start of impl

data/patch-taxonomy/.gitignore

@@ -0,0 +1 @@
+*.pickle

data/patch-taxonomy/about.json

@@ -0,0 +1,3 @@
+{
+    "inputs": []
+}

data/patch-taxonomy/conflicts.tsv

@@ -0,0 +1 @@
+

data/patch-taxonomy/deprecated.tsv

@@ -0,0 +1 @@
+

data/patch-taxonomy/forwards.tsv

@@ -0,0 +1,2 @@
+id	replacement
+2002	1001

data/patch-taxonomy/synonyms.tsv

@@ -0,0 +1,2 @@
+name	|	uid	|	type	|	uniqname	|	sourceinfo	|	
+Camaryllis major	|	21	|	synonym	|		|		|	

data/patch-taxonomy/taxonomy.tsv

@@ -0,0 +1,16 @@
+uid	|	parent_uid	|	name	|	rank	|	sourceinfo	|	uniqname	|	flags	|	
+1000000	|		|	Exampleroot	|	no rank	|	ncbi:10239,gbif:8	|		|		|	
+999999	|	1000000	|	Nototuexample	|	no rank	|		|		|	not_otu	|	
+1001	|	1000000	|	Amaryllidaceae	|	no rank	|		|		|		|	
+100	|	1001	|	Amaryllis	|	no rank	|		|		|		|	
+200	|	1001	|	Bamaryllis	|	no rank	|		|		|		|	
+300	|	1001	|	Amaryllis Amaryllis	|	no rank	|		|	Amaryllis (subgenus Amaryllis)	|		|	
+1	|	100	|	Amaryllis belladonna	|	no rank	|		|		|		|	
+2	|	100	|	Amaryllis minor	|	no rank	|		|		|	hybrid,edited	|	
+3	|	100	|	Amaryllis someλodd	|	no rank	|		|		|		|	
+11	|	200	|	Bamaryllis belladonna	|	no rank	|	ncbi:1,gbif:3	|		|		|	
+12	|	200	|	Bamaryllis major	|	no rank	|	ncbi:2,irmng:5	|		|		|	
+13	|	200	|	Bamarylis minor	|	no rank	|		|		|		|	
+21	|	300	|	Amaryllis Amaryllis major	|	no rank	|		|		|		|	
+22	|	300	|	Amaryllis Amaryllis minor	|	no rank	|		|		|		|	
+23	|	300	|	Amaryllis somelodd	|	no rank	|		|		|		|	

data/patch-taxonomy/version.txt

@@ -0,0 +1,2 @@
+0.0draft0
+

data/sink.json

@@ -0,0 +1,9 @@
+[
+  {
+    "action": "sink",
+    "taxon": {
+      "ott_id_to_be_jr_syn": 12,
+      "ott_id_of_sr_syn": 11
+    }
+  }
+]

expected/taxonomy-patcher/sink/output

@@ -0,0 +1,31 @@
+loading taxonomy
+loaded
+1 amendments to be processed.
+1/1 amendments applied.
+version.txt
+0.0draft0
+taxonomy.tsv
+uid	|	parent_uid	|	name	|	rank	|	sourceinfo	|	uniqname	|	flags	|	
+1000000	|		|	Exampleroot	|	no rank	|	ncbi:10239,gbif:8	|		|		|	
+999999	|	1000000	|	Nototuexample	|	no rank	|		|		|	not_otu	|	
+1001	|	1000000	|	Amaryllidaceae	|	no rank	|		|		|		|	
+100	|	1001	|	Amaryllis	|	no rank	|		|		|		|	
+1	|	100	|	Amaryllis belladonna	|	no rank	|		|		|		|	
+2	|	100	|	Amaryllis minor	|	no rank	|		|		|	edited,hybrid	|	
+3	|	100	|	Amaryllis someλodd	|	no rank	|		|		|		|	
+200	|	1001	|	Bamaryllis	|	no rank	|		|		|		|	
+11	|	200	|	Bamaryllis belladonna	|	no rank	|	ncbi:1,irmng:5,gbif:3	|		|		|	
+13	|	200	|	Bamarylis minor	|	no rank	|		|		|		|	
+300	|	1001	|	Amaryllis Amaryllis	|	no rank	|		|	Amaryllis (subgenus Amaryllis)	|		|	
+21	|	300	|	Amaryllis Amaryllis major	|	no rank	|		|		|		|	
+22	|	300	|	Amaryllis Amaryllis minor	|	no rank	|		|		|		|	
+23	|	300	|	Amaryllis somelodd	|	no rank	|		|		|		|	
+synonyms.tsv
+name	|	uid	|	type	|	uniqname	|	sourceinfo	|	
+Camaryllis major	|	21	|		|		|		|	
+Bamaryllis major	|	11	|		|		|		|	
+forwards.tsv
+id	replacement
+6520249	100
+2002	1001
+12	11

