6 Commits

Author SHA1 Message Date
cf1f707243 update test plan with TOC + autoformatting changes from pandoc 2018-08-24 10:26:33 -07:00
c0f087a549 fix document title 2018-08-24 10:23:02 -07:00
907e70f953 add table of contents and autoformatting.
This commit was the result of running a pandocs command
to clean up the formatting and generate a table of contents
for the markdown document.
2018-08-24 10:21:48 -07:00
96e4e7e662 improve local tests idea 2018-08-23 12:44:54 -07:00
c790babe80 flesh out test plans in greater detail 2018-08-23 12:36:29 -07:00
adaf25d751 add QE and testing readmes 2018-08-23 11:18:45 -07:00
4 changed files with 554 additions and 275 deletions

View File

@@ -21,8 +21,6 @@ import dateutil.parser
from whoosh.qparser import MultifieldParser, QueryParser
from whoosh.analysis import StemmingAnalyzer
from whoosh.qparser.dateparse import DateParserPlugin
from whoosh import fields, index
"""
@@ -182,38 +180,30 @@ class Search:
# is defined.
schema = Schema(
id = fields.ID(stored=True, unique=True),
kind = fields.ID(stored=True),
id = ID(stored=True, unique=True),
kind = ID(stored=True),
created_time = fields.DATETIME(stored=True),
modified_time = fields.DATETIME(stored=True),
indexed_time = fields.DATETIME(stored=True),
created_time = ID(stored=True),
modified_time = ID(stored=True),
indexed_time = ID(stored=True),
title = fields.TEXT(stored=True, field_boost=100.0),
title = TEXT(stored=True, field_boost=100.0),
url = ID(stored=True, unique=True),
url = fields.ID(stored=True),
mimetype=ID(stored=True),
owner_email=ID(stored=True),
owner_name=TEXT(stored=True),
mimetype = fields.TEXT(stored=True),
repo_name=TEXT(stored=True),
repo_url=ID(stored=True),
owner_email = fields.ID(stored=True),
owner_name = fields.TEXT(stored=True),
# mainly for email threads, groups.io, hypothesis
group = fields.ID(stored=True),
repo_name = fields.TEXT(stored=True),
repo_url = fields.ID(stored=True),
github_user = fields.TEXT(stored=True),
tags = fields.KEYWORD(commas=True,
stored=True,
lowercase=True),
github_user=TEXT(stored=True),
# comments only
issue_title = fields.TEXT(stored=True, field_boost=100.0),
issue_url = fields.ID(stored=True),
issue_title=TEXT(stored=True, field_boost=100.0),
issue_url=ID(stored=True),
content = fields.TEXT(stored=True, analyzer=stemming_analyzer)
content=TEXT(stored=True, analyzer=stemming_analyzer)
)
@@ -253,22 +243,17 @@ class Search:
writer.delete_by_term('id',item['id'])
# Index a plain google drive file
created_time = dateutil.parser.parse(item['createdTime'])
modified_time = dateutil.parser.parse(item['modifiedTime'])
indexed_time = datetime.now().replace(microsecond=0)
try:
writer.add_document(
id = item['id'],
kind = 'gdoc',
created_time = created_time,
modified_time = modified_time,
indexed_time = indexed_time,
created_time = item['createdTime'],
modified_time = item['modifiedTime'],
indexed_time = datetime.now().replace(microsecond=0).isoformat(),
title = item['name'],
url = item['webViewLink'],
mimetype = mimetype,
owner_email = item['owners'][0]['emailAddress'],
owner_name = item['owners'][0]['displayName'],
group='',
repo_name='',
repo_url='',
github_user='',
@@ -276,9 +261,6 @@ class Search:
issue_url='',
content = content
)
except ValueError as e:
print(repr(e))
print(" > XXXXXX Failed to index Google Drive file \"%s\""%(item['name']))
else:
@@ -332,7 +314,7 @@ class Search:
)
assert output == ""
except RuntimeError:
print(" > XXXXXX Failed to index Google Drive document \"%s\""%(item['name']))
print(" > XXXXXX Failed to index document \"%s\""%(item['name']))
# If export was successful, read contents of markdown
@@ -360,22 +342,17 @@ class Search:
else:
print(" > Creating a new record")
try:
created_time = dateutil.parser.parse(item['createdTime'])
modified_time = dateutil.parser.parse(item['modifiedTime'])
indexed_time = datetime.now()
writer.add_document(
id = item['id'],
kind = 'gdoc',
created_time = created_time,
modified_time = modified_time,
indexed_time = indexed_time,
created_time = item['createdTime'],
modified_time = item['modifiedTime'],
indexed_time = datetime.now().replace(microsecond=0).isoformat(),
title = item['name'],
url = item['webViewLink'],
mimetype = mimetype,
owner_email = item['owners'][0]['emailAddress'],
owner_name = item['owners'][0]['displayName'],
group='',
repo_name='',
repo_url='',
github_user='',
@@ -383,10 +360,6 @@ class Search:
issue_url='',
content = content
)
except ValueError as e:
print(repr(e))
print(" > XXXXXX Failed to index Google Drive file \"%s\""%(item['name']))
@@ -420,14 +393,13 @@ class Search:
issue_comment_content += comment.body.rstrip()
issue_comment_content += "\n"
