refactor to better file structure (close #100)

.gitignore

@@ -1,5 +1,6 @@
-gnverifier/gnverifier
+gnverifier
 debug.test
+coverage.txt
 t
 t.json
 .env

CHANGELOG.md

@@ -1,16 +1,20 @@
 # Changelog
 
+## [v1.0.2] - 2023-03-09 Thu
+
+- Add [#100]: refactor to a better file organization.
+
 ## [v1.0.1] - 2022-09-30 Fri
 
-- Add: update all modules
+- Add: update all modules.
 
 ## [v1.0.0] - 2022-08-24 Wed
 
-- Add: prepare for v1.0.0
+- Add: prepare for v1.0.0.
 
 ## [v1.0.0-RC1] - 2022-05-10 Tue
 
-- Add: update gnmatcher, gnames to v1.0.0-RC1
+- Add: update gnmatcher, gnames to v1.0.0-RC1.
 
 ## [v0.9.5] - 2022-05-02 Mon
 
@@ -193,6 +197,9 @@ This document follows [changelog guidelines]
 
 <!-- VERSIONS -->
 
+[v1.0.2]: https://github.com/gnames/gnverifier/compare/v1.0.1...v1.0.2
+[v1.0.1]: https://github.com/gnames/gnverifier/compare/v1.0.0...v1.0.1
+[v1.0.0]: https://github.com/gnames/gnverifier/compare/v1.0.0-RC1...v1.0.0
 [v1.0.0-rc1]: https://github.com/gnames/gnverifier/compare/v0.9.5...v1.0.0-RC1
 [v0.9.5]: https://github.com/gnames/gnverifier/compare/v0.9.4...v0.9.5
 [v0.9.4]: https://github.com/gnames/gnverifier/compare/v0.9.3...v0.9.4
@@ -233,6 +240,16 @@ This document follows [changelog guidelines]
 
 <!-- Issues -->
 
+[#110]: https://github.com/gnames/gnverifier/issues/110
+[#109]: https://github.com/gnames/gnverifier/issues/109
+[#108]: https://github.com/gnames/gnverifier/issues/108
+[#107]: https://github.com/gnames/gnverifier/issues/107
+[#106]: https://github.com/gnames/gnverifier/issues/106
+[#105]: https://github.com/gnames/gnverifier/issues/105
+[#104]: https://github.com/gnames/gnverifier/issues/104
+[#103]: https://github.com/gnames/gnverifier/issues/103
+[#102]: https://github.com/gnames/gnverifier/issues/102
+[#101]: https://github.com/gnames/gnverifier/issues/101
 [#100]: https://github.com/gnames/gnverifier/issues/100
 [#99]: https://github.com/gnames/gnverifier/issues/99
 [#98]: https://github.com/gnames/gnverifier/issues/98

Dockerfile

@@ -1,12 +1,10 @@
-FROM alpine:3.14
+FROM alpine:3.17
 
 LABEL maintainer="Dmitry Mozzherin"
 
-ENV LAST_FULL_REBUILD 2021-04-09
-
 WORKDIR /bin
 
-COPY ./gnverifier/gnverifier /bin
+COPY ./gnverifier /bin
 
 ENTRYPOINT [ "gnverifier" ]
 

LICENSE

@@ -1,6 +1,6 @@
-MIT License
+The MIT License (MIT)
 
-Copyright (c) 2020-2022 gnames
+Copyright © 2020-2022 Dmitry Mozzherin <[email protected]>
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -9,13 +9,13 @@ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 copies of the Software, and to permit persons to whom the Software is
 furnished to do so, subject to the following conditions:
 
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
 
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

Makefile

@@ -1,14 +1,21 @@
+PROJ_NAME = gnverifier
+
 VERSION = $(shell git describe --tags)
 VER = $(shell git describe --tags --abbrev=0)
 DATE = $(shell date -u '+%Y-%m-%d_%H:%M:%S%Z')
-FLAG_MODULE = GO111MODULE=on
-FLAGS_SHARED = $(FLAG_MODULE) CGO_ENABLED=0 GOARCH=amd64
+
+NO_C = CGO_ENABLED=0
+FLAGS_SHARED = $(NO_C) GOARCH=amd64
 FLAGS_LD=-ldflags "-w -s \
-                  -X github.com/gnames/gnverifier.Build=${DATE} \
-                  -X github.com/gnames/gnverifier.Version=${VERSION}"
+                  -X github.com/gnames/$(PROJ_NAME)/pkg.Build=$(DATE) \
+                  -X github.com/gnames/$(PROJ_NAME)/pkg.Version=$(VERSION)"
+FLAGS_REL = -trimpath -ldflags "-s -w \
+						-X github.com/gnames/$(PROJ_NAME)/pkg.Build=$(DATE)"
+
 GOCMD=go
 GOINSTALL=$(GOCMD) install $(FLAGS_LD)
 GOBUILD=$(GOCMD) build $(FLAGS_LD)
+GORELEASE = $(GOCMD) build $(FLAGS_REL)
 GOCLEAN=$(GOCMD) clean
 GOGENERATE=$(GOCMD) generate
 GOGET = $(GOCMD) get
@@ -17,48 +24,57 @@ all: install
 
