + urllib.parse.quote_plus(token)
return url
else:
return ""

2
crc/services/task_logging_service.py
View File

@ -89,7 +89,7 @@ class TaskLoggingService(object):
sort_column = desc(task_log_query.sort_column)
else:
sort_column = task_log_query.sort_column
paginator = sql_query.order_by(sort_column).paginate(task_log_query.page, task_log_query.per_page,
paginator = sql_query.order_by(sort_column).paginate(task_log_query.page + 1, task_log_query.per_page,
error_out=False)
task_log_query.update_from_sqlalchemy_paginator(paginator)
return task_log_query

6
tests/scripts/test_task_logging.py
View File

@ -153,7 +153,7 @@ class TestTaskLogging(BaseTest):
logs = TaskLoggingService().get_logs_for_study_paginated(study.id, TaskLogQuery(per_page=5))
self.assertEqual(40, logs.total)
self.assertEqual(5, len(logs.items), "I can limit results to 5")
self.assertEqual(1, logs.page)
self.assertEqual(0, logs.page)
self.assertEqual(8, logs.pages)
self.assertEqual(5, logs.per_page)
self.assertEqual(True, logs.has_next)
@ -165,4 +165,6 @@ class TestTaskLogging(BaseTest):
logs = TaskLoggingService.get_logs_for_study_paginated(study.id, TaskLogQuery(per_page=5, sort_column="level", sort_reverse=True))
for i in range(0, 5):
self.assertEqual('info', logs.items[i].level, "It is possible to sort on a column")
self.assertEqual('info', logs.items[i].level, "It is possible to sort on a column")

20
tests/study/test_study_download_logs.py
View File

@ -1,7 +1,10 @@
import json
from tests.base_test import BaseTest
from crc import session
from crc.models.task_log import TaskLogModel
from crc.models.task_log import TaskLogModel, TaskLogQuery, TaskLogQuerySchema
from crc.models.user import UserModel
from openpyxl import load_workbook
from io import BytesIO
@ -40,10 +43,19 @@ class TestDownloadLogsForStudy(BaseTest):
'message': 'This is a third message.'}
self.add_log(study_id, workflow.id, task.name, 'empty_workflow', log_data)
rv = self.app.get(f'/v1.0/study/{study_id}/log/download',
content_type="application/json",
headers=self.logged_in_headers())
# Run the query, which should include a 'download_url' link that we can click on.
url = f'/v1.0/study/{workflow.study_id}/log'
task_log_query = TaskLogQuery()
user = session.query(UserModel).filter_by(uid=self.test_uid).first()
rv = self.app.put(url, headers=self.logged_in_headers(user), content_type="application/json",
data=TaskLogQuerySchema().dump(task_log_query))
self.assert_success(rv)
log_query = json.loads(rv.get_data(as_text=True))
self.assertIsNotNone(log_query['download_url'])
# Use the provided link to get the file.
rv = self.app.get(log_query['download_url'])
self.assert_success(rv)
wb = load_workbook(BytesIO(rv.data))
ws = wb.active