[med-svn] [Git][med-team/plip][upstream] New upstream version 2.1.6+dfsg

[Nilesh Patra]

Nilesh Patra pushed to branch upstream at Debian Med / plip


Commits:
a768dc00 by Nilesh Patra at 2020-11-11T19:26:03+05:30
New upstream version 2.1.6+dfsg
- - - - -


4 changed files:

- CHANGES.txt
- plip/basic/config.py
- plip/exchange/webservices.py
- plip/test/test_command_line.py


Changes:

=====================================
CHANGES.txt
=====================================
@@ -1,5 +1,8 @@
 Changelog
 ---------
+# 2.1.6
+* fetch URL for PDB files updated to avoid issues with RCSB API changes
+
 # 2.1.5
 * option added to handle specific model in NMR structures
 * fixes a bug in alt-location handling


=====================================
plip/basic/config.py
=====================================
@@ -1,4 +1,4 @@
-__version__ = '2.1.5'
+__version__ = '2.1.6'
 __maintainer__ = 'PharmAI GmbH (2020) - www.pharm.ai - hello at pharm.ai'
 
 import logging


=====================================
plip/exchange/webservices.py
=====================================
@@ -27,7 +27,7 @@ def check_pdb_status(pdbid):
 def fetch_pdb(pdbid):
     """Get the newest entry from the RCSB server for the given PDB ID. Exits with '1' if PDB ID is invalid."""
     pdbid = pdbid.lower()
-    logger.info(f'checking status of PDB-ID {pdbid}')
+    # logger.info(f'checking status of PDB-ID {pdbid}')
     # @todo re-implement state check with ew RCSB API, see https://www.rcsb.org/news?year=2020&article=5eb18ccfd62245129947212a&feature=true
     # state, current_entry = check_pdb_status(pdbid)  # Get state and current PDB ID
     #
@@ -41,7 +41,7 @@ def fetch_pdb(pdbid):
     logger.info('downloading file from PDB')
     # get URL for current entry
     # @todo needs update to react properly on response codes of RCSB servers
-    pdburl = f'http://www.rcsb.org/pdb/files/{pdbid}.pdb'
+    pdburl = f'https://files.rcsb.org/download/{pdbid}.pdb'
     try:
         pdbfile = urlopen(pdburl).read().decode()
         # If no PDB file is available, a text is now shown with "We're sorry, but ..."


=====================================
plip/test/test_command_line.py
=====================================
@@ -40,6 +40,11 @@ class CommandLineTest(unittest.TestCase):
         exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -i 4v59 -o {self.tmp_dir.name}', shell=True)
         self.assertEqual(exitcode, 1)
 
+    def test_pdb_format_available(self):
+        """A valid PDB ID is provided, but there is no entry in PDB format from wwPDB"""
+        exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -i 1acj -o {self.tmp_dir.name}', shell=True)
+        self.assertEqual(exitcode, 0)
+
     def test_valid_pdb(self):
         """A PDB ID with no valid PDB record is provided."""
         exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -x -f ./pdb/1eve.pdb -o {self.tmp_dir.name}',



View it on GitLab: https://salsa.debian.org/med-team/plip/-/commit/a768dc00c77828ada9d16c06147786c880369d93

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View it on GitLab: https://salsa.debian.org/med-team/plip/-/commit/a768dc00c77828ada9d16c06147786c880369d93
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