 test: deps install
 	@echo Run tests
-	$(FLAG_MODULE) go test -race ./...
+	$(GOCMD) test -shuffle=on -count=1 -race -coverprofile=coverage.txt ./...
+
+tools: deps
+	@echo Installing tools from tools.go
+	@cat tools.go | grep _ | awk -F'"' '{print $$2}' | xargs -tI % go install %
 
 deps:
 	@echo Download go.mod dependencies
 	$(GOCMD) mod download; \
 	$(GOGENERATE)
 
-tools: deps
-	@echo Installing tools from tools.go
-	@cat gnverifier/tools.go | grep _ | awk -F'"' '{print $$2}' | xargs -tI % go install %
-
 build:
+	@echo Building
 	$(GOGENERATE)
-	cd gnverifier; \
 	$(GOCLEAN); \
-	$(FLAGS_SHARED) $(GOBUILD);
+	$(NO_C) $(GOBUILD);
+
+buildrel:
+	@echo Building release binary
+	$(GOGENERATE)
+	$(GOCLEAN); \
+	$(NO_C) $(GORELEASE);
+
+install:
+	@echo Build and install locally
+	$(GOGENERATE)
+	$(NO_C) $(GOINSTALL);
 
 release: dockerhub
 	@echo Building releases for Linux, Mac, Windows
-	cd gnverifier; \
 	$(GOCLEAN); \
 	$(FLAGS_SHARED) GOOS=linux $(GOBUILD); \
-	tar zcvf /tmp/gnverifier-${VER}-linux.tar.gz gnverifier; \
+	tar zcvf /tmp/$(PROJ_NAME)-${VER}-linux.tar.gz $(PROJ_NAME); \
 	$(GOCLEAN); \
 	$(FLAGS_SHARED) GOOS=darwin $(GOBUILD); \
-	tar zcvf /tmp/gnverifier-${VER}-mac.tar.gz gnverifier; \
+	tar zcvf /tmp/$(PROJ_NAME)-${VER}-mac.tar.gz $(PROJ_NAME); \
+	$(GOCLEAN); \
+	$(NO_C) GOOS=darwin GOARCH=arm64 $(GOBUILD); \
+	tar zcvf /tmp/$(PROJ_NAME)-${VER}-mac-arm64.tar.gz $(PROJ_NAME); \
 	$(GOCLEAN); \
 	$(FLAGS_SHARED) GOOS=windows $(GOBUILD); \
-	zip -9 /tmp/gnverifier-${VER}-win-64.zip gnverifier.exe; \
+	zip -9 /tmp/$(PROJ_NAME)-${VER}-win-64.zip $(PROJ_NAME).exe; \
 	$(GOCLEAN);
 
-install:
-	$(GOGENERATE)
-	cd gnverifier; \
-	$(FLAGS_SHARED) $(GOINSTALL);
-
 docker: build
-	docker build -t gnames/gnverifier:latest -t gnames/gnverifier:$(VERSION) .; \
-	cd gnverifier; \
+	@echo Build Docker images
+	docker buildx build -t gnames/$(PROJ_NAME):latest -t gnames/$(PROJ_NAME):$(VERSION) .; \
 	$(GOCLEAN);
 
 dockerhub: docker
-	docker push gnames/gnverifier; \
-	docker push gnames/gnverifier:$(VERSION)
+	@echo Push Docker images to DockerHub
+	docker push gnames/$(PROJ_NAME); \
+	docker push gnames/$(PROJ_NAME):$(VERSION)
 

