Close #94, close #96 new noparse names

Do not parse names that have "bacterium" as "epithet".
Do not parse names that start with "Candidatus".

CHANGELOG.md

@@ -2,7 +2,11 @@
 
 ## Unreleased
 
+## [v.0.14.2]
+
+- Add [#96]: Do not parse names starting with "Candidatus".
 - Add [#95]: Remove make depenency on gRPC tooling.
+- Add [#94]: Do not parse names with "bacterium" "epithet.
 - Add [#90]: Allow `ß` in names.
 - Add [#89]: Support `subspec.` as a rank.
 - Add [#82]: Support authors with prefix `zu`.
@@ -136,6 +140,7 @@ array of names instead of a stream.
 
 This document follows [changelog guidelines]
 
+[v0.14.3]: https://gitlab.com/gogna/gnparser/compare/v0.14.2...v0.14.3
 [v0.14.2]: https://gitlab.com/gogna/gnparser/compare/v0.14.1...v0.14.2
 [v0.14.1]: https://gitlab.com/gogna/gnparser/compare/v0.14.0...v0.14.1
 [v0.14.0]: https://gitlab.com/gogna/gnparser/compare/v0.13.1...v0.14.0
@@ -155,6 +160,14 @@ This document follows [changelog guidelines]
 [v0.6.0]: https://gitlab.com/gogna/gnparser/compare/v0.5.1...v0.6.0
 [v0.5.1]: https://gitlab.com/gogna/gnparser/tree/v0.5.1
 
+[#100]: https://gitlab.com/gogna/gnparser/issues/100
+[#99]: https://gitlab.com/gogna/gnparser/issues/99
+[#98]: https://gitlab.com/gogna/gnparser/issues/98
+[#97]: https://gitlab.com/gogna/gnparser/issues/97
+[#96]: https://gitlab.com/gogna/gnparser/issues/96
+[#95]: https://gitlab.com/gogna/gnparser/issues/95
+[#94]: https://gitlab.com/gogna/gnparser/issues/94
+[#93]: https://gitlab.com/gogna/gnparser/issues/93
 [#92]: https://gitlab.com/gogna/gnparser/issues/92
 [#91]: https://gitlab.com/gogna/gnparser/issues/91
 [#90]: https://gitlab.com/gogna/gnparser/issues/90

README.md

@@ -71,7 +71,6 @@ gnparser -h
 
 <!-- vim-markdown-toc -->
 
-
 ## Introduction
 
 Global Names Parser or ``gnparser`` is a program written in Go for breaking up
@@ -112,19 +111,19 @@ more efficient JSON conversion.
 
 ## Features
 
-- Fastest parser ever.
-- Very easy to install, just placing executable somewhere in the PATH is
+* Fastest parser ever.
+* Very easy to install, just placing executable somewhere in the PATH is
   sufficient.
-- Extracts all elements from a name, not only canonical forms.
-- Works with very complex scientific names, including hybrid formulas.
-- Includes gRPC server that can be used as if a native method call from C++,
-  C#, Java, Python, Ruby, PHP, JavaScript, Objective C, Dart.
-- Use as a native library from Go projects.
-- Can run as a command line application.
-- Can be scaled to many CPUs and computers (if 300 millions names an
-   hour is not enough).
-- Calculates a stable UUID version 5 ID from the content of a string.
-- Provides C-binding to incorporate parser into other languages.
+* Extracts all elements from a name, not only canonical forms.
+* Works with very complex scientific names, including hybrid formulas.
+* Includes gRPC server that can be used as if a native method call from C++,
+* C#, Java, Python, Ruby, PHP, JavaScript, Objective C, Dart.
+* Use as a native library from Go projects.
+* Can run as a command line application.
+* Can be scaled to many CPUs and computers (if 300 millions names an
+  hour is not enough).
+* Calculates a stable UUID version 5 ID from the content of a string.
+* Provides C-binding to incorporate parser into other languages.
 
