From 21ad7b17910c82002888d57bf2ea4b584da46a27 Mon Sep 17 00:00:00 2001 From: "R. S. Doiel" Date: Tue, 12 Sep 2023 16:28:34 -0700 Subject: [PATCH 01/11] feat: implemented very fast clone of part of EPrint REST API for the eprint dataset, eprintrest --- .gitignore | 2 + Makefile | 2 +- cmd/eprintrest/eprintrest.go | 166 +++++++++ doi2rdm.1.md | 2 +- eprint2rdm.1.md | 2 +- eprintrest.1.html | 115 ++++++ eprintrest.1.md | 81 +++++ eprintrest.go | 336 ++++++++++++++++++ man/man1/doi2rdm.1 | 2 +- man/man1/eprint2rdm.1 | 2 +- man/man1/eprintrest.1 | 101 ++++++ man/man1/people2vocabulary.1 | 2 +- man/man1/rdmutil.1 | 2 +- pagefind/fragment/unknown_7cf1198.pf_fragment | Bin 0 -> 922 bytes pagefind/index/unknown_68fceb6.pf_index | Bin 0 -> 17900 bytes pagefind/pagefind-entry.json | 2 +- .../pagefind.unknown_29fa54e2969ebdb.pf_meta | Bin 0 -> 215 bytes people2vocabulary.1.md | 2 +- rdmutil.1.md | 2 +- version.go | 2 +- 20 files changed, 812 insertions(+), 11 deletions(-) create mode 100644 cmd/eprintrest/eprintrest.go create mode 100644 eprintrest.1.html create mode 100644 eprintrest.1.md create mode 100644 eprintrest.go create mode 100644 man/man1/eprintrest.1 create mode 100644 pagefind/fragment/unknown_7cf1198.pf_fragment create mode 100644 pagefind/index/unknown_68fceb6.pf_index create mode 100644 pagefind/pagefind.unknown_29fa54e2969ebdb.pf_meta diff --git a/.gitignore b/.gitignore index c404eeef..7fd0ec6d 100644 --- a/.gitignore +++ b/.gitignore @@ -107,3 +107,5 @@ test-*.txt *.yaml s3_uploads/ migration/ +testdata +*.bash diff --git a/Makefile b/Makefile index fcf7b9d9..e7b4b60c 100644 --- a/Makefile +++ b/Makefile @@ -9,7 +9,7 @@ RELEASE_DATE = $(shell date +%Y-%m-%d) RELEASE_HASH=$(shell git log --pretty=format:'%h' -n 1) -PROGRAMS = rdmutil eprint2rdm doi2rdm people2vocabulary # $(shell ls -1 cmd) +PROGRAMS = rdmutil eprint2rdm eprintrest doi2rdm people2vocabulary # $(shell ls -1 cmd) MAN_PAGES = $(shell ls -1 *.1.md | sed -E 's/\.1.md/.1/g') diff --git a/cmd/eprintrest/eprintrest.go b/cmd/eprintrest/eprintrest.go new file mode 100644 index 00000000..6e972812 --- /dev/null +++ b/cmd/eprintrest/eprintrest.go @@ -0,0 +1,166 @@ +// eprintrest is a command line program that re-creates a EPrints 3.x REST +// API running on localhost. It requires access to the repository's +// "archives" directory as well as the MySQL database. +// +// @author R. S. Doiel, +// @author Tom Morrell, +// +// Copyright (c) 2023, Caltech +// All rights not granted herein are expressly reserved by Caltech. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// 1. Redistributions of source code must retain the above copyright notice, +// this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright notice, +// this list of conditions and the following disclaimer in the documentation +// and/or other materials provided with the distribution. +// +// 3. Neither the name of the copyright holder nor the names of its contributors +// may be used to endorse or promote products derived from this software without +// specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE +// LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +// SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +// INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +// CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +// ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +// POSSIBILITY OF SUCH DAMAGE. +package main + +import ( + "flag" + "fmt" + "os" + "path" + + // Caltech Library packages + "github.com/caltechlibrary/irdmtools" +) + +var ( + helpText = `%{app_name}(1) irdmtools user manual | version {version} {release_hash} +% R. S. Doiel and Tom Morrell +% {release_date} + +# NAME + +{app_name} + +# SYNOPSIS + +{app_name} [OPTIONS] + +# DESCRIPTION + +{app_name} is a Caltech Library centric localhost web service +that creates a funcionally similar replica of the EPrints REST API +for EPrints 3.3.x based repositories. It uses the path to the +"archives" directory and a MySQL Database for the repository. +It only supports "archive" eprint.eprint_status records and +only the complete XML. Start up time is slow because it builds +the data structures representing the content in memory. This +makes the response times to request VERY fast compared to +the EPrints REST API. + +NOTE: the rest API does not enforce user permissions, restrictions +or roles. It is a minimal READ ONLY re-implementation of the EPrints 3.3 +REST API! + +The application is configured from the environment. The following +environment variables need to be set. + +REPO_ID +: The repository id string (e.g. caltechauthors). Also the name of the database for the repository. + +EPRINT_ARCHIVES_PATH +: A path to the "archives" directory holding your repository content +(e.g. /usr/local/eprints/archives) + +DB_USER +: The user name needed to access the MySQL database[^1] + +DB_PASSWORD +: The password needed to access the MySQL database[^1] + +REST_PORT +: The localhost port to use for the read only REST API. + +[^1]: MySQL, like this REST service assumes to be running on localhost. + + +# OPTIONS + +-help +: display help + +-license +: display license + +-version +: display version + + +# EXAMPLE + +This is an example environment + +~~~ +REPO_ID="caltechauthors" +EPRINT_ARCHIVES_PATH="/code/eprints3.3/archives" +REST_PORT=80 +DB_USER="eprints" +DB_PASSWORD="something_secret_here" +~~~ + +Running the localhost REST API clone + +~~~ +{app_name} +~~~ + +` +) + +func main() { + appName := path.Base(os.Args[0]) + // NOTE: The following are set when version.go is generated + version := irdmtools.Version + releaseDate := irdmtools.ReleaseDate + releaseHash := irdmtools.ReleaseHash + fmtHelp := irdmtools.FmtHelp + + showHelp, showVersion, showLicense := false, false, false + flag.BoolVar(&showHelp, "help", false, "display help") + flag.BoolVar(&showVersion, "version", false, "display version") + flag.BoolVar(&showLicense, "license", false, "display license") + + flag.Parse() + + if showHelp { + fmt.Fprintf(os.Stdout, "%s\n", fmtHelp(helpText, appName, version, releaseDate, releaseHash)) + os.Exit(0) + } + if showVersion { + fmt.Fprintf(os.Stdout, "%s %s %s\n", appName, version, releaseHash) + os.Exit(0) + } + if showLicense { + fmt.Fprintf(os.Stdout, "%s\n", irdmtools.LicenseText) + os.Exit(0) + } + + // Create a appity object + app := new(irdmtools.EPrintRest) + if err := app.Run(os.Stdin, os.Stdout, os.Stderr); err != nil { + fmt.Fprintf(os.Stderr, "%s\n", err) + os.Exit(1) + } +} diff --git a/doi2rdm.1.md b/doi2rdm.1.md index ef856150..4ca7b598 100644 --- a/doi2rdm.1.md +++ b/doi2rdm.1.md @@ -1,4 +1,4 @@ -%doi2rdm(1) irdmtools user manual | version 0.0.48 fb9e58e +%doi2rdm(1) irdmtools user manual | version 0.0.48 0238bfa % R. S. Doiel and Tom Morrell % 2023-09-12 diff --git a/eprint2rdm.1.md b/eprint2rdm.1.md index c90a7668..6f6e760d 100644 --- a/eprint2rdm.1.md +++ b/eprint2rdm.1.md @@ -1,4 +1,4 @@ -%eprint2rdm(1) irdmtools user manual | version 0.0.48 fb9e58e +%eprint2rdm(1) irdmtools user manual | version 0.0.48 0238bfa % R. S. Doiel and Tom Morrell % 2023-09-12 diff --git a/eprintrest.1.html b/eprintrest.1.html new file mode 100644 index 00000000..007b8e86 --- /dev/null +++ b/eprintrest.1.html @@ -0,0 +1,115 @@ + + + + Institutional Repository Data Management + + + + +
+Caltech Library logo +
+ + +
+