# Now create the actual search index record.
# Now create the actual search index record
created_time = clean_timestamp(issue.created_at)
modified_time = clean_timestamp(issue.updated_at)
indexed_time = clean_timestamp(datetime.now())
# Add one document per issue thread,
# containing entire text of thread.
created_time = issue.created_at
modified_time = issue.updated_at
indexed_time = datetime.now()
try:
writer.add_document(
id = issue.html_url,
kind = 'issue',
@@ -439,7 +411,6 @@ class Search:
mimetype='',
owner_email='',
owner_name='',
group='',
repo_name = repo_name,
repo_url = repo_url,
github_user = issue.user.login,
@@ -447,9 +418,6 @@ class Search:
issue_url = issue.html_url,
content = issue_comment_content
)
except ValueError as e:
print(repr(e))
print(" > XXXXXX Failed to index Github issue \"%s\""%(issue.title))
@@ -479,8 +447,7 @@ class Search:
print(" > XXXXXXXX Failed to find file info.")
return
indexed_time = datetime.now()
indexed_time = clean_timestamp(datetime.now())
if fext in MARKDOWN_EXTS:
print("Indexing markdown doc %s from repo %s"%(fname,repo_name))
@@ -509,19 +476,17 @@ class Search:
usable_url = "https://github.com/%s/blob/master/%s"%(repo_name, fpath)
# Now create the actual search index record
try:
writer.add_document(
id = fsha,
kind = 'markdown',
created_time = None,
modified_time = None,
created_time = '',
modified_time = '',
indexed_time = indexed_time,
title = fname,
url = usable_url,
mimetype='',
owner_email='',
owner_name='',
group='',
repo_name = repo_name,
repo_url = repo_url,
github_user = '',
@@ -529,11 +494,6 @@ class Search:
issue_url = '',
content = content
)
except ValueError as e:
print(repr(e))
print(" > XXXXXX Failed to index Github markdown file \"%s\""%(fname))
else:
print("Indexing github file %s from repo %s"%(fname,repo_name))
@@ -541,19 +501,17 @@ class Search:
key = fname+"_"+fsha
# Now create the actual search index record
try:
writer.add_document(
id = key,
kind = 'ghfile',
created_time = None,
modified_time = None,
created_time = '',
modified_time = '',
indexed_time = indexed_time,
title = fname,
url = repo_url,
mimetype='',
owner_email='',
owner_name='',
group='',
repo_name = repo_name,
repo_url = repo_url,
github_user = '',
@@ -561,9 +519,6 @@ class Search:
issue_url = '',
content = ''
)
except ValueError as e:
print(repr(e))
print(" > XXXXXX Failed to index Github file \"%s\""%(fname))
@@ -577,32 +532,20 @@ class Search:
Use a Github file API record to add a filename
to the search index.