 ## Use Cases
 
@@ -213,12 +212,12 @@ If there are problems with parsing a name, parser generates ``qualityWarnings``
 messages and lowers parsing ``quality`` of the name.  Quality values mean the
 following:
 
-- ``"quality": 1`` - No problems were detected
-- ``"quality": 2`` - There were small problems, normalized result
+* ``"quality": 1`` - No problems were detected
+* ``"quality": 2`` - There were small problems, normalized result
   should still be good
-- ``"quality": 3`` - There were serious problems with the name, and the
+* ``"quality": 3`` - There were serious problems with the name, and the
   final result is rather doubtful
-- ``"quality": 0`` - A string could not be recognized as a scientific
+* ``"quality": 0`` - A string could not be recognized as a scientific
   name and parsing fails
 
 ### Creating stable GUIDs for name-strings
@@ -435,8 +434,8 @@ to parser. API calls would be accessibe on ``http://0.0.0.0:9000/api``.
 Make sure to CGI-escape name-strings for GET requests. An '&' character
 needs to be converted to '%26'
 
-- ``GET /api?q=Aus+bus|Aus+bus+D.+%26+M.,+1870``
-- ``POST /api`` with request body of JSON array of strings
+* ``GET /api?q=Aus+bus|Aus+bus+D.+%26+M.,+1870``
+* ``POST /api`` with request body of JSON array of strings
 
 ```ruby
 require 'json'
@@ -478,22 +477,22 @@ docker run gnames/gognparser "Amaurorhinus bewichianus (Wollaston,1860) (s.str.)
 package main
 
 import (
-	"fmt"
+  "fmt"
 
-	"gitlab.com/gogna/gnparser"
+  "gitlab.com/gogna/gnparser"
 )
 
 func main() {
-	opts := []gnparser.Option{
-		gnparser.Format("csv"),
-		gnparser.WorkersNum(100),
-	}
-	gnp := gnparser.NewGNparser(opts...)
-	res, err := gnp.ParseAndFormat("Bubo bubo")
-	if err != nil {
-		fmt.Println(err)
-	}
-	fmt.Println(res)
+  opts := []gnparser.Option{
+    gnparser.Format("csv"),
+    gnparser.WorkersNum(100),
+  }
+  gnp := gnparser.NewGNparser(opts...)
+  res, err := gnp.ParseAndFormat("Bubo bubo")
+  if err != nil {
+    fmt.Println(err)
+  }
+  fmt.Println(res)
 }
 ```
 
