update README.md and go.mod

.gitignore

@@ -7,3 +7,5 @@ vendor
 .DS_Store
 _log
 go.sum
+
+.XML.tmp*

ChangeLog

@@ -1,3 +1,7 @@
+2020-04-29 Li Jianfeng <[email protected]>
+
+		* support covid19 api
+
 2020-04-22 Li Jianfeng <[email protected]>
 
 		* bio.tools API support --from and --size flag

README.md

@@ -25,23 +25,23 @@ For website spider (optional):
 
 For raw sequencing data query (optional):
 
-- [sra-tools](https://github.com/ncbi/sra-tools) for SRA and dbGAP database: MAC and Windows user `bget i base/[email protected]`, Linux user `bget i base/sratools`;
+- [sra-tools](https://github.com/ncbi/sra-tools) for SRA and dbGAP database: `bget i sratools`;
 - [pyega3](https://github.com/EGA-archive/ega-download-client) for EGA database: `pip3 install pyega3`;
-- [gdc-client](https://gdc.cancer.gov/access-data/gdc-data-transfer-tool) for GDC portal: `bget i base/gdc-client@1.4.0 -u`.
+- [gdc-client](https://gdc.cancer.gov/access-data/gdc-data-transfer-tool) for GDC portal: `bget i gdc-client@1.5.0 -u`.
 
 ## Installation
 
 ```bash
 # windows
-wget https://github.com/openanno/bget/releases/download/v0.2.4/bget.exe
+wget https://github.com/openanno/bget/releases/download/v0.3.0/bget.exe
 
 # osx
-wget https://github.com/openanno/bget/releases/download/v0.2.4/bget_osx
+wget https://github.com/openanno/bget/releases/download/v0.3.0/bget_osx
 mv bget_osx bget
 chmod a+x bget
 
 # linux
-wget https://github.com/openanno/bget/releases/download/v0.2.4/bget_linux64
+wget https://github.com/openanno/bget/releases/download/v0.3.0/bget_linux64
 mv bget_linux64 bget
 chmod a+x bget
 
@@ -142,6 +142,41 @@ bget api mgrast anno --info
 bget api mgrast anno --evalue 100 --type organism --source SwissProt --seq mgm4447943.3
 
 bget api mgrast compute --info
+
+# returns all data in the system. Warning: this request returns 8MB+ and takes 5+ seconds
+bget api covid19 --all
+# returns all countries and associated provinces
+bget api covid19 --cts
+# returns all cases by case type for a country from the first recorded case.
+bget api covid19 --ct --name China
+# returns all cases by case type for a country from the first recorded case.
+bget api covid19 --ct-d-one --name China
+# returns all cases by case type for a country.
+bget api covid19 --ct-d-one-total --name China
+# returns all cases by case type for a country from the first recorded case with the latest record being the live count.
+bget api covid19 --ct-st-d-one --name China --status confirmed
+# returns all cases by case type for a country from the first recorded case.
+bget api covid19 --ct-st-d-one-live --name China --status confirmed
+# returns all cases by case type for a country from the first recorded case
+bget api covid19 --ct-st-d-one-total --name China --status confirmed
+# returns all cases by case type for a country with the latest record being the live count.
+bget api covid19 --ct-st-live --name China --status confirmed
+# returns all cases by case type for a country.
+bget api covid19 --ct-st --name China --status confirmed
+# returns all cases by case type for a country.
+bget api covid19 --ct-st-total --name China --status confirmed
+# returns all cases of a country.
+bget api covid19 --ct-total --name China
+# returns all live cases by case type for a country.
+bget api covid19 --live-ct --name China
+# returns all live cases by case type for a country after a given date.
+bget api covid19 --live-ct-st-date --name China --status confirmed --date 2020-04-20T06:20:47Z
+# returns all live cases by case type for a country.
+bget api covid19 --live-ct-st --name China --status confirmed
+# a summary of new and total cases per country
+bget api covid19 --summary
+bget api covid19 --export
+bget api covid19 --webhook https://your_webhook.com
 ```
 