README.md

@@ -67,10 +67,10 @@ If you want to cite GNverifier, use [DOI generated by Zenodo][zenodo doi]:
   manual curation have priority over auto-curated and uncurated datasets. For
   example [Catalogue of Life] or [WoRMS] are considered curated,
   [GBIF] auto-curated, [uBio] not curated.
-- Fine-tunng the match score by matching authors, years, ranks etc.
+- Fine-tuning the match score by matching authors, years, ranks etc.
 - It is possible to map any name-strings checklist to any of registered
   Data Sources.
-- If a Data Source provides a classification for a name, it will be returned in
+- If a Data Source provides a classification for a name, it will be returned to
   the output.
 - The app works for checking just one name-string, or multiple ones written in
   a file.
@@ -151,7 +151,7 @@ go get github.com/gnames/gnverifier/gnverifier
 
 [GNverifier] takes one name-string or a text file with one name-string per
 line as an argument, sends a query with these data to a [remote GNames
-server][gnames] to match the name-strigs against many different biodiversity
+server][gnames] to match the name-strings against many biodiversity
 databases and returns results to STDOUT either in JSON, CSV or TSV format.
 
 The app can alto take a query string like
@@ -293,7 +293,7 @@ gnverifier -f tsv file.csv
 
 Note that a separate JSON "document" is returned for each separate record,
 instead of returning one big JSON document for all records. For large lists it
-significantly speeds up parsin of the JSON on the user side.
+significantly speeds up parsing of the JSON on the user side.
 
 #### jobs
 
@@ -372,7 +372,7 @@ gnverifier -p 8777 --web-logs
 
 ### nsqd-tcp
 
-Requires `--port`. Allows to redirect web-service log output to [NSQ]
+Requires `--port`. Allows redirecting web-service log output to [NSQ]
 messaging server's TCP-based endpoint. It is handy for aggregations of logs
 from [GNverifier] web-services running inside of Docker containers or in
 Kubernetes pods.
@@ -444,7 +444,7 @@ It includes following operators:
 option, if given, will overwrite this setting (`ds:1,2,172`).
 
 `tx:`
-: Parent taxon. Limits results to names that contain a particular higher taxon
+: Parent taxon. Limit results to names that contain a particular higher taxon
 in their classification. If `ds:` is given, uses the classification of the
 first data-source in the setting. If `ds:` is not given, uses managerial
 classification of the Catalogue of Life (`tx:Hemiptera`, `tx:Animalia`,
@@ -463,7 +463,7 @@ to enter several settings at once loosely following rules of nomenclature
 is possible to have abbreviated specific epithets or range in
 years: `n:Mono. gall. Oliv. 1750-1800`.
 
-Often there are errors in species eptithets gender. Because of that search
+Often there are errors in species epithets gender. Because of that search
 will try to detect names in any gender that correspond to the epithet.
 
 The search requires to have either `sp:`, `isp:` or `asp:` setting,

gnverifier/cmd/root.go → cmd/root.go

@@ -20,11 +20,11 @@ import (
 	"github.com/gnames/gnquery"
 	"github.com/gnames/gnquery/ent/search"
 	"github.com/gnames/gnsys"
-	"github.com/gnames/gnverifier"
-	"github.com/gnames/gnverifier/config"
-	"github.com/gnames/gnverifier/ent/output"
-	"github.com/gnames/gnverifier/io/verifrest"
-	"github.com/gnames/gnverifier/io/web"
+	"github.com/gnames/gnverifier/internal/ent/output"
+	"github.com/gnames/gnverifier/internal/io/verifrest"
+	"github.com/gnames/gnverifier/internal/io/web"
+	gnverifier "github.com/gnames/gnverifier/pkg"
+	"github.com/gnames/gnverifier/pkg/config"
 	"github.com/rs/zerolog"
 	"github.com/rs/zerolog/log"
 	"github.com/spf13/cobra"

go.mod

@@ -1,64 +1,62 @@
 module github.com/gnames/gnverifier
 
-go 1.19
+go 1.20
 
 require (
 	github.com/dnaeon/go-vcr v1.2.0
-	github.com/dustin/go-humanize v1.0.0
-	github.com/gnames/gnfmt v0.3.0
+	github.com/dustin/go-humanize v1.0.1
+	github.com/gnames/gnfmt v0.4.1
 	github.com/gnames/gnlib v0.14.0
 	github.com/gnames/gnquery v0.3.3
 	github.com/gnames/gnsys v0.2.2
 	github.com/gnames/gnuuid v0.1.1
-	github.com/labstack/echo/v4 v4.9.0
-	github.com/labstack/gommon v0.3.1
-	github.com/maxbrunsfeld/counterfeiter/v6 v6.5.0
-	github.com/rs/zerolog v1.28.0
+	github.com/labstack/echo/v4 v4.10.2
+	github.com/labstack/gommon v0.4.0
+	github.com/maxbrunsfeld/counterfeiter/v6 v6.6.1
+	github.com/rs/zerolog v1.29.0
 	github.com/sfgrp/lognsq v0.1.1
-	github.com/spf13/cobra v1.5.0
-	github.com/spf13/viper v1.13.0
-	github.com/stretchr/testify v1.8.0
+	github.com/spf13/cobra v1.6.1
+	github.com/spf13/viper v1.15.0
+	github.com/stretchr/testify v1.8.2
 	gopkg.in/yaml.v2 v2.4.0
 )
 
