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90339fd
skeleton for demoing
squirrelo Mar 20, 2015
72267a0
add conformation to removing proc data
squirrelo Mar 25, 2015
10f077d
Merge branch 'master' of https://github.com/biocore/qiita into cart-a…
squirrelo Mar 28, 2015
f1ca570
add patch to create default analyses for all existing users
squirrelo Mar 28, 2015
e362c25
add default analysis on user creation
squirrelo Mar 28, 2015
cfe9ba2
streamline UI for cart
squirrelo Mar 30, 2015
28f8480
further refining IU
squirrelo Mar 30, 2015
f0c3f80
add default analyses using only SQL
squirrelo Mar 31, 2015
6d30936
changes to tests to reflect patch
squirrelo Mar 31, 2015
4f3756f
fix more tests, add analysis_workflow steps for carts
squirrelo Mar 31, 2015
b5bf4ed
update user private_analyses to ignore default cart
squirrelo Mar 31, 2015
68488c7
update test again to reflect change
squirrelo Mar 31, 2015
90b3de2
merge upstream/master
squirrelo Apr 1, 2015
bd3d513
Merge branch 'master' of https://github.com/biocore/qiita into cart-a…
squirrelo Apr 2, 2015
f5026f8
move default analysis pull to user object
squirrelo Apr 2, 2015
874632b
implement the default_analysis in qiita_pet
squirrelo Apr 2, 2015
ddf2ff4
more comments addressed
squirrelo Apr 2, 2015
1dc1440
pep8
squirrelo Apr 2, 2015
cf1123f
remove magic numbers from tests
squirrelo Apr 2, 2015
15c71dc
replace processed_date retriveal
squirrelo Apr 3, 2015
8e129e6
add info modal for proc data
squirrelo Apr 3, 2015
e784006
more UI changes
squirrelo Apr 3, 2015
d7b4778
couple small UI changes
squirrelo Apr 3, 2015
ba42c6a
use info glyph
squirrelo Apr 3, 2015
dc9ff3a
add from_default flag for analysis creation
squirrelo Apr 6, 2015
2274b0d
queue analysis creation
squirrelo Apr 6, 2015
d8f4738
Merge branch 'cart-analysis-changes' into create-analysis-from-cart
squirrelo Apr 6, 2015
bc9321a
fix queues and tests
squirrelo Apr 6, 2015
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remove magic numbers from tests
  • Loading branch information
squirrelo committed Apr 2, 2015
commit cf1123f532d17149f8dd576b0d4bc066b41f9025
42 changes: 22 additions & 20 deletions qiita_db/test/test_analysis.py
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
from qiita_db.job import Job
from qiita_db.user import User
from qiita_db.exceptions import QiitaDBStatusError
from qiita_db.util import get_mountpoint
from qiita_db.util import get_mountpoint, get_count
from qiita_db.study import Study, StudyPerson
from qiita_db.data import ProcessedData
from qiita_db.metadata_template import SampleTemplate
Expand Down Expand Up @@ -92,36 +92,36 @@ def test_has_access_no_access(self):
def test_create(self):
sql = "SELECT EXTRACT(EPOCH FROM NOW())"
time1 = float(self.conn_handler.execute_fetchall(sql)[0][0])

new_id = get_count("qiita.analysis") + 1
new = Analysis.create(User("admin@foo.bar"), "newAnalysis",
"A New Analysis")
self.assertEqual(new.id, 7)
self.assertEqual(new.id, new_id)
sql = ("SELECT analysis_id, email, name, description, "
"analysis_status_id, pmid, EXTRACT(EPOCH FROM timestamp) "
"FROM qiita.analysis WHERE analysis_id = 7")
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs[0][:-1], [7, 'admin@foo.bar', 'newAnalysis',
"FROM qiita.analysis WHERE analysis_id = %s")
obs = self.conn_handler.execute_fetchall(sql, [new_id])
self.assertEqual(obs[0][:-1], [new_id, 'admin@foo.bar', 'newAnalysis',
'A New Analysis', 1, None])
self.assertTrue(time1 < float(obs[0][-1]))

def test_create_parent(self):
sql = "SELECT EXTRACT(EPOCH FROM NOW())"
time1 = float(self.conn_handler.execute_fetchall(sql)[0][0])