 ### Query DOI resources

_examples/bapi.sh

@@ -35,6 +35,24 @@ bget api gdc -m -q "5b2974ad-f932-499b-90a3-93577a9f0573,556e5e3f-0ab9-4b6c-aa62
 bget api gdc -m -q "5b2974ad-f932-499b-90a3-93577a9f0573,556e5e3f-0ab9-4b6c-aa62-c42f6a6cf20c" -n
 bget api gdc -d -q "5b2974ad-f932-499b-90a3-93577a9f0573" -n
 bget api ncbi -q "Galectins control MTOR and AMPK in response to lysosomal damage to induce autophagy OR MTOR-independent autophagy induced by interrupted endoplasmic reticulum-mitochondrial Ca2+ communication: a dead end in cancer cells. OR The PARK10 gene USP24 is a negative regulator of autophagy and ULK1 protein stability OR Coordinate regulation of autophagy and the ubiquitin proteasome system by MTOR." | bioctl cvrt  --xml2json pubmed -
+bget api covid19 --all
+bget api covid19 --cts
+bget api covid19 --ct --name China
+bget api covid19 --ct-d-one --name China
+bget api covid19 --ct-d-one-total --name China
+bget api covid19 --ct-st-d-one --name China --status confirmed
+bget api covid19 --ct-st-d-one-live --name China --status confirmed
+bget api covid19 --ct-st-d-one-total --name China --status confirmed
+bget api covid19 --ct-st-live --name China --status confirmed
+bget api covid19 --ct-st --name China --status confirmed
+bget api covid19 --ct-st-total --name China --status confirmed
+bget api covid19 --ct-total --name China
+bget api covid19 --live-ct --name China
+bget api covid19 --live-ct-st-date --name China --status confirmed --date 2020-04-20T06:20:47Z
+bget api covid19 --live-ct-st --name China --status confirmed
+bget api covid19 --summary
+bget api covid19 --export
+bget api covid19 --webhook https://your_webhook.com
 
 cd ..
 bget --clean

_meta/tools/main.json

@@ -236,6 +236,9 @@
     "Name": "golang",
     "Description": "",
     "Versions": [
+      "1.14.2",
+      "1.14.1",
+      "1.14",
       "1.13.4",
       "1.13.3",
       "1.13.2",