 require (
 	github.com/davecgh/go-spew v1.1.1 // indirect
-	github.com/fsnotify/fsnotify v1.5.4 // indirect
+	github.com/fsnotify/fsnotify v1.6.0 // indirect
 	github.com/gnames/gnstats v0.1.0 // indirect
 	github.com/golang-jwt/jwt v3.2.2+incompatible // indirect
 	github.com/golang/snappy v0.0.3 // indirect
 	github.com/google/uuid v1.2.0 // indirect
 	github.com/hashicorp/hcl v1.0.0 // indirect
-	github.com/inconshreveable/mousetrap v1.0.0 // indirect
+	github.com/inconshreveable/mousetrap v1.0.1 // indirect
 	github.com/json-iterator/go v1.1.12 // indirect
-	github.com/magiconair/properties v1.8.6 // indirect
-	github.com/mattn/go-colorable v0.1.12 // indirect
-	github.com/mattn/go-isatty v0.0.14 // indirect
+	github.com/magiconair/properties v1.8.7 // indirect
+	github.com/mattn/go-colorable v0.1.13 // indirect
+	github.com/mattn/go-isatty v0.0.17 // indirect
 	github.com/mitchellh/mapstructure v1.5.0 // indirect
 	github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd // indirect
 	github.com/modern-go/reflect2 v1.0.2 // indirect
 	github.com/nsqio/go-nsq v1.1.0 // indirect
-	github.com/pelletier/go-toml v1.9.5 // indirect
-	github.com/pelletier/go-toml/v2 v2.0.5 // indirect
+	github.com/pelletier/go-toml/v2 v2.0.6 // indirect
 	github.com/pmezard/go-difflib v1.0.0 // indirect
 	github.com/pointlander/compress v1.1.1-0.20190518213731-ff44bd196cc3 // indirect
 	github.com/pointlander/jetset v1.0.1-0.20190518214125-eee7eff80bd4 // indirect
 	github.com/pointlander/peg v1.0.1 // indirect
-	github.com/spf13/afero v1.8.2 // indirect
+	github.com/spf13/afero v1.9.3 // indirect
 	github.com/spf13/cast v1.5.0 // indirect
 	github.com/spf13/jwalterweatherman v1.1.0 // indirect
 	github.com/spf13/pflag v1.0.5 // indirect
-	github.com/subosito/gotenv v1.4.1 // indirect
+	github.com/subosito/gotenv v1.4.2 // indirect
 	github.com/valyala/bytebufferpool v1.0.0 // indirect
-	github.com/valyala/fasttemplate v1.2.1 // indirect
-	golang.org/x/crypto v0.0.0-20220411220226-7b82a4e95df4 // indirect
-	golang.org/x/mod v0.6.0-dev.0.20220106191415-9b9b3d81d5e3 // indirect
-	golang.org/x/net v0.0.0-20220520000938-2e3eb7b945c2 // indirect
-	golang.org/x/sys v0.0.0-20220520151302-bc2c85ada10a // indirect
-	golang.org/x/text v0.3.7 // indirect
-	golang.org/x/time v0.0.0-20201208040808-7e3f01d25324 // indirect
-	golang.org/x/tools v0.1.10 // indirect
-	golang.org/x/xerrors v0.0.0-20220517211312-f3a8303e98df // indirect
+	github.com/valyala/fasttemplate v1.2.2 // indirect
+	golang.org/x/crypto v0.6.0 // indirect
+	golang.org/x/mod v0.7.0 // indirect
+	golang.org/x/net v0.7.0 // indirect
+	golang.org/x/sys v0.5.0 // indirect
+	golang.org/x/text v0.7.0 // indirect
+	golang.org/x/time v0.3.0 // indirect
+	golang.org/x/tools v0.5.0 // indirect
 	gopkg.in/ini.v1 v1.67.0 // indirect
 	gopkg.in/yaml.v3 v3.0.1 // indirect
 )