"""
if 'created_time' in d.keys() and d['created_time'] is not None:
created_time = d['created_time']
else:
created_time = None
if 'modified_time' in d.keys() and d['modified_time'] is not None:
modified_time = d['modified_time']
else:
modified_time = None
indexed_time = datetime.now()
indexed_time = clean_timestamp(datetime.now())
# Now create the actual search index record
try:
writer.add_document(
id = d['permalink'],
kind = 'emailthread',
created_time = created_time,
modified_time = modified_time,
created_time = '',
modified_time = '',
indexed_time = indexed_time,
title = d['subject'],
url = d['permalink'],
mimetype='',
owner_email='',
owner_name=d['original_sender'],
group=d['subgroup'],
repo_name = '',
repo_url = '',
github_user = '',
@@ -610,9 +553,7 @@ class Search:
issue_url = '',
content = d['content']
)
except ValueError as e:
print(repr(e))
print(" > XXXXXX Failed to index Groups.io thread \"%s\""%(d['subject']))
@@ -690,10 +631,10 @@ class Search:
full_items[f['id']] = f
## Shorter:
#break
# Longer:
if nextPageToken is None:
break
## Longer:
#if nextPageToken is None:
# break
writer = self.ix.writer()
@@ -701,7 +642,7 @@ class Search:
temp_dir = tempfile.mkdtemp(dir=os.getcwd())
print("Temporary directory: %s"%(temp_dir))
try:
# Drop any id in indexed_ids
# not in remote_ids
@@ -729,13 +670,6 @@ class Search:
self.add_drive_file(writer, item, temp_dir, config, update=False)
count += 1
except Exception as e:
print("ERROR: While adding Google Drive files to search index")
print("-"*40)
print(repr(e))
print("-"*40)
print("Continuing...")
pass
print("Cleaning temporary directory: %s"%(temp_dir))
subprocess.call(['rm','-fr',temp_dir])
@@ -1140,7 +1074,7 @@ class Search:
elif doctype=='issue':
item_keys = ['title','repo_name','repo_url','url','created_time','modified_time']
elif doctype=='emailthread':
item_keys = ['title','owner_name','url','created_time','modified_time']
item_keys = ['title','owner_name','url']
elif doctype=='ghfile':
item_keys = ['title','repo_name','repo_url','url']
elif doctype=='markdown':
@@ -1157,6 +1091,10 @@ class Search:
for r in results:
d = {}
for k in item_keys:
if k=='created_time' or k=='modified_time':
#d[k] = r[k]
d[k] = dateutil.parser.parse(r[k]).strftime("%Y-%m-%d")
else:
d[k] = r[k]
json_results.append(d)
@@ -1170,9 +1108,7 @@ class Search:
query_string = " ".join(query_list)
query = None
if ":" in query_string:
query = QueryParser("content", self.schema)
query.add_plugin(DateParserPlugin(free=True))
query = query.parse(query_string)
query = QueryParser("content", self.schema).parse(query_string)
elif len(fields) == 1 and fields[0] == "filename":
pass
elif len(fields) == 2:
@@ -1180,12 +1116,9 @@ class Search:
else:
# If the user does not specify a field,
# these are the fields that are actually searched
fields = ['title', 'content','owner_name','owner_email','url','created_date','modified_date']
fields = ['title', 'content','owner_name','owner_email','url']
if not query:
query = MultifieldParser(fields, schema=self.ix.schema)
query.add_plugin(DateParserPlugin(free=True))
query = query.parse(query_string)
#query = MultifieldParser(fields, schema=self.ix.schema).parse(query_string)
query = MultifieldParser(fields, schema=self.ix.schema).parse(query_string)
parsed_query = "%s" % query
print("query: %s" % parsed_query)
results = searcher.search(query, terms=False, scored=True, groupedby="kind")

View File

@@ -1,7 +1,5 @@
import requests, os, re
from bs4 import BeautifulSoup
import dateutil.parser
import datetime
class GroupsIOException(Exception):
pass
@@ -66,7 +64,7 @@ class GroupsIOArchivesCrawler(object):
## Short circuit
## for debugging purposes
break
#break
return subgroups
@@ -253,7 +251,7 @@ class GroupsIOArchivesCrawler(object):
subject = soup.find('title').text
# Extract information for the schema:
# - permalink for thread (done above)
# - permalink for thread (done)
# - subject/title (done)
# - original sender email/name (done)
# - content (done)
@@ -268,35 +266,11 @@ class GroupsIOArchivesCrawler(object):
pass
else:
# found an email!
# this is a maze, not amazing.
# thanks groups.io!
# this is a maze, thanks groups.io
td = tr.find('td')
sender_divrow = td.find('div',{'class':'row'})
sender_divrow = sender_divrow.find('div',{'class':'pull-left'})
divrow = td.find('div',{'class':'row'}).find('div',{'class':'pull-left'})
if (i+1)==1:
original_sender = sender_divrow.text.strip()
date_divrow = td.find('div',{'class':'row'})
date_divrow = date_divrow.find('div',{'class':'pull-right'})
date_divrow = date_divrow.find('font',{'class':'text-muted'})
date_divrow = date_divrow.find('script').text
try:
time_seconds = re.search(' [0-9]{1,} ',date_divrow).group(0)
time_seconds = time_seconds.strip()
# Thanks groups.io for the weird date formatting
time_seconds = time_seconds[:10]
mmicro_seconds = time_seconds[10:]
if (i+1)==1:
created_time = datetime.datetime.utcfromtimestamp(int(time_seconds))
modified_time = datetime.datetime.utcfromtimestamp(int(time_seconds))
else:
modified_time = datetime.datetime.utcfromtimestamp(int(time_seconds))
except AttributeError:
created_time = None
modified_time = None
original_sender = divrow.text.strip()
for div in td.find_all('div'):
if div.has_attr('id'):
@@ -325,10 +299,7 @@ class GroupsIOArchivesCrawler(object):
thread = {
'permalink' : permalink,
'created_time' : created_time,
'modified_time' : modified_time,
'subject' : subject,
'subgroup' : subgroup_name,
'original_sender' : original_sender,
'content' : full_content
}
@@ -353,13 +324,11 @@ class GroupsIOArchivesCrawler(object):
results = []
for row in rows:
# This is where we extract
# a list of thread titles
# and corresponding links.
# We don't care about anything except title and ugly link
subject = row.find('span',{'class':'subject'})
title = subject.get_text()
link = row.find('a')['href']
#print(title)
results.append((title,link))
return results

181
quality/Readme.md Normal file
View File

@@ -0,0 +1,181 @@
# Centillion Quality Engineering Plan
Table of Contents
-------
* [Centillion Quality Engineering Plan](#centillion-quality-engineering-plan)
* [Summary](#summary)
* [Tracking Bugs and Issues](#tracking-bugs-and-issues)
* [Branches, Versioning, and Git Workflow](#branches-versioning-and-git-workflow)
* [Communication and Mailing Lists](#communication-and-mailing-lists)
* [Checklists](#checklists)
* [Documentation](#documentation)
* [Configuration Management Tools](#configuration-management-tools)
* [Tests](#tests)
* [Code Reviews](#code-reviews)
* [Formal Release Process](#formal-release-process)
* [Continual Process Improvement](#continual-process-improvement)
Summary
-------
This document contains a quality engineering plan for centillion, the
Data Commons search engine.
Tracking Bugs and Issues
------------------------
We utilize the [issues
section](https://github.com/dcppc/centillion/issues) of the centillion
repository to keep track of bugs and feature requests.
Branches, Versioning, and Git Workflow
--------------------------------------
All code is kept under version control in the
[dcppc/centillion](https://github.com/dcppc/centillion) Github
repository.
**Primary Git Branches:**
We utillize a git branch pattern that has two primary branches: a
development branch and a stable branch.
- The primary **development branch** is `dcppc` and is actively
developed and deployed to <https://betasearch.nihdatacommons.us>.
- The primary **stable branch** is `releases/v1` and is stable and
deployed to <https://search.nihdatacommons.us>.
All tagged versions of Centillion exist on the stable branch. Only
tagged versions of centillion are run on
<https://search.nihdatacommons.us>.
**Other Branches:**
Features are developed by creating a new branch from `dcppc`, working on
the feature, and opening a pull request. When the pull request is
approved, it can be merged into the `dcppc` branch.
When features have accumulated and a new version is ready, a new
pre-release branch will be made to prepare for a new release. When the
pre-release branch is ready, it is merged into the stable branch in a
single merge commit and a new version of centillion is tagged. The new
version is deployed on <https://search.nihdatacommons.us>.