api/cmd/covid19.go

@@ -0,0 +1,87 @@
+package cmd
+
+import (
+	"github.com/openanno/bget/api/fetch"
+	"github.com/openanno/bget/api/types"
+	"github.com/spf13/cobra"
+)
+
+var covid19Endp types.Covid19Endpoints
+var Covid19Cmd = &cobra.Command{
+	Use:   "covid19",
+	Short: "Query covid19api.com website APIs.",
+	Long:  `Query covid19api.com website APIs. Detail see https://covid19api.com`,
+	Run: func(cmd *cobra.Command, args []string) {
+		Covid19CmdRunOptions(cmd, args)
+	},
+}
+
+func Covid19CmdRunOptions(cmd *cobra.Command, args []string) {
+	if fetch.Covid19(&covid19Endp, &bapiClis, func() { initCmd(cmd, args) }, nil) {
+		bapiClis.HelpFlags = false
+	}
+	if bapiClis.HelpFlags {
+		cmd.Help()
+	}
+}
+
+func init() {
+	setGlobalFlag(Covid19Cmd, &bapiClis)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.AllRoute, "all", "", false, `Get all Data.`)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.CountriesRoute, "cts", "", false, `Get list of countries.`)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.CountryDayOneRoute, "ct-d-one", "", false, `Get list of cases per country per province by case type from the first recorded case.`)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.CountryDayOneTotalRoute, "ct-d-one-total", "", false, `Get list of cases per country by case type from the first recorded case.`)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.CountryRoute, "ct", "", false, `Get list of cases per country per province by case type.`)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.CountryStatusDayOneLiveRoute, "ct-st-d-one-live", "", false, `Get list of cases per country per province by case type from the first recorded case,  updated with latest live count.`)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.CountryStatusDayOneRoute, "ct-st-d-one", "", false, `Get list of cases per country per province by case type from the first recorded case".`)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.CountryStatusDayOneTotalRoute, "ct-st-d-one-total", "", false, `Get list of cases per country by case type from the first recorded case.`)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.CountryStatusLiveRoute, "ct-st-live", "", false, `Daily list of cases per country per province by case type, updated with latest live count.`)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.CountryStatusRoute, "ct-st", "", false, `Get list of cases per country per province by case type.`)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.CountryStatusTotalRoute, "ct-st-total", "", false, `Get list of cases per country by case type.`)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.CountryTotalRoute, "ct-total", "", false, `Get list of cases per country by case type.`)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.ExportRoute, "export", "", false, `Get all data as a zip file.`)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.LiveCountryRoute, "live-ct", "", false, `Get live list of cases per country per province by case type.`)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.LiveCountryStatusAfterDateRoute, "live-ct-st-date", "", false, `Get a time series of cases per country per province by case type after a date.`)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.LiveCountryStatusRoute, "live-ct-st", "", false, `Get a time series of cases per country per province by case type.`)
+	Covid19Cmd.Flags().BoolVarP(&covid19Endp.SummaryRoute, "summary", "", false, `Summary of new and total cases per country.`)
+	Covid19Cmd.Flags().StringVarP(&covid19Endp.WebhookRoute, "webhook", "", "", `Add a webhook to be notified when new data becomes available.`)
+
+	Covid19Cmd.Flags().StringVarP(&covid19Endp.Country, "name", "", "", `Country name.`)
+	Covid19Cmd.Flags().StringVarP(&covid19Endp.Status, "status", "", "", `Patient status [confirmed, recovered, deaths].`)
+	Covid19Cmd.Flags().StringVarP(&covid19Endp.Date, "date", "", "", `After a given date.`)
+
+	Covid19Cmd.Example = `  # returns all data in the system. Warning: this request returns 8MB+ and takes 5+ seconds
+  bget api covid19 --all
+  # returns all countries and associated provinces
+  bget api covid19 --cts
+  # returns all cases by case type for a country from the first recorded case.
+  bget api covid19 --ct --name China
+  # returns all cases by case type for a country from the first recorded case.
+  bget api covid19 --ct-d-one --name China
+  # returns all cases by case type for a country.
+  bget api covid19 --ct-d-one-total --name China
+  # returns all cases by case type for a country from the first recorded case with the latest record being the live count.
+  bget api covid19 --ct-st-d-one --name China --status confirmed
+  # returns all cases by case type for a country from the first recorded case.
+  bget api covid19 --ct-st-d-one-live --name China --status confirmed
+  # returns all cases by case type for a country from the first recorded case
+  bget api covid19 --ct-st-d-one-total --name China --status confirmed
+  # returns all cases by case type for a country with the latest record being the live count.
+  bget api covid19 --ct-st-live --name China --status confirmed
+  # returns all cases by case type for a country.
+  bget api covid19 --ct-st --name China --status confirmed
+  # returns all cases by case type for a country.
+  bget api covid19 --ct-st-total --name China --status confirmed
+  # returns all cases of a country.
+  bget api covid19 --ct-total --name China
+  # returns all live cases by case type for a country. 
+  bget api covid19 --live-ct --name China
+  # returns all live cases by case type for a country after a given date.
+  bget api covid19 --live-ct-st-date --name China --status confirmed --date 2020-04-20T06:20:47Z
+  # returns all live cases by case type for a country.
+  bget api covid19 --live-ct-st --name China --status confirmed
+  # a summary of new and total cases per country
+  bget api covid19 --summary
+  bget api covid19 --export
+  bget api covid19 --webhook https://your_webhook.com`
+}

api/cmd/root.go

@@ -44,6 +44,7 @@ func init() {
 	BapiCmd.AddCommand(Dataset2toolsCmd)
 	BapiCmd.AddCommand(CligovCmd)
 	BapiCmd.AddCommand(CrossRefCmd)
+	BapiCmd.AddCommand(Covid19Cmd)
 	wd, _ := os.Getwd()
 
