28005 update urllib3v1.26.5

brdm/BaseRefData.py

@@ -51,11 +51,12 @@ def backup_dir(self):
     def backup_dir(self, value):
         self._backup_dir = value
 
-    def load_config(self, config_file):
+    @staticmethod
+    def load_config(config_file):
         """Load the parameters in config file."""
         try:
             with open(config_file, 'r') as stream:
-                config = yaml.load(stream)
+                config = yaml.safe_load(stream)
         except yaml.YAMLError as e:
             print('Could not load configuration file. Error: {}'.format(e))
             exit(1)

rdm_env_setting.yaml

@@ -3,82 +3,14 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - _libgcc_mutex=0.1
-  - asn1crypto=0.24.0
-  - beautifulsoup4=4.6.3
-  - biopython=1.72
-  - blas=1.0
-  - blast=2.7.1
-  - boost=1.67.0
-  - boost-cpp=1.67.0
-  - bzip2=1.0.6
-  - ca-certificates=2019.10.16
-  - certifi=2019.9.11
-  - chardet=3.0.4
-  - cryptography-vectors=2.3.1
-  - cython=0.29
-  - gmp=6.1.2
-  - gnutls=3.5.19
-  - icu=58.2
-  - idna=2.7
-  - intel-openmp=2019.0
-  - libffi=3.2.1
-  - libgcc-ng=7.2.0
-  - libgfortran-ng=7.2.0
-  - libstdcxx-ng=7.2.0
-  - mkl=2018.0.3
-  - mkl_fft=1.0.6
-  - mkl_random=1.0.1
-  - ncurses=6.1
-  - nettle=3.3
-  - numpy=1.15.0
-  - numpy-base=1.15.0
-  - openssl=1.0.2p
-  - pcre=8.41
-  - perl=5.26.2
-  - perl-archive-tar=2.18
-  - perl-carp=1.38
-  - perl-compress-raw-bzip2=2.074
-  - perl-compress-raw-zlib=2.081
-  - perl-data-dumper=2.161
-  - perl-encode=2.88
-  - perl-exporter=5.72
-  - perl-exporter-tiny=1.000000
-  - perl-extutils-makemaker=7.34
-  - perl-io-compress=2.069
-  - perl-io-zlib=1.10
-  - perl-list-moreutils=0.428
-  - perl-list-moreutils-xs=0.428
-  - perl-parent=0.236
-  - perl-pathtools=3.73
-  - perl-scalar-list-utils=1.45
-  - perl-test-more=1.001002
-  - perl-xsloader=0.24
-  - pip=18.1
-  - pkginfo=1.4.2
-  - pycparser=2.19
-  - pyopenssl=18.0.0
-  - pysocks=1.6.8
-  - python=3.6.6
-  - readline=7.0
-  - requests=2.22.0
-  - requests-ftp=0.3.1
-  - requests-toolbelt=0.8.0
-  - setuptools=40.5.0
-  - six=1.11.0
-  - sqlite=3.25.2
-  - tbb=2019.3
-  - tbb4py=2019.3
-  - tk=8.6.8
-  - tqdm=4.28.1
-  - twine=1.11.0
-  - wheel=0.32.2
-  - xz=5.2.4
-  - yaml=0.1.7
-  - zlib=1.2.11
+  - python=3.9.12
+  - biopython=1.78
+  - blast=2.12
+  - certifi=2022.6.15
+  - requests=2.27
+  - beautifulsoup4=4.11
+  - pyyaml
+  - requests-ftp=0.3
+  - twine=3
   - pip:
-    - cffi==1.14.5
-    - cryptography==3.3.2
-    - reference-data-manager
-    - pyyaml==4.2b1
-    - urllib3==1.25.2
+      - reference-data-manager

requirements.txt

@@ -1,25 +1,12 @@
-asn1crypto==0.24.0
-beautifulsoup4==4.6.3
-biopython==1.72
-certifi==2019.9.11
-cffi==1.14.5
-chardet==3.0.4
-cryptography==3.3.2
-cryptography-vectors==2.3.1
-Cython==0.29
-idna==2.7
-mkl-fft==1.0.6
-mkl-random==1.0.1
-numpy==1.15.0
-pkginfo==1.4.2
-pycparser==2.19
-pyOpenSSL==18.0.0
-PySocks==1.6.8
-PyYAML==5.4
-requests==2.22.0
+beautifulsoup4==4.11.1
+biopython==1.78
+certifi==2022.6.15
+blast==2.12.0
+chardet==4.0.0
+pyyaml==6.0
+requests==2.27.1
 requests-ftp==0.3.1
-requests-toolbelt==0.8.0
-six==1.11.0
-tqdm==4.28.1
-twine==1.11.0
-urllib3==1.25.2
+requests-toolbelt==0.9.1
+six==1.16.0
+tqdm==4.64.0
+twine==3.7.1

tests/TestGreenGene.py

@@ -6,10 +6,10 @@
 
 class TestGreenGene(unittest.TestCase):
     @classmethod
-    def setUpClass(self):
+    def setUpClass(cls):
         dir_path = os.path.dirname(os.path.realpath(__file__))
-        self.fixture = GreenGeneData('{}/test_config.yaml'
-                                     .format(dir_path))
+        cls.fixture = GreenGeneData('{}/test_config.yaml'
+                                    .format(dir_path))
 