NAME

+

eprintrest

+

SYNOPSIS

+

eprintrest OPTIONS

+

DESCRIPTION

+

eprintrest is a Caltech Library centric localhost web service that +creates a funcionally similar replica of the EPrints REST API for +EPrints 3.3.x based repositories. It uses the path to the “archives” +directory and a MySQL Database for the repository. It only supports +“archive” eprint.eprint_status records and only the complete XML. Start +up time is slow because it builds the data structures representing the +content in memory. This makes the response times to request VERY fast +compared to the EPrints REST API.

+

NOTE: the rest API does not enforce user permissions, restrictions or +roles. It is a minimal READ ONLY re-implementation of the EPrints 3.3 +REST API!

+

The application is configured from the environment. The following +environment variables need to be set.

+
+
REPO_ID
+
+The repository id string (e.g. caltechauthors). Also the name of the +database for the repository. +
+
EPRINT_ARCHIVES_PATH
+
+A path to the “archives” directory holding your repository content +(e.g. /usr/local/eprints/archives) +
+
DB_USER
+
+The user name needed to access the MySQL database1 +
+
DB_PASSWORD
+
+The password needed to access the MySQL database2 +
+
REST_PORT
+
+The localhost port to use for the read only REST API. +
+
+

OPTIONS

+
+
-help
+
+display help +
+
-license
+
+display license +
+
-version
+
+display version +
+
+

EXAMPLE

+

This is an example environment

+
REPO_ID="caltechauthors"
+EPRINT_ARCHIVES_PATH="/code/eprints3.3/archives"
+REST_PORT=80
+DB_USER="eprints"
+DB_PASSWORD="something_secret_here"
+

Running the localhost REST API clone

+
eprintrest
+ +
+ + + + diff --git a/eprintrest.1.md b/eprintrest.1.md new file mode 100644 index 00000000..6838b4c8 --- /dev/null +++ b/eprintrest.1.md @@ -0,0 +1,81 @@ +%eprintrest(1) irdmtools user manual | version 0.0.48 0238bfa +% R. S. Doiel and Tom Morrell +% 2023-09-12 + +# NAME + +eprintrest + +# SYNOPSIS + +eprintrest [OPTIONS] + +# DESCRIPTION + +eprintrest is a Caltech Library centric localhost web service +that creates a funcionally similar replica of the EPrints REST API +for EPrints 3.3.x based repositories. It uses the path to the +"archives" directory and a MySQL Database for the repository. +It only supports "archive" eprint.eprint_status records and +only the complete XML. Start up time is slow because it builds +the data structures representing the content in memory. This +makes the response times to request VERY fast compared to +the EPrints REST API. + +NOTE: the rest API does not enforce user permissions, restrictions +or roles. It is a minimal READ ONLY re-implementation of the EPrints 3.3 +REST API! + +The application is configured from the environment. The following +environment variables need to be set. + +REPO_ID +: The repository id string (e.g. caltechauthors). Also the name of the database for the repository. + +EPRINT_ARCHIVES_PATH +: A path to the "archives" directory holding your repository content +(e.g. /usr/local/eprints/archives) + +DB_USER +: The user name needed to access the MySQL database[^1] + +DB_PASSWORD +: The password needed to access the MySQL database[^1] + +REST_PORT +: The localhost port to use for the read only REST API. + +[^1]: MySQL, like this REST service assumes to be running on localhost. + + +# OPTIONS + +-help +: display help + +-license +: display license + +-version +: display version + + +# EXAMPLE + +This is an example environment + +~~~ +REPO_ID="caltechauthors" +EPRINT_ARCHIVES_PATH="/code/eprints3.3/archives" +REST_PORT=80 +DB_USER="eprints" +DB_PASSWORD="something_secret_here" +~~~ + +Running the localhost REST API clone + +~~~ +eprintrest +~~~ + + diff --git a/eprintrest.go b/eprintrest.go new file mode 100644 index 00000000..0bb4a095 --- /dev/null +++ b/eprintrest.go @@ -0,0 +1,336 @@ +// irdmtools is a package for working with institutional repositories and +// data management systems. Current implementation targets Invenio-RDM. +// +// @author R. S. Doiel, +// @author Tom Morrell, +// +// Copyright (c) 2023, Caltech +// All rights not granted herein are expressly reserved by Caltech. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// 1. Redistributions of source code must retain the above copyright notice, +// this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright notice, +// this list of conditions and the following disclaimer in the documentation +// and/or other materials provided with the distribution. +// +// 3. Neither the name of the copyright holder nor the names of its contributors +// may be used to endorse or promote products derived from this software without +// specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE +// LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +// SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +// INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +// CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +// ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +// POSSIBILITY OF SUCH DAMAGE. +package irdmtools + +import ( + "database/sql" + "fmt" + "io" + "log" + "net/http" + "os" + "strings" + "time" + + // 3rd Party packages + _ "github.com/go-sql-driver/mysql" +) + +// EPrintRest the "app" structure for the service. +type EPrintRest struct { + RepoID string `json:"repo_id,required"` + EPrintArchivesPath string `json:"eprint_archives_path,required"` + Port string `json:"rest_port,omitempty"` + DbHost string `json:"db_host,omitempty` + DbUser string `json:"db_user,omitempty` + DbPassword string `json:"db_password,omitempty` + in io.Reader + out io.Writer + eout io.Writer +} + +var ( + restPage = ` + + + {repo_id} REST: Datasets + + +