 	BapiCmd.PersistentFlags().StringVarP(&(bapiClis.TaskID), "task-id", "k", stringo.RandString(15), "Task ID (random).")

api/fetch/covid19.go

@@ -0,0 +1,95 @@
+package fetch
+
+import (
+	"encoding/json"
+	"io"
+	"strings"
+
+	"github.com/openbiox/ligo/stringo"
+
+	"github.com/openanno/bget/api/types"
+)
+
+const Covid19Host = "https://api.covid19api.com/"
+
+// Covid19 access api.covid19api.com API
+func Covid19(endpoints *types.Covid19Endpoints, bapiClis *types.BapiClisT, f func(), of io.Writer) bool {
+	setLog(bapiClis)
+	if bapiClis.Format == "" {
+		bapiClis.Format = "json"
+	}
+	netopt := setNetOpt(bapiClis)
+	url := Covid19Host + setCovid19QuerySuffix(endpoints, bapiClis)
+	if url == Covid19Host || url == Covid19Host+"?fmt=json" {
+		return false
+	}
+	f()
+	if endpoints.WebhookRoute != "" {
+		val := make(map[string]string)
+		val["URL"] = endpoints.WebhookRoute
+		postData, _ := json.MarshalIndent(val, "", " ")
+
+		PostReq("api.mg-rast.org", url, postData, bapiClis, netopt, of)
+	} else {
+		GetReq("api.covid19api.com", url, bapiClis, netopt, of)
+	}
+
+	return true
+}
+
+func setCovid19QuerySuffix(endpoints *types.Covid19Endpoints, BapiClis *types.BapiClisT) (suffix string) {
+	suffixList := []string{}
+	if endpoints.AllRoute {
+		suffix = "all"
+	} else if endpoints.CountriesRoute {
+		suffix = "countries"
+	} else if endpoints.CountryDayOneRoute {
+		suffix = "dayone/country/:country"
+	} else if endpoints.CountryDayOneTotalRoute {
+		suffix = "total/dayone/country/:country"
+	} else if endpoints.CountryRoute {
+		suffix = "country/:country"
+	} else if endpoints.CountryStatusDayOneLiveRoute {
+		suffix = "dayone/country/:country/status/:status/live"
+	} else if endpoints.CountryStatusDayOneRoute {
+		suffix = "dayone/country/:country/status/:status"
+	} else if endpoints.CountryStatusDayOneTotalRoute {
+		suffix = "total/dayone/country/:country/status/:status"
+	} else if endpoints.CountryStatusLiveRoute {
+		suffix = "country/:country/status/:status/live"
+	} else if endpoints.CountryStatusRoute {
+		suffix = "country/:country/status/:status"
+	} else if endpoints.CountryStatusTotalRoute {
+		suffix = "total/country/:country/status/:status"
+	} else if endpoints.CountryTotalRoute {
+		suffix = "total/country/:country"
+	} else if endpoints.ExportRoute {
+		suffix = "export"
+	} else if endpoints.LiveCountryRoute {
+		suffix = "live/country/:country"
+	} else if endpoints.LiveCountryStatusAfterDateRoute {
+		suffix = "live/country/:country/status/:status/date/:date"
+	} else if endpoints.LiveCountryStatusRoute {
+		suffix = "live/country/:country/status/:status"
+	} else if endpoints.SummaryRoute {
+		suffix = "summary"
+	} else if endpoints.WebhookRoute != "" {
+		suffix = "webhook"
+	}
+	if strings.Contains(suffix, ":country") {
+		suffix = stringo.StrReplaceAll(suffix, ":country", endpoints.Country)
+	}
+	if strings.Contains(suffix, ":status") {
+		suffix = stringo.StrReplaceAll(suffix, ":status", endpoints.Status)
+	}
+	if strings.Contains(suffix, ":date") {
+		suffix = stringo.StrReplaceAll(suffix, ":date", endpoints.Date)
+	}
+	if BapiClis.Extra != "" {
+		suffixList = append(suffixList, BapiClis.Extra)
+	}
+	if len(suffixList) > 0 {
+		suffix = suffix + "?" + strings.Join(suffixList, "&")
+	}
+	return suffix
+}