new_id = get_count("qiita.analysis") + 1
new = Analysis.create(User("admin@foo.bar"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.id, 7)
self.assertEqual(new.id, new_id)
sql = ("SELECT analysis_id, email, name, description, "
"analysis_status_id, pmid, EXTRACT(EPOCH FROM timestamp) "
"FROM qiita.analysis WHERE analysis_id = 7")
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs[0][:-1], [7, 'admin@foo.bar', 'newAnalysis',
"FROM qiita.analysis WHERE analysis_id = %s")
obs = self.conn_handler.execute_fetchall(sql, [new_id])
self.assertEqual(obs[0][:-1], [new_id, 'admin@foo.bar', 'newAnalysis',
'A New Analysis', 1, None])
self.assertTrue(time1 < float(obs[0][-1]))

sql = "SELECT * FROM qiita.analysis_chain WHERE child_id = 7"
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs, [[1, 7]])
sql = "SELECT * FROM qiita.analysis_chain WHERE child_id = %s"
obs = self.conn_handler.execute_fetchall(sql, [new_id])
self.assertEqual(obs, [[1, new_id]])

def test_retrieve_owner(self):
self.assertEqual(self.analysis.owner, "test@foo.bar")
Expand Down Expand Up @@ -242,21 +242,23 @@ def test_retrieve_biom_tables_none(self):
self.assertEqual(new.biom_tables, None)

def test_set_step(self):
new_id = get_count("qiita.analysis") + 1
new = Analysis.create(User("admin@foo.bar"), "newAnalysis",
"A New Analysis", Analysis(1))
new.step = 2
sql = "SELECT * FROM qiita.analysis_workflow WHERE analysis_id = 7"
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs, [[7, 2]])
sql = "SELECT * FROM qiita.analysis_workflow WHERE analysis_id = %s"
obs = self.conn_handler.execute_fetchall(sql, [new_id])
self.assertEqual(obs, [[new_id, 2]])

def test_set_step_twice(self):
new_id = get_count("qiita.analysis") + 1
new = Analysis.create(User("admin@foo.bar"), "newAnalysis",
"A New Analysis", Analysis(1))
new.step = 2
new.step = 4
sql = "SELECT * FROM qiita.analysis_workflow WHERE analysis_id = 7"
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs, [[7, 4]])
sql = "SELECT * FROM qiita.analysis_workflow WHERE analysis_id = %s"
obs = self.conn_handler.execute_fetchall(sql, [new_id])
self.assertEqual(obs, [[new_id, 4]])

def test_retrieve_step(self):
new = Analysis.create(User("admin@foo.bar"), "newAnalysis",
Expand Down
11 changes: 6 additions & 5 deletions qiita_db/test/test_job.py
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
from qiita_core.util import qiita_test_checker
from qiita_db.job import Job, Command
from qiita_db.user import User
from qiita_db.util import get_mountpoint
from qiita_db.util import get_mountpoint, get_count
from qiita_db.analysis import Analysis
from qiita_db.exceptions import (QiitaDBDuplicateError, QiitaDBStatusError,
QiitaDBUnknownIDError)
Expand Down Expand Up @@ -219,16 +219,17 @@ def test_create_exists(self):

def test_create_exists_return_existing(self):
"""Makes sure creation doesn't duplicate a job by returning existing"""
new_id = get_count("qiita.analysis") + 1
Analysis.create(User("demo@microbio.me"), "new", "desc")
self.conn_handler.execute(
"INSERT INTO qiita.analysis_sample "
"(analysis_id, processed_data_id, sample_id) VALUES "
"(7, 1, '1.SKB8.640193'), (7, 1, '1.SKD8.640184'), "
"(7, 1, '1.SKB7.640196'), (7, 1, '1.SKM9.640192'), "
"(7, 1, '1.SKM4.640180')")
"({0}, 1, '1.SKB8.640193'), ({0}, 1, '1.SKD8.640184'), "
"({0}, 1, '1.SKB7.640196'), ({0}, 1, '1.SKM9.640192'), "
"({0}, 1, '1.SKM4.640180')".format(new_id))
new = Job.create("18S", "Beta Diversity",
{"--otu_table_fp": 1, "--mapping_fp": 1},
Analysis(7), return_existing=True)
Analysis(new_id), return_existing=True)
self.assertEqual(new.id, 2)

def test_retrieve_datatype(self):
Expand Down