{repo_id} REST: Datasets

+ + +` + + datasetPage = ` + + + {repo_id} REST: {dataset} DataSet + + +

{repo_id} REST: {dataset} DataSet

+
    + {list_of_li} +
+ +` + + idFields = map[string]string{ + "eprint": "eprintid", + "user": "userid", + "subject": "subjectid", + } +) + +// LoadEnv settings from the enviroment to run a local host clone +// of the EPrints REST API using the archives content and MySQL database. +func (app *EPrintRest) LoadEnv() { + app.RepoID = os.Getenv("REPO_ID") + app.EPrintArchivesPath = os.Getenv("EPRINT_ARCHIVES_PATH") + app.Port = os.Getenv("REST_PORT") + if app.Port == "" { + app.Port = ":8003" + } else if ! strings.HasPrefix(app.Port, ":") { + app.Port = ":" + app.Port + } + app.DbUser = os.Getenv("DB_USER") + app.DbPassword = os.Getenv("DB_PASSWORD") +} + +func transformTxt(s string, target string, dest string) string { + return strings.ReplaceAll(s, target, dest) +} + +// MkDatasetPage takes the simple page template and maps the dataset and label +// rendering the HTML page as a string +func (app *EPrintRest) MkDatasetPage(db *sql.DB, tmpl string, dataset string, label string) (string, error) { + src := transformTxt(transformTxt(tmpl, "{repo_id}", app.RepoID), "{dataset}", label) + // Figure out which dataset we're working with and retrieve the ids building a list of + // LI elements in the form `
  • {id}.xml
    • ` + items := []string{} + idField, ok := idFields[dataset] + if !ok { + return "", fmt.Errorf("%q is not a supported dataset", dataset) + } + queryTxt := transformTxt(transformTxt(`SELECT {idField} AS id FROM {dataset} ORDER BY {idField}`, `{idField}`, idField), `{dataset}`, dataset) + rows, err := db.Query(queryTxt) + if err != nil { + return "", err + } + defer rows.Close() + liTmpl := transformTxt(`
  • {id}.xml
    • `, `{dataset}`, dataset) + for rows.Next() { + var id string + if err := rows.Scan(&id); err != nil { + return "", err + } + items = append(items, transformTxt(liTmpl, `{id}`, id)) + + } + return transformTxt(src, "{list_of_li}", strings.Join(items, "\n")), nil +} + +// RequestLogger logs http request to service +func RequestLogger(targetMux http.Handler) http.Handler { + return http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) { + start := time.Now() + targetMux.ServeHTTP(w, r) + + // log request by who(IP address) + requesterIP := r.RemoteAddr + + log.Printf( + "%s\t\t%s\t\t%s\t\t%v", + r.Method, + r.RequestURI, + requesterIP, + time.Since(start), + ) + }) + } + +// EPrintXMLPath takes the app setup and generates the path do the EPrintXML document from +// an id. +func (app *EPrintRest) EPrintXMLPath(db *sql.DB, id string) (string, error) { + queryTxt := `SELECT IFNULL(dir, "") AS dir, IFNULL(rev_number, "") AS rev_number FROM eprint WHERE eprintid = ?` + rows, err := db.Query(queryTxt, id) + if err != nil { + return "", err + } + defer rows.Close() + for rows.Next() { + var ( + dir string + revNumber string + ) + if err := rows.Scan(&dir, &revNumber); err != nil { + return "", err + } + return fmt.Sprintf("%s/%s/documents/%s/revisions/%s.xml", app.EPrintArchivesPath, app.RepoID, dir, revNumber), nil + } + return "", fmt.Errorf("failed to get next row for eprintid %q", id) +} + +func getIds(db *sql.DB, dataset string) ([]string, error) { + idField, ok := idFields[dataset] + if ! ok { + return nil, fmt.Errorf("unsupported dataset %q", dataset) + } + whereClause := "" + if dataset == "eprint" { + whereClause = `WHERE eprint_status = "archive"` + } + queryTxt := fmt.Sprintf(`SELECT %s FROM %s %s ORDER BY %s`, idField, dataset, whereClause, idField) + ids := []string{} + rows, err := db.Query(queryTxt) + if err != nil { + return nil, err + } + defer rows.Close() + for rows.Next() { + var id string + if err := rows.Scan(&id); err != nil { + return nil, err + } + ids = append(ids, id) + } + return ids, nil +} + +// Serve runs the web service minimally replicating the EPrints 