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Merge branch 'dev' of github.com:biocore/qiita into dev
2 parents 9613bdb + 751e559 commit bcb4433

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-614
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‎notebooks/resource-allocation/generate-allocation-summary-arrays.py

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from qiita_core.util import MaxRSS_helper
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from qiita_db.util import MaxRSS_helper
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from qiita_db.software import Software
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import datetime
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from io import StringIO

‎notebooks/resource-allocation/generate-allocation-summary.py

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from json import loads
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from os.path import join
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from qiita_core.util import MaxRSS_helper
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from qiita_db.util import MaxRSS_helper
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from qiita_db.exceptions import QiitaDBUnknownIDError
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from qiita_db.processing_job import ProcessingJob
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from qiita_db.software import Software

‎qiita_core/support_files/cert.conf

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authorityKeyIdentifier=keyid,issuer
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basicConstraints=CA:FALSE
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keyUsage = digitalSignature, nonRepudiation, keyEncipherment, dataEncipherment
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subjectAltName = @alt_names
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[alt_names]
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DNS.1 = localhost

‎qiita_core/support_files/ci_rootca.crt

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-----BEGIN CERTIFICATE-----
2-
MIIDSzCCAjOgAwIBAgIUMpJXCX29kpvz+72BzsmGaOl8+TowDQYJKoZIhvcNAQEL
2+
MIIDSzCCAjOgAwIBAgIUNZa06QPa5si7H/HCG2E4s0opIO0wDQYJKoZIhvcNAQEL
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2020
-----END CERTIFICATE-----

‎qiita_core/support_files/ci_rootca.key

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-----BEGIN PRIVATE KEY-----
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4+5t5RSoyHDQeIc4OKiCdA==
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-----END PRIVATE KEY-----

‎qiita_core/support_files/ci_rootca.srl

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‎qiita_core/support_files/ci_server.crt

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-----BEGIN CERTIFICATE-----
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2222
-----END CERTIFICATE-----

‎qiita_core/support_files/ci_server.csr

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-----END CERTIFICATE REQUEST-----

‎qiita_core/support_files/ci_server.key

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-----BEGIN PRIVATE KEY-----
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16-
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19-
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20-
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21-
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22-
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23-
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24-
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26-
r2wH35ScNDiuF03q0cf0DoAq/baQ2woNg2gTV5FcEaf1DuLCqiNXsAOfWPyY6hTu
27-
71mg/F74UlfLqZLjgM0Hb8JO
2+
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19+
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27+
LEluqA2De7Zc9mdvWENRT00=
2828
-----END PRIVATE KEY-----

‎qiita_core/support_files/csr.conf

Lines changed: 21 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,21 @@
1+
[ req ]
2+
default_bits = 2048
3+
prompt = no
4+
default_md = sha256
5+
req_extensions = req_ext
6+
distinguished_name = dn
7+
8+
[ dn ]
9+
C = US
10+
ST = California
11+
L = San Diego
12+
O = UCSD
13+
OU = Knight Lab
14+
CN = localhost
15+
16+
[ req_ext ]
17+
subjectAltName = @alt_names
18+
19+
[ alt_names ]
20+
DNS.1 = localhost
21+
IP.1 = 127.0.0.1

‎qiita_core/tests/test_util.py

Lines changed: 1 addition & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@
1010

1111
from qiita_core.util import (
1212
qiita_test_checker, execute_as_transaction, get_qiita_version,
13-
is_test_environment, get_release_info, MaxRSS_helper)
13+
is_test_environment, get_release_info)
1414
from qiita_db.meta_util import (
1515
generate_biom_and_metadata_release, generate_plugin_releases)
1616
import qiita_db as qdb
@@ -82,20 +82,6 @@ def test_get_release_info(self):
8282
self.assertEqual(biom_metadata_release, ('', '', ''))
8383
self.assertNotEqual(archive_release, ('', '', ''))
8484

85-
def test_MaxRSS_helper(self):
86-
tests = [
87-
('6', 6.0),
88-
('6K', 6000),
89-
('6M', 6000000),
90-
('6G', 6000000000),
91-
('6.9', 6.9),
92-
('6.9K', 6900),
93-
('6.9M', 6900000),
94-
('6.9G', 6900000000),
95-
]
96-
for x, y in tests:
97-
self.assertEqual(MaxRSS_helper(x), y)
98-
9985

10086
if __name__ == '__main__':
10187
main()

‎qiita_core/util.py

Lines changed: 0 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -151,15 +151,3 @@ def get_release_info(study_status='public'):
151151
archive_release = ((md5sum, filepath, timestamp))
152152

153153
return (biom_metadata_release, archive_release)
154-
155-
156-
def MaxRSS_helper(x):
157-
if x[-1] == 'K':
158-
y = float(x[:-1]) * 1000
159-
elif x[-1] == 'M':
160-
y = float(x[:-1]) * 1000000
161-
elif x[-1] == 'G':
162-
y = float(x[:-1]) * 1000000000
163-
else:
164-
y = float(x)
165-
return y

‎qiita_db/handlers/tests/test_user.py

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -51,10 +51,14 @@ def test_get(self):
5151

5252
obs = loads(obs.body)
5353
exp = {'data': [
54-
{'email': '[email protected]', 'name': 'Dude'},
5554
{'email': '[email protected]', 'name': 'Shared'},
5655
{'email': '[email protected]', 'name': 'Admin'},
57-
{'email': '[email protected]', 'name': 'Demo'}]}
56+
{'email': '[email protected]', 'name': 'Demo'},
57+
{'email': '[email protected]', 'name': 'Dude'},
58+
{'email': '[email protected]', 'name': 'JustNow'},
59+
{'email': '[email protected]', 'name': 'Oldie'},
60+
{'email': '[email protected]', 'name': 'TooLate'}
61+
]}
5862
self.assertEqual(obs, exp)
5963

6064

‎qiita_db/support_files/patches/92.sql

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -10,6 +10,9 @@ CREATE TABLE qiita.slurm_resource_allocations (
1010
extra_info varchar DEFAULT NULL,
1111
memory_used bigint,
1212
walltime_used integer,
13+
job_start TIMESTAMP,
14+
node_name varchar DEFAULT NULL,
15+
node_model varchar DEFAULT NULL,
1316
CONSTRAINT pk_slurm_resource_allocations_processing_job_id PRIMARY KEY (
1417
processing_job_id )
1518
);
@@ -27,3 +30,12 @@ ALTER TABLE qiita.prep_template ADD current_human_filtering boolean DEFAULT Fals
2730
-- Adding a new column: reprocess_job_id to qiita.prep_template to keep track of
2831
-- the job that reprocessed this prep
2932
ALTER TABLE qiita.prep_template ADD reprocess_job_id uuid DEFAULT NULL;
33+
34+
-- Jun 19, 2024
35+
-- Adding a new column to the user table that logs when this account was created
36+
-- Usefull e.g. to prune non-verified=inactive user or to plot user growth
37+
38+
ALTER TABLE qiita.qiita_user
39+
ADD creation_timestamp timestamp without time zone DEFAULT NOW();
40+
41+
COMMENT ON COLUMN qiita.qiita_user.creation_timestamp IS 'The date the user account was created';

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