Commits to fix bugs (hotfixes) may need to be applied to both the stable
and development branches. In this case, a hotfix branch should be
created from the head commit of the stable branch, and the appropriate
changes should be made on the branch. A pull request should be opened to
merge the hotfix into the release branch. A second pull request should
be opened to merge the hotfix into the development branch. Once the
hotfix is merged into the stable branch, a new version should be tagged.
Communication and Mailing Lists
-------------------------------
- No mailing list currently exists for centillion.
- Github issues are the primary form of communication about
development of centillion. This is the best method for communicating
bug reports or detailed information.
- The Send Feedback button on the centillion page is the primary way
of getting quick feedback from users about the search engine.
- The [\#centillion](https://nih-dcppc.slack.com/messages/CCD64QD6G)
Slack channel in the DCPPC slack workspace is the best place for
conversations about centillion (providing feedback, answering quick
questions, etc.)
Checklists
----------
We plan to utilize the Wiki feature of the Github repository to develop
checlists:
- Checklist for releases
- Checklist for deployment of https://search.nihdatacommons.us nginx
etc.
Documentation
-------------
The documentation is a pile of markdown documents, turned into a static
site using mkdocs.
Configuration Management Tools
------------------------------
We do not currently utilize any configuration management software,
because centillion is not packaged as an importable Python module.
Packaging centillion is a future goal that is closely related to the
need to improve and modularize the internal search schema/document type
abstraction. These improvements would allow the types of collections
being indexed to be separated from "core centillion", and core
centillion would be packaged.
Tests
-----
See (ref) for a full test plan with more detail.
Summary of test plan:
- Implement tests for the four major pages/components
- Login/authentication
- Search
- Master List
- Control Panel
- Test authentication with two bot accounts (yammasnake and florence
python)
- Separate frontend and backend tests
- Add a test flag in the flask config file to change the backend
behavior of the server
Code Reviews
------------
CI tests will be implemented for all pull requests.
Pull requests to the **stable branch** have the following checks in
place:
- PRs to the stable branch require at least 1 PR review
- PRs to the stable branch must pass CI tests
Pull requests to the **development branch** have the following checks in
place:
- PRs to the development branch must pass CI tests
Formal Release Process
----------------------
In order to ensure a stable, consistent product, we utilize the
branching pattern described above to implement new features in the
development branch and test them out on
<https://betasearch.nihdatacommons.us>.
Once features and bug fixes have been tested and reviewed internally,
they are ready to be deployed. A new pre-release branch is created from
the development branch. The pre-release branch has a feature freeze in
place. Changes are made to the pre-release branch to prepare it for the
next major version release.
When the pre-release branch is finished, it is merged into the stable
branch. The head commit of the stable version is tagged with the lastest
release number.
Finally, the new version is deployed on
<https://search.nihdatacommons.us>.
Continual Process Improvement
-----------------------------
We will utilize the centillion wiki on Github to keep track of repeated
processes and opportunities for improvement. Feedback and ideas for
process improvement can also be submitted via Github issues.

196
tests/Readme.md Normal file
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@@ -0,0 +1,196 @@
Centillion Tests
================
Table of Contents
------------------
* [Centillion Tests](#centillion-tests)
* [Test Plan](#test-plan)
* [Local Tests](#local-tests)
* [Short Tests](#short-tests)
* [Long Tests](#long-tests)
* [Credentials](#credentials)
* [Detailed Description of Tests](#detailed-description-of-tests)
* [Authentication Layer Tests](#authentication-layer-tests)
* [Search Function Tests](#search-function-tests)
* [Master List Endpoint Tests](#master-list-endpoint-tests)
* [Control Panel Endpoint Tests](#control-panel-endpoint-tests)
* [Continuous Integration Plan](#continuous-integration-plan)
* [Procedure/Checklist](#procedurechecklist)
Test Plan
---------
Related: <https://github.com/dcppc/centillion/issues/82>
The test suite for centillion needs to check each of the major
components of centillion, as well as check the authentication mechanism
using multiple login credentials.
