Merge pull request #3210 from antgonza/minor-changes-09.2022

minor changes after qiita-rc 09.2022

Author: charles-cowart

qiita_db/support_files/patches/87.sql

@@ -1,6 +1,6 @@
 -- Aug 11, 2022
 -- updating resource allocations to use slurm
-UPDATE qiita.processing_job_resource_allocation processing_job_resource_allocation SET allocation =
+UPDATE qiita.processing_job_resource_allocation SET allocation =
 REPLACE(
   REPLACE(
     REPLACE(
@@ -13,4 +13,6 @@ REPLACE(
       '-l pmem=', '--mem-per-cpu '),
     '-l mem=', '--mem '),
   '-l walltime=', '--time '),
-'-p 1023', '--priority 1023');
+'-p 1023', '--qos=qiita_prio');
+
+INSERT INTO qiita.filepath_type (filepath_type) VALUES ('bam');

qiita_db/test/test_setup.py

@@ -36,7 +36,7 @@ def test_filepath(self):
         self.assertEqual(get_count("qiita.filepath"), 23)
 
     def test_filepath_type(self):
-        self.assertEqual(get_count("qiita.filepath_type"), 24)
+        self.assertEqual(get_count("qiita.filepath_type"), 25)
 
     def test_study_prep_template(self):
         self.assertEqual(get_count("qiita.study_prep_template"), 2)

qiita_db/test/test_util.py

@@ -135,6 +135,7 @@ def test_get_filepath_types(self):
                'directory': 8, 'plain_text': 9, 'reference_seqs': 10,
                'reference_tax': 11, 'reference_tree': 12, 'log': 13,
                'sample_template': 14, 'prep_template': 15, 'qiime_map': 16,
+               'bam': 17
                }
         with qdb.sql_connection.TRN:
             qdb.sql_connection.TRN.add("SELECT filepath_type,filepath_type_id "

setup.py

@@ -108,7 +108,7 @@
                         'networkx', 'humanize', 'wtforms<3.0.0', 'nltk',
                         'openpyxl', 'sphinx-bootstrap-theme', 'Sphinx<3.0',
                         'gitpython', 'redbiom', 'pyzmq', 'sphinx_rtd_theme',
-                        'paramiko', 'seaborn',  'matplotlib', 'scipy<1.8',
+                        'paramiko<2.9', 'seaborn',  'matplotlib', 'scipy<1.8',
                         'nose',
                         'flake8', 'six', 'qiita-files @ https://github.com/'
                         'qiita-spots/qiita-files/archive/master.zip', 'mock',