Changes to existing files for taxonomic amendments

.gitignore

@@ -4,6 +4,7 @@ peyotl.egg-info
 peyotl/test/data/mini_phyl
 peyotl/test/data/mini_system
 peyotl/test/data/mini_collections
+peyotl/test/data/mini_amendments
 env
 dist
 *~

bootstrap.sh

@@ -29,5 +29,11 @@ then
 else
     git clone https://github.com/jimallman/mini_collections.git || exit
 fi
+if test -d mini_amendments
+then
+    echo "mini_amendments exists"
+else
+    git clone https://github.com/jimallman/mini_amendments.git || exit
+fi
 cd .. || exit
 cp -r template_mini_par mini_par

extras/lock-phylesystem.py

@@ -8,7 +8,7 @@
     git_dir = os.path.join(repo, '.git')
     assert os.path.isdir(git_dir)
 except:
-    sys.exit('''Expecting a phylesystem or collections shard as the only argument.
+    sys.exit('''Expecting a phylesystem shard (or one for collections, amendments, etc.) as the only argument.
 This script looks for the .git dir in the first argument, and locks that .git
   dir to prevent simultaneous operations by the phylesystem-api.
 
@@ -30,4 +30,4 @@
     finally:
       print 'Lock released'
     sys.exit(0)
-sys.exit('timeout waiting for lock\n')
+sys.exit('timeout waiting for lock\n')

peyotl/api/__init__.py

@@ -5,5 +5,6 @@
 from peyotl.api.phylografter import Phylografter
 from peyotl.api.phylesystem_api import PhylesystemAPI
 from peyotl.api.collections_api import TreeCollectionsAPI
+from peyotl.api.amendments_api import TaxonomicAmendmentsAPI
 from peyotl.api.oti import OTI
 

peyotl/api/wrapper.py

@@ -65,6 +65,7 @@ def __init__(self, **kwargs):
         self._phylografter = 'http://www.reelab.net/phylografter'
         self._phylesystem_api = kwargs.get('phylesystem')
         self._collections_api = kwargs.get('collections')
+        self._amendments_api = kwargs.get('amendments')
         self._taxomachine = kwargs.get('taxomachine')
         self._treemachine = kwargs.get('treemachine')
     @property
@@ -89,6 +90,13 @@ def collections_api(self):
                                                                     'https://api.opentreeoflife.org')
         return self._collections_api
     @property
+    def amendments_api(self):
+        if self._amendments_api is None:
+            self._amendments_api = self._config.get_config_setting('apis',
+                                                                    'amendments_api',
+                                                                    'https://api.opentreeoflife.org')
+        return self._amendments_api
+    @property
     def phylografter(self):
         return self._phylografter
     @property
@@ -115,13 +123,15 @@ class APIWrapper(object):
     # deprecated service
     # see https://github.com/OpenTreeOfLife/treemachine/issues/170
     SUPPORTING_GET_SOURCE_TREE = False
-    def __init__(self, domains=None, phylesystem_api_kwargs=None, collections_api_kwargs=None, **kwargs):
+    def __init__(self, domains=None, phylesystem_api_kwargs=None, collections_api_kwargs=None, amendments_api_kwargs=None, **kwargs):
         if domains is None:
             domains = get_domains_obj(**kwargs)
         self.domains = domains
         self._phylografter = None
         self._phylesystem_api = None
         self._collections_api = None
+        self._amendments_api = None
+        self._amendments = None
         self._taxomachine = None
         self._treemachine = None
         self._oti = None
@@ -140,6 +150,10 @@ def __init__(self, domains=None, phylesystem_api_kwargs=None, collections_api_kw
             self._collections_api_kwargs = {}
         else:
             self._collections_api_kwargs = dict(collections_api_kwargs)
+        if amendments_api_kwargs is None:
+            self._amendments_api_kwargs = {}
+        else:
+            self._amendments_api_kwargs = dict(amendments_api_kwargs)
     @property
     def oti(self):
         from peyotl.api.oti import _OTIWrapper #pylint: disable=R0401
@@ -191,12 +205,19 @@ def wrap_collections_api(self, **kwargs):
         kwargs['config'] = self._config
         self._collections_api = _TreeCollectionsAPIWrapper(self.domains.collections_api, **kwargs)
         return self._collections_api
+    def wrap_amendments_api(self, **kwargs):
+        raise NotImplementedError("wrap_amendments_api not implemented yet!") 
     @property
     def collections_api(self):
         if self._collections_api is None:
             self.wrap_collections_api()
         return self._collections_api
     @property
+    def amendments_api(self):
+        if self._amendments_api is None:
+            self.wrap_amendments_api()
+        return self._amendments_api
+    @property
     def phylografter(self):
         from peyotl.api.phylografter import _PhylografterWrapper
         if self._phylografter is None:

peyotl/collections/collections_umbrella.py

@@ -87,7 +87,7 @@ def __init__(self,
         Repos can be found by passing in a `repos_par` (a directory that is the parent of the repos)
             or by trusting the `repos_dict` mapping of name to repo filepath.
         `with_caching` should be True for non-debugging uses.
-        `assumed_doc_version` is optional. If specified all TreeCollectionStoreShard repos are assumed to store
+        `assumed_doc_version` is optional. If specified all TreeCollectionsShard repos are assumed to store
             files of this version of nexson syntax.
         `git_ssh` is the path of an executable for git-ssh operations.
         `pkey` is the PKEY that has to be in the env for remote, authenticated operations to work

peyotl/default.conf

@@ -6,6 +6,7 @@ formatter = rich
 [apis]
 phylesystem_api = https://devapi.opentreeoflife.org
 collections_api = https://devapi.opentreeoflife.org
+amendments_api = https://devapi.opentreeoflife.org
 oti = https://devapi.opentreeoflife.org
 taxomachine = https://api.opentreeoflife.org
 treemachine = https://api.opentreeoflife.org

peyotl/git_storage/git_action.py

@@ -437,7 +437,7 @@ def _remove_document(self, gh_user, doc_id, parent_sha, author, commit_msg=None)
                 doc_dir = os.path.split(doc_filepath)[0]
                 #_LOG.debug("@@@@@@@@ GitActionBase._remove_document, doc_dir={}".format(doc_dir))
                 git(self.gitdir, self.gitwd, "rm", "-rf", doc_dir)
-            elif self.doc_type in ('collection', 'favorites'):
+            elif self.doc_type in ('collection', 'favorites', 'amendment'):
                 # delete just the target file
                 git(self.gitdir, self.gitwd, "rm", doc_filepath)
             else:

peyotl/sugar/__init__.py

@@ -9,6 +9,7 @@
 taxomachine = None
 phylesystem_api = None
 collections_api = None
+amendments_api = None
 #favorites_api = None
 oti = None
 tnrs = None
@@ -19,7 +20,7 @@
 
 
 def _populate_globals():
-    global treemachine, oti, phylesystem_api, collections_api, taxomachine, tnrs, \
+    global treemachine, oti, phylesystem_api, collections_api, amendments_api, taxomachine, tnrs, \
         taxonomy, tree_of_life, graph_of_life, studies
     from peyotl.api import APIWrapper
     api_wrapper = APIWrapper()
@@ -28,6 +29,7 @@ def _populate_globals():
     taxomachine = api_wrapper.taxomachine
     phylesystem_api = api_wrapper.phylesystem_api
     collections_api = api_wrapper.collections_api
+    amendments_api = api_wrapper.amendments_api
     #global favorites_api
     #favorites_api = api_wrapper.favorites_api
     tnrs = api_wrapper.tnrs