We implement the following checks:
1. Check authentication mechanism(s) (yamasnake and florence python)
2. Check search function
3. Check master list endpoint
4. Check control panel endpoint
5. Check update search index endpoints
The tests are written such that the back end and front end are tested
separately.
We need also need different tiers of tests, so we don't max out API
calls by making lots of commits to multiple PRs.
We have three tiers of tests: \* Local tests - quick tests for CI, no
API calls \* Short tests - tests using dummy API accounts \* Long tests
- tests using DCPPC API accounts
### Local Tests
Local tests can be run locally without any interaction with APIs. These
will still utilize centillion's search schema, but will load the search
index with fake documents rather than fetching them from an API.
Uncle Archie, which runs CI tests, runs local tests only (unless you
request it to run short test or long test.)
### Short Tests
Short tests utilize credentials for bot accounts that have intentionally
been set up to have a "known" corpus of test documents. These would
provide unit-style tests for centillion - are the mechanics of indexing
a particular type of document from a particular API working?
### Long Tests
Long tests are indexing the real deal, utilizing the credentials used in
the final production centillion. This test takes longer but is more
likely to catch corner cases specific to the DCPPC documents.
Credentials
-----------
Running tests on centillion requires multiple sets of credentials. Let's
lay out what is needed:
- The Flask app requires a token/secret token API key pair to allow
users to authenticate through Github and confirm they are members of
the DCPPC organization. This OAuth application is owned by Charles
Reid (@charlesreid1).
- The search index needs a Github access token so that it can
interface with the Github API to index files and issues. This access
token is specified (along with other secrets) in the Flask
configuration file. The access key comes from Florence Python
(@fp9695253).
- The search index also requires a Google Drive API access token. This
must be an access token for a user who has authenticated with the
Centillion Google Drive OAuth application. This access token comes
from <mailroom@nihdatacommons.com>.
- The search index requires API credentials for any other APIs
associated with other document collections (Groups.io, Hypothesis,
Disqus).
- The backend test requires the credentials provided to Flask.
- The frontend test (Selenium) needs two Github username/passwords:
one for Florence Python (@fp9695253) and one for Yamma Snake
(@yammasnake). These are required to simulate the user
authenticating with Github through the browser.
- The frontend test credentials are a special case.
- The frontend tests expect credentials to come from environment
variables.
- These environment variables get passed in at test time.
- Tests are all run on [Uncle
Archie](https://github.com/dcppc/uncle-archie).
- Uncle Archie already has to protect a confidential config file
containing Github credentials, so add additional credentials for
frontend tests there.
- Logical separation: these credentials are not needed to
*operate* centillion, these credentials are needed to *test*
centillion
- Uncle Archie already requires github credentials, already
protects sensitive info.
- Google Drive requiring its own credentials file on disk is a
pain.
In summary: tests use the `config_flask.py` and `config_centillion.py`
files to provide it with the API keys it needs and to instruct it on
what to index. The credentials and config files will control what the
search index will actually index. The Uncle Archie CI tester config file
contains the credentials needed to run frontend tests (check the
login/authentication layer).
Detailed Description of Tests
-----------------------------
### Authentication Layer Tests
Frontend tests run as Florence Python:
- Can we log in via github and reach centillion
- Can we reach the control panel
Frontend tests run as Yamma Snake (DCPPC member):
- Can we log in via github and reach centillion
- Can we reach the control panel
### Search Function Tests
Frontend tests:
- Can we enter something into search box and submit
- Can we sort the results
- Do the results look okay
Backend tests:
- Load the search index and run a query using whoosh API
### Master List Endpoint Tests
Frontend tests:
- Can we get to the master list page
- Can we sort the results
- Do the results look okay
Backend tests:
- Check the output of the `/list` API endpoint
### Control Panel Endpoint Tests
Frontend tests:
- Can we get to the control panel page
- Can we click the button to trigger an indexing event
Backend tests:
- Trigger a re-index of the search index from the backend.
### Continuous Integration Plan
Tests are automatically run using Uncle Archie for continuous
integration and deployment.
Procedure/Checklist
-------------------
Pre-release procedure:
- prepare to run all test
- run short tests
- deploy to beta
- run long tests
- test out