expected/taxonomy-patcher/taxonomy-patcher.json

@@ -1,4 +1,9 @@
 [
+  {
+    "invocation" : ["otc-taxonomy-patcher", "--amend-status-to-stdout", "--write-to-stdout", "--edits", "<INFILELIST>"],
+    "infile_list": ["sink.json", "patch-taxonomy"],
+    "expected": "sink"
+  },
   {
     "invocation" : ["otc-taxonomy-patcher", "--amend-status-to-stdout", "--write-to-stdout", "--edits", "<INFILELIST>"],
     "infile_list": ["unmarked-homonym.json", "tnrs-taxonomy"],

tools/taxonomy-patcher.cpp

@@ -221,7 +221,7 @@ class BaseTaxonAmendment: public TaxonomyAmendment {
 class TaxonAdditionAmendment: public BaseTaxonAmendment {
     public:
     TaxonAdditionAmendment(const json & taxon_obj)
-        :BaseTaxonAmendment(taxon_obj,true) {
+        :BaseTaxonAmendment(taxon_obj, true) {
     }
 
     virtual ~TaxonAdditionAmendment(){
@@ -235,6 +235,27 @@ class TaxonAdditionAmendment: public BaseTaxonAmendment {
     }
 };
 
+class TaxonSinkAmendment: public TaxonomyAmendment {
+    public:
+    TaxonSinkAmendment(const json & taxon_obj)
+        :TaxonomyAmendment() {
+        this->ott_id_to_be_jr_syn = get_unsigned_property(taxon_obj, "ott_id_to_be_jr_syn", true).second;
+        this->ott_id_of_sr_syn = get_unsigned_property(taxon_obj, "ott_id_of_sr_syn", true).second;
+
+    }
+
+    virtual ~TaxonSinkAmendment(){
+    }
+
+    virtual std::pair<bool, std::string> patch(PatchableTaxonomy &t) {
+        throw OTCError("Sink action not implemented yet")  ; 
+    }
+
+    protected:
+        OttId ott_id_to_be_jr_syn;
+        OttId ott_id_of_sr_syn;
+};
+
 class TaxonEditAmendment: public BaseTaxonAmendment {
     public:
     TaxonEditAmendment(const json & taxon_obj)
@@ -369,6 +390,12 @@ TaxonomyAmendmentPtr parse_taxon_amendment_obj(const json & edit_obj) {
             return std::make_shared<TaxonEditAmendment>(*(taxon_j.second));
         }
         throw OTCError() << "Expecting edit action to contain taxon object.";
+    } else if (action == "sink") {
+        auto taxon_j = get_object_property(edit_obj, "taxon", false);
+        if (taxon_j.first) {
+            return std::make_shared<TaxonSinkAmendment>(*(taxon_j.second));
+        }
+        throw OTCError() << "Expecting edit action to contain taxon object.";
     } else {
         throw OTCError() << "Taxon amendment with action \"" << action << "\" not implemented.";
     }