     '''
     @classmethod
@@ -22,9 +22,13 @@ def tearDownClass(self):
 
         pass
     '''
+
     def test_1_download(self):
         print('Check method download...')
-        success = self.fixture.download(test=True)
+        try:
+            success = self.fixture.download(test=True)
+        except Exception as e:
+            print(e)
         self.assertTrue(success, 'Failed in GreenGene download.')
 
     def test_2_update(self):

tests/TestNcbiBlastData.py

@@ -7,9 +7,9 @@
 class TestNcbiBlastData(unittest.TestCase):
 
     @classmethod
-    def setUpClass(self):
+    def setUpClass(cls):
         dir_path = os.path.dirname(os.path.realpath(__file__))
-        self.fixture = NcbiBlastData('{}/test_config.yaml'.format(dir_path))
+        cls.fixture = NcbiBlastData('{}/test_config.yaml'.format(dir_path))
 
     '''
     @classmethod
@@ -81,6 +81,5 @@ def test_5_download(self):
                                    'Downloaded file is empty')
 
 
-
 if __name__ == '__main__':
     unittest.main()

tests/TestNcbiTaxonomy.py

@@ -6,10 +6,10 @@
 
 class TestNcbiTaxonomyData(unittest.TestCase):
     @classmethod
-    def setUpClass(self):
+    def setUpClass(cls):
         dir_path = os.path.dirname(os.path.realpath(__file__))
-        self.fixture = NcbiTaxonomyData('{}/test_config.yaml'
-                                        .format(dir_path))
+        cls.fixture = NcbiTaxonomyData('{}/test_config.yaml'
+                                       .format(dir_path))
 
     '''
     @classmethod
@@ -54,8 +54,8 @@ def test_5_restore(self):
         print('Restore ncbi taxonomy...')
         success = self.fixture.restore(strftime('%Y-%m-%d', gmtime()),
                                        os.path.join(
-                                            self.fixture.destination_dir,
-                                            'restoreTaxonomy')
+                                           self.fixture.destination_dir,
+                                           'restoreTaxonomy')
                                        )
         self.assertTrue(success, 'Failed in NCBI taxonomy restore.')
 

tests/TestNcbiWholeGenome.py

@@ -6,10 +6,10 @@
 
 class TestNcbiWholeGenome(unittest.TestCase):
     @classmethod
-    def setUpClass(self):
+    def setUpClass(cls):
         dir_path = os.path.dirname(os.path.realpath(__file__))
-        self.fixture = NcbiWholeGenome('{}/test_config.yaml'
-                                       .format(dir_path))
+        cls.fixture = NcbiWholeGenome('{}/test_config.yaml'
+                                      .format(dir_path))
 
     '''
     @classmethod
@@ -54,8 +54,8 @@ def test_5_restore(self):
         print('Restore ncbi taxonomy...')
         success = self.fixture.restore(strftime('%Y-%m-%d', gmtime()),
                                        os.path.join(
-                                            self.fixture.destination_dir,
-                                            'restoreTaxonomy')
+                                           self.fixture.destination_dir,
+                                           'restoreTaxonomy')
                                        )
         self.assertTrue(success, 'Failed in NCBI taxonomy restore.')
 

tests/TestSilvaData.py

@@ -7,16 +7,16 @@
 
 class TestSilvaData(unittest.TestCase):
     @classmethod
-    def setUpClass(self):
+    def setUpClass(cls):
         dir_path = os.path.dirname(os.path.realpath(__file__))
-        self.fixture = SilvaData('{}/test_config.yaml'.format(dir_path))
+        cls.fixture = SilvaData('{}/test_config.yaml'.format(dir_path))
 
     @classmethod
-    def tearDownClass(self):
-        if os.path.exists(self.fixture.destination_dir):
-            shutil.rmtree(self.fixture.destination_dir)
-        if os.path.exists(self.fixture.backup_dir):
-            shutil.rmtree(self.fixture.backup_dir)
+    def tearDownClass(cls):
+        if os.path.exists(cls.fixture.destination_dir):
+            shutil.rmtree(cls.fixture.destination_dir)
+        if os.path.exists(cls.fixture.backup_dir):
+            shutil.rmtree(cls.fixture.backup_dir)
         pass
 
     def test_1_download(self):

tests/TestSubsetData.py

@@ -7,9 +7,9 @@
 class TestNcbiSebsetData(unittest.TestCase):
 
     @classmethod
-    def setUpClass(self):
+    def setUpClass(cls):
         dir_path = os.path.dirname(os.path.realpath(__file__))
-        self.fixture = NcbiSubsetData('{}/test_config.yaml'.format(dir_path))
+        cls.fixture = NcbiSubsetData('{}/test_config.yaml'.format(dir_path))
 
     '''
     @classmethod