finish up separation and Corymorpha changes

Author: jar398

Makefile

@@ -13,7 +13,7 @@
 JAVAFLAGS=-Xmx14G
 
 # Modify as appropriate
-WHICH=3.0draft5
+WHICH=3.0draft6
 PREV_WHICH=2.10
 
 # ----- Taxonomy source locations -----
@@ -111,7 +111,7 @@ tax/ott/log.tsv: $(CLASS) make-ott.py assemble_ott.py adjustments.py amendments.
 		    bin/jython \
 		    inclusions.csv \
 		    feed/amendments/amendments-1/next_ott_id.json \
-		    tax/skel/taxonomy.tsv \
+		    tax/separation/taxonomy.tsv \
 		    feed/ott_id_list/by_qid.csv
 	@date
 	@rm -f *py.class

adjustments.py

@@ -16,7 +16,8 @@ def deal_with_polysemies(ott):
     # ncbi 10197 	|	6072	|	Ctenophora	|	phylum	|	= comb jellies  OTT 641212
     # ncbi 516519	|	702682	|	Ctenophora	|	genus	|	= cranefly      OTT 1043126
 
-    # The comb jellies are already in the taxonomy at this point (from skeleton).
+    # The comb jellies are already in the taxonomy at this point (from
+    # separation taxonomy).
 
     # Add the diatom to OTT so that SILVA has something to map its diatom to
     # that's not the comb jellies.
@@ -28,7 +29,7 @@ def deal_with_polysemies(ott):
     # Diatom.  Contains e.g. Ctenophora pulchella.
     establish('Ctenophora', ott, ancestor='Bacillariophyta', ott_id='103964')
 
-    # The comb jelly should already be in skeleton, but include the code for symmetry.
+    # The comb jelly should already be in separation, but include the code for symmetry.
     # Contains e.g. Leucothea multicornis
     establish('Ctenophora', ott, parent='Metazoa', ott_id='641212')
 
@@ -72,6 +73,10 @@ def deal_with_polysemies(ott):
     # not sure why this is needed.
     establish('Stereopsidaceae', ott, division='Fungi', source='gbif:7717211')
 
+    # 3.0draft5 problem
+    establish('Corymorpha', ott, division='Cnidaria', source='ncbi:264057', ott_id='183501')
+    establish('Corymorpha', ott, division='Nematoda', source='ncbi:364543', ott_id='860265')
+
 def load_silva():
     silva = Taxonomy.getTaxonomy('tax/silva/', 'silva')
 
@@ -199,7 +204,7 @@ def fix_name(bad, good):
     # JAR 2014-05-13 scrutinizing pin() and BarrierNodes.  Wikipedia
     # confirms this synonymy.  Dail L. prefers -phyta to -phyceae
     # but says -phytina would be more correct per code.
-    # Skeleton taxonomy has -phyta (on Dail's advice).
+    # Separation taxonomy has -phyta (on Dail's advice).
     silva.taxon('Rhodophyceae').synonym('Rhodophyta')    # moot now?
 
     silva.taxon('Florideophycidae', 'Rhodophyceae').synonym('Florideophyceae')
@@ -651,7 +656,7 @@ def patch_ncbi(ncbi):
         if ncbi.maybeTaxon(toplevel) != None:
             ncbi.taxon(toplevel).prune(this_source)
 
-    # - Canonicalize division names (cf. skeleton) -
+    # - Canonicalize division names (cf. separation) -
     # JAR 2014-05-13 scrutinizing pin() and BarrierNodes.  Wikipedia
     # confirms these synonymies.
     ncbi.taxon('Glaucocystophyceae').rename('Glaucophyta')

assemble_ott.py

@@ -34,8 +34,7 @@ def create_ott(version):
     for name in names_of_interest:
         ott.eventLogger.namesOfInterest.add(name)
 
-    # idspace string 'skel' is magical, see Taxon.addSource
-    ott.setSkeleton(Taxonomy.getTaxonomy('tax/skel/', 'skel'))
+    ott.setSkeleton(Taxonomy.getTaxonomy('tax/separation/', 'separation'))
 
     # These are particularly hard cases; create alignment targets up front
     adjustments.deal_with_polysemies(ott)
@@ -87,7 +86,7 @@ def merge_sources(ott):
     # higher priority to Worms for Malacostraca, Cnidaria so we split out
     # those clades from worms and absorb them before NCBI
     worms = adjustments.load_worms()
-    # Malacostraca instead of Decapoda because M. is in the skeleton
+    # Malacostraca instead of Decapoda because M. is in the separation taxonomy
     (malacostraca, worms_sans_malacostraca) = split_taxonomy(worms, 'Malacostraca')
     align_and_merge(ott.alignment(malacostraca))
     (cnidaria, low_priority_worms) = split_taxonomy(worms_sans_malacostraca, 'Cnidaria')

doc/method/data-package/Makefile

@@ -14,8 +14,8 @@ ott3.0.tgz: $(REF)/tarballs/ott3.0draft3.tgz
 alt-ott3.0.tgz:
 	wget http://files.opentreeoflife.org/ott/ott3.0/ott3.0draft3.tgz
 
-separation.tgz: $(REF)/tax/skel/taxonomy.tsv
-	tar czf $@ -C $(REF) tax/skel
+separation.tgz: $(REF)/tax/separation/taxonomy.tsv
+	tar czf $@ -C $(REF) tax/separation
 
 silva.tgz: $(REF)/tax/silva/taxonomy.tsv
 	tar czf $@ -C $(REF) tax/silva

inclusions.csv

@@ -108,3 +108,5 @@ Equisetidae,Equisetopsida,5662213,"issue 281"
 Acropora,Cnidaria,712401,"issue reftax#298"
 Acropora,Bryozoa,4149092,"issue reftax#298 (syn of Porina)"
 Dermocystidium salmonis,Ichthyosporea,5653696,"issue reftax #301"
+Corymorpha,Cnidaria,183501,"fallout from setting Cnidarian priority"
+Corymorpha,Nematoda,860265,"fallout from setting Cnidarian priority"