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josemduarte
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So the tests have been failing a few times and still are. I've solved some of the issues related to the changes introduced in #537 and pushed the commits. However the CATH server is not working at the moment and the build still fails because of that. In any case this solves issue #517, so the related tests that were failing for the last week or so are now fine with this. I've also back-ported the cloning fix to bugfixes-4.2 (see 46b30b3) |
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Thank you @josemduarte! I checked out your branch and the tests work fine. From my side, this PR can be merged. About the CATH problem I created a new issue #544. |
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merging although unit tests fail (related to CATH, so not related to this pull request( |
andreasprlic
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* 'master' of github.com:biojava/biojava: (36 commits) Add some tests for negative residue ranges Minor javadoc & warnings fixes Fix compilation errors from merge Fix MultipleAlignmentJmol resizing bug Fixed bug where bonds from struct conn records were not made for multiple models. Latest ECOD now contains string quotes around some data fields. Need to remove them for junit tests to parse. update test for type of group based on comments from @josemduarte Fixing cath urls according to their final layout [maven-release-plugin]prepare for next development iteration [maven-release-plugin]prepare release biojava-4.2.4 new utility class for chromosome mappings. adding new dependency on guava new utility class for chromosome mappings. new utility class for chromosome mappings. Adding test for genome mapping Complete new CATH file names biojava#546 and biojava#544 Fixing biojava#544 and improving logging Some work towards fixing biojava#544 Back-porting cloning fix (see biojava#541) into bugfixes-4.2 biojava#542 changing default SCOP download location to Berkeley- SCOP. ...
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As mentioned in the discussion in #517 the issue was with seqres groups not having set the chem component. The mmtf inflator was actually setting them correctly (without a 3-letter code though, a known limitation), but the problem was in cloning of groups (needed to create the bioassembly) where the chem comp wasn't cloned properly.