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Relaxing metadata requirements #1021

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ee28b13
Adding patch
josenavas Mar 28, 2015
5c60e61
Fixing populate test db
josenavas Mar 28, 2015
39d2429
Fixing base objects
josenavas Mar 28, 2015
5cc71a0
New metadata template code layout
josenavas Mar 28, 2015
1b8dbdb
Improving base class and tests
josenavas Mar 28, 2015
2bc0117
Solving SampleTemplate creation issues
josenavas Mar 29, 2015
4212b04
Adding few files that I forgot on the previous commit
josenavas Mar 29, 2015
9b1b9d7
Fixing the sample template class
josenavas Mar 29, 2015
ad1948f
Moving read only tests to their own class
josenavas Mar 29, 2015
09eca70
Moving some code to the base class
josenavas Mar 29, 2015
cc2be6b
Fixing tests for PrepSample
josenavas Mar 29, 2015
1a2c955
Fixing all prep template tests
josenavas Mar 29, 2015
2ce7f65
Fixing pep8
josenavas Mar 29, 2015
6c728c8
Adding utilities
josenavas Mar 30, 2015
03be340
Moving db read only tests to its own class
josenavas Mar 30, 2015
af5f5de
Creating constants module for holding metadata constants
josenavas Mar 30, 2015
a67a71c
Adding squirrelo's code
josenavas Mar 30, 2015
7254b68
Removing unneeded files
josenavas Mar 30, 2015
fd7608a
Fixing bug on delete and reducing code duplication
josenavas Mar 30, 2015
4260c39
Adding column checker
josenavas Mar 31, 2015
8c3d32e
linkerprimersequnce->primer & barcodesequence->barcode
josenavas Mar 31, 2015
d3fedea
Add datatype specific column checking
josenavas Mar 31, 2015
47aac33
reducing code duplication
josenavas Mar 31, 2015
d3fe0ac
Reducing code duplicatio on object creation
josenavas Mar 31, 2015
6402e10
Adding comments
josenavas Mar 31, 2015
91e67ef
constants.py -> column_restriction.py
josenavas Mar 31, 2015
336f470
Enforcing lowercasing when loading templates
josenavas Mar 31, 2015
58422b8
Fixing search tests
josenavas Mar 31, 2015
ab0c7ae
Exposing needed functions
josenavas Mar 31, 2015
879d53f
Fixing setup tests
josenavas Mar 31, 2015
71b08f5
Fixing util tests
josenavas Mar 31, 2015
b091863
Removing functions that are no longer needed
josenavas Mar 31, 2015
a4cc4ab
Simplifying to_file function
josenavas Mar 31, 2015
8711478
Adding missing prep template to the repo and to the database + fix al…
josenavas Apr 1, 2015
29ef682
Forgot the tests for the job object
josenavas Apr 1, 2015
242293d
Fixing analysis object...
josenavas Apr 1, 2015
9d61f9a
Adding metadata_template to setup.py
josenavas Apr 1, 2015
e443d30
Adding qiime_map_fp property to prep template
josenavas Apr 1, 2015
b4462ca
Adding regenerate files function to prep template
josenavas Apr 1, 2015
bb2193e
Fixing bug in prep template creation
josenavas Apr 1, 2015
8e8de2a
Fixing qiita_ware for requirement changes
josenavas Apr 1, 2015
c9eb332
Fixing one remaining test
josenavas Apr 1, 2015
4a0d797
Adding check_restrictions func to base metadata template
josenavas Apr 1, 2015
9af44f6
exposing all the needed things
josenavas Apr 1, 2015
944818a
Disabling ebi submission if missing columns
josenavas Apr 1, 2015
2084f39
Disabling preprocessing and processed data approval based on missing …
josenavas Apr 1, 2015
3d0687e
Updating dbs and html files
josenavas Apr 1, 2015
3a1aef4
Merge branch 'master' of github.com:qiime/QiiTa into relaxing-metadat…
josenavas Apr 1, 2015
303a747
Addressing @squirrelo's comment
josenavas Apr 1, 2015
7d81c2c
Adding missing comma that was breaking flake8 but not the code?
josenavas Apr 1, 2015
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Forgot the tests for the job object
  • Loading branch information
josenavas committed Apr 1, 2015
commit 29ef682f4a11f08ae7022881151107ad4d9eeadb
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 @@ -123,8 +123,7 @@ def test_delete_files(self):
Job(1)

obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.filepath WHERE filepath_id = 12 OR "
"filepath_id = 19")
"SELECT * FROM qiita.filepath WHERE filepath_id = 12")
self.assertEqual(obs, [])

obs = self.conn_handler.execute_fetchall(
Expand Down Expand Up @@ -292,16 +291,18 @@ def test_retrieve_error_exists(self):
self.assertEqual(self.job.error.msg, "TESTERROR")

def test_add_results(self):
file_count = get_count('qiita.filepath')
self.job.add_results([(join(self._job_folder, "1_job_result.txt"),
"plain_text")])

# make sure files attached to job properly
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.job_results_filepath WHERE job_id = 1")

self.assertEqual(obs, [[1, 12], [1, 19]])
self.assertEqual(obs, [[1, 12], [1, file_count+1]])

def test_add_results_dir(self):
file_count = get_count('qiita.filepath')
# Create a test directory
test_dir = join(self._job_folder, "2_test_folder")

Expand All @@ -311,7 +312,7 @@ def test_add_results_dir(self):
# make sure files attached to job properly
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.job_results_filepath WHERE job_id = 1")
self.assertEqual(obs, [[1, 12], [1, 19]])
self.assertEqual(obs, [[1, 12], [1, file_count+1]])

def test_add_results_completed(self):
self.job.status = "completed"
Expand Down