@@ -507,9 +506,9 @@ o := gnp.ParseToObject("Homo sapiens")
 fmt.Println(o.Canonical.Simple)
 switch d := o.Details.(type) {
 case *pb.Parsed_Species:
-	fmt.Println(d.Species.Genus)
+  fmt.Println(d.Species.Genus)
 case *pb.Parsed_Uninomial:
-	fmt.Println(d.Uninomial.Value)
+  fmt.Println(d.Uninomial.Value)
 ...
 }
 ```
@@ -554,13 +553,12 @@ provide a warning "Possible ICN author instead of subgenus".
 
 ## Authors
 
-- [Dmitry Mozzherin]
+* [Dmitry Mozzherin]
 
 ## Contributors
 
-- [Geoff Ower]
-- [Hernan Lucas Pereira]
-
+* [Geoff Ower]
+* [Hernan Lucas Pereira]
 
 If you want to submit a bug or add a feature read
 [CONTRIBUTING] file.
@@ -568,10 +566,11 @@ If you want to submit a bug or add a feature read
 ## References
 
 Rees, T. (compiler) (2019). The Interim Register of Marine and Nonmarine
-Genera. Available from http://www.irmng.org at VLIZ.
+Genera. Available from `http://www.irmng.org` at VLIZ.
 Accessed 2019-04-10
 
 ## License
+
 Released under [MIT license]
 
 [releases]: https://gitlab.com/gogna/gnparser/-/releases

preprocess/noparse.rl

@@ -21,7 +21,7 @@ func NoParse(data []byte) bool {
 
     noparse1 = ("Not" | "None" | "Un" ("n"? "amed" | "identified"));
     noparse2 = any* [Ii] "nc" ("." | "ertae") space* [Ss] "ed" ("." | "is");
-    noparse3 = any* ("phytoplasma" | "plasmid" "s"? | [^A-Z] "RNA" [^A-Z]*);
+    noparse3 = any* ("phytoplasma" | space "bacterium"| "plasmid" "s"? | [^A-Z] "RNA" [^A-Z]*);
 
 
     main := (noparse1 | noparse2 | noparse3) %/setMatch

preprocess/preprocess.go

@@ -63,6 +63,9 @@ func Preprocess(bs []byte) *Preprocessor {
 		pr.NoParse = true
 		return pr
 	}
+	if name == "Candidatus" || strings.HasPrefix("Candidatus ", name) {
+		return pr
+	}
 	pr.NoParse = NoParse(bs[0:i])
 	if pr.NoParse {
 		return pr

testdata/test_data.txt

@@ -3065,6 +3065,33 @@ noparse
 3bf556bb-ea7c-536e-8b62-93ba329c559d,Uropodoideaincertaesedis,0,,,,,,0
 #>
 
+#SECTION: No parsing -- bacterium, Candidatus<
+Acidobacteria bacterium
+noparse
+{"parsed":false,"quality":0,"verbatim":"Acidobacteria bacterium","cardinality":0,"surrogate":false,"virus":false,"hybrid":false,"bacteria":false,"nameStringId":"c982b4fd-c41a-5987-bcc8-989c4164b9ec","parserVersion":"test_version"}
+c982b4fd-c41a-5987-bcc8-989c4164b9ec,Acidobacteria bacterium,0,,,,,,0
+
+Acidimicrobiales bacterium JGI 01_E13
+noparse
+{"parsed":false,"quality":0,"verbatim":"Acidimicrobiales bacterium JGI 01_E13","cardinality":0,"surrogate":false,"virus":false,"hybrid":false,"bacteria":false,"nameStringId":"8b71a29b-4271-5a83-8a92-5dab1d9dc4c3","parserVersion":"test_version"}
+8b71a29b-4271-5a83-8a92-5dab1d9dc4c3,Acidimicrobiales bacterium JGI 01_E13,0,,,,,,0
+
+Acidobacterium ailaaui Myers & King, 2016
+Acidobacterium ailaaui Myers & King, 2016
+{"parsed":true,"quality":1,"verbatim":"Acidobacterium ailaaui Myers \u0026 King, 2016","normalized":"Acidobacterium ailaaui Myers \u0026 King 2016","cardinality":2,"canonicalName":{"full":"Acidobacterium ailaaui","simple":"Acidobacterium ailaaui","stem":"Acidobacterium ailaau"},"authorship":"Myers \u0026 King 2016","details":[{"genus":{"value":"Acidobacterium"},"specificEpithet":{"value":"ailaaui","authorship":{"value":"Myers \u0026 King 2016","basionymAuthorship":{"authors":["Myers","King"],"year":{"value":"2016"}}}}}],"positions":[["genus",0,14],["specificEpithet",15,22],["authorWord",23,28],["authorWord",31,35],["year",37,41]],"surrogate":false,"virus":false,"hybrid":false,"bacteria":true,"nameStringId":"b9f4555f-d2e0-5d40-acde-2b546a28a7fc","parserVersion":"test_version"}
+b9f4555f-d2e0-5d40-acde-2b546a28a7fc,"Acidobacterium ailaaui Myers & King, 2016",2,Acidobacterium ailaaui,Acidobacterium ailaaui,Acidobacterium ailaau,Myers & King 2016,2016,1
+
+Candidatus Amesbacteria bacterium GW2011_GWC1_46_24
+noparse
+{"parsed":false,"quality":0,"verbatim":"Candidatus Amesbacteria bacterium GW2011_GWC1_46_24","cardinality":0,"surrogate":false,"virus":false,"hybrid":false,"bacteria":false,"nameStringId":"83382178-94bf-5bf3-a8c8-fdbca4af927c","parserVersion":"test_version"}
+83382178-94bf-5bf3-a8c8-fdbca4af927c,Candidatus Amesbacteria bacterium GW2011_GWC1_46_24,0,,,,,,0
+
+Candidatus
+noparse
+{"parsed":false,"quality":0,"verbatim":"Candidatus","cardinality":0,"surrogate":false,"virus":false,"hybrid":false,"bacteria":false,"nameStringId":"fb9138ac-ae7a-58c9-a912-d31d0a4eeed3","parserVersion":"test_version"}
+fb9138ac-ae7a-58c9-a912-d31d0a4eeed3,Candidatus,0,,,,,,0
+#>
+
 #SECTION: No parsing -- 'Not', 'None', 'Unidentified'  phrases<
 
 None recorded