[med-svn] [Git][med-team/spades][master] 2 commits: More yaml.load issues fixed

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / spades


Commits:
68470522 by Andreas Tille at 2019-11-13T14:32:17Z
More yaml.load issues fixed

- - - - -
0c6e72d1 by Andreas Tille at 2019-11-13T15:29:31Z
Fix location of docs

- - - - -


2 changed files:

- debian/docs
- debian/patches/yaml_load.patch


Changes:

=====================================
debian/docs
=====================================
@@ -1,2 +1,2 @@
-*manual.html
+assembler/*manual.html
 README.md


=====================================
debian/patches/yaml_load.patch
=====================================
@@ -14,3 +14,23 @@ Description: Specify yaml loader
          dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(cfg["dataset"].yaml_filename))
          support.pretty_print_reads(dataset_data, log)
  
+--- a/assembler/src/spades_pipeline/hammer_logic.py
++++ b/assembler/src/spades_pipeline/hammer_logic.py
+@@ -94,7 +94,7 @@ def prepare_config_ih(filename, cfg, ext
+     elif sys.version.startswith('3.'):
+         import pyyaml3 as pyyaml
+ 
+-    data = pyyaml.load(open(filename, 'r'))
++    data = pyyaml.load(open(filename, 'r'), Loader=pyyaml.FullLoader)
+     data["dataset"] = cfg.dataset_yaml_filename
+     data["working_dir"] = cfg.tmp_dir
+     data["output_dir"] = cfg.output_dir
+@@ -153,7 +153,7 @@ def run_hammer(corrected_dataset_yaml_fi
+         log.info("\n===== Skipping %s (already processed). \n" % "read error correction tool")
+         support.continue_from_here(log)
+ 
+-    corrected_dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'))
++    corrected_dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'), Loader=pyyaml.FullLoader)
+     remove_not_corrected_reads(cfg.output_dir)
+     is_changed = False
+     if cfg.gzip_output:



View it on GitLab: https://salsa.debian.org/med-team/spades/compare/639914be81dc5d563998c58ee9c98d64640d6369...0c6e72d195e43f8019b879d884d90eb308181406

-- 
View it on GitLab: https://salsa.debian.org/med-team/spades/compare/639914be81dc5d563998c58ee9c98d64640d6369...0c6e72d195e43f8019b879d884d90eb308181406
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