api/types/api.go

@@ -139,3 +139,29 @@ type MgRastEndpoints struct {
 
 	Auth string
 }
+
+// Covid19Endpoints is https://api.covid19api.com/ website endpoints
+type Covid19Endpoints struct {
+	AllRoute                        bool
+	CountriesRoute                  bool
+	CountryDayOneRoute              bool
+	CountryDayOneTotalRoute         bool
+	CountryRoute                    bool
+	CountryStatusDayOneLiveRoute    bool
+	CountryStatusDayOneRoute        bool
+	CountryStatusDayOneTotalRoute   bool
+	CountryStatusLiveRoute          bool
+	CountryStatusRoute              bool
+	CountryStatusTotalRoute         bool
+	CountryTotalRoute               bool
+	ExportRoute                     bool
+	LiveCountryRoute                bool
+	LiveCountryStatusAfterDateRoute bool
+	LiveCountryStatusRoute          bool
+	SummaryRoute                    bool
+	WebhookRoute                    string
+
+	Country string
+	Status  string
+	Date    string
+}

go.mod

@@ -9,26 +9,23 @@ require (
 	github.com/biogo/ncbi v1.0.2
 	github.com/bitly/go-simplejson v0.5.0 // indirect
 	github.com/bmizerany/assert v0.0.0-20160611221934-b7ed37b82869 // indirect
-	github.com/chromedp/cdproto v0.0.0-20200209033844-7e00b02ea7d2 // indirect
+	github.com/chromedp/cdproto v0.0.0-20200424080200-0de008e41fa0 // indirect
 	github.com/chromedp/chromedp v0.5.3
 	github.com/gobwas/ws v1.0.3 // indirect
 	github.com/gocolly/colly v1.2.0
 	github.com/google/go-github/v27 v27.0.6
+	github.com/konsorten/go-windows-terminal-sequences v1.0.3 // indirect
 	github.com/mailru/easyjson v0.7.1 // indirect
 	github.com/mattn/go-runewidth v0.0.9 // indirect
-	github.com/nwaples/rardecode v1.1.0 // indirect
 	github.com/olekukonko/tablewriter v0.0.4
 	github.com/onsi/ginkgo v1.11.0 // indirect
 	github.com/onsi/gomega v1.8.1 // indirect
-	github.com/openbiox/ligo v0.0.0-20200422182023-2b3120cef2ab
-	github.com/pierrec/lz4 v2.5.2+incompatible // indirect
+	github.com/openbiox/ligo v0.0.0-20200429101038-6db14930de2a
 	github.com/sirupsen/logrus v1.5.0
 	github.com/spf13/cobra v1.0.0
-	github.com/spf13/pflag v1.0.5 // indirect
 	github.com/tidwall/pretty v1.0.1
-	github.com/ulikunitz/xz v0.5.7 // indirect
-	github.com/vbauerster/mpb/v5 v5.0.3
-	golang.org/x/net v0.0.0-20200421231249-e086a090c8fd // indirect
+	github.com/vbauerster/mpb/v5 v5.0.4
+	golang.org/x/crypto v0.0.0-20200427165652-729f1e841bcc // indirect
 	golang.org/x/oauth2 v0.0.0-20200107190931-bf48bf16ab8d
-	google.golang.org/appengine v1.6.6 // indirect
+	golang.org/x/sys v0.0.0-20200428200454-593003d681fa // indirect
 )