3.x +// REST API. +func (app *EPrintRest) ListenAndServe() error { + db, err := sql.Open("mysql", fmt.Sprintf("%s:%s@/%s", app.DbUser, app.DbPassword, app.RepoID)) + if err != nil { + return err + } + defer db.Close() + + // Preload set pages, content and cache the id list pages + eprintSrc, err := app.MkDatasetPage(db, datasetPage, "eprint", "EPrints") + if err != nil { + return err + } + userSrc, err := app.MkDatasetPage(db, datasetPage, "user", "Users") + if err != nil { + return err + } + subjectSrc, err := app.MkDatasetPage(db, datasetPage, "subject", "Subjects") + if err != nil { + return err + } + restPageSrc := transformTxt(restPage, "{repo_id}", app.RepoID) + + + // Set up our server Mux + mux := http.NewServeMux() + + // Map the on URLs to the disk path to EPrint XML files with the latest version. + eprintXML := map[string]string{} + ids, err := getIds(db, "eprint") + tot := len(ids) + cnt := 0 + for i, id := range ids { + var ( + fName string + src []byte + err error + ) + apiPath := fmt.Sprintf("/rest/eprint/%s.xml", id) + fName, err = app.EPrintXMLPath(db, id) + if err != nil { + return err + } + src, err = os.ReadFile(fName) + if err != nil { + log.Printf("skipping, failed to read record %s from %s", id, fName) + continue + } + eprintXML[apiPath] = fmt.Sprintf("%s", src) + cnt += 1 + if (i % 1000) == 0 { + log.Printf("scanned %d/%d records, read %d", i, tot, cnt) + } + } + log.Printf("found %d/%d records", cnt, tot) + // Handle `/rest/eprint/` and the individual EPrint XML responses + mux.HandleFunc("/rest/eprint/", func(w http.ResponseWriter, req *http.Request) { + // FIXME: Set content type to HTML + if req.URL.Path == "/rest/eprint/" { + io.WriteString(w, eprintSrc) + return + } + if txt, ok := eprintXML[req.URL.Path]; ok { + io.WriteString(w, txt) + return + } + http.Error(w, http.StatusText(http.StatusNotFound), http.StatusNotFound) + }) + + // Handle `/rest/user/` + mux.HandleFunc("/rest/user/", func(w http.ResponseWriter, req *http.Request) { + // FIXME: Set content type to HTML + if req.URL.Path == "/rest/user/" { + io.WriteString(w, userSrc) + return + } + http.Error(w, http.StatusText(http.StatusNotFound), http.StatusNotFound) + }) + + // Handle `/rest/subject/` + mux.HandleFunc("/rest/subject/", func(w http.ResponseWriter, req *http.Request) { + // FIXME: Set content type to HTML + if req.URL.Path == "/rest/subject/" { + io.WriteString(w, subjectSrc) + return + } + http.Error(w, http.StatusText(http.StatusNotFound), http.StatusNotFound) + }) + + // Handle of REST API page `/rest/` and '/' with restPage + mux.HandleFunc("/rest/", func(w http.ResponseWriter, req *http.Request) { + // FIXME: Set content type to HTML + io.WriteString(w, restPageSrc) + }) + /* + mux.HandleFunc("/", func(w http.ResponseWriter, req *http.Request) { + // FIXME: Set content type to HTML + io.WriteString(w, restPageSrc) + }) + */ + // FIXME need to setup a 404 error page response. + log.Printf("Starting REST API for %q up listening on http://localhost%s", app.RepoID, app.Port) + return http.ListenAndServe(app.Port, RequestLogger(mux)) +} + +// Run loads a configuration from the environment and does a sanity check of the service setup +// maps standard in, out and error to the service then invokes app.ListenAndServe(). +func (app *EPrintRest) Run(in io.Reader, out io.Writer, eout io.Writer) error { + app.LoadEnv() + // Sanity check the application's settings. + if app.RepoID == "" || app.EPrintArchivesPath == "" || app.Port == "" { + return fmt.Errorf("repoID, eprint archives path or rest port number missing") + } + if app.DbUser == "" || app.DbPassword == "" { + return fmt.Errorf("MySQL EPrint database access not configured") + } + app.in = in + app.out = out + app.eout = eout + return app.ListenAndServe() +} diff --git a/man/man1/doi2rdm.1 b/man/man1/doi2rdm.1 index b1b4f72e..88040c2b 100644 --- a/man/man1/doi2rdm.1 +++ b/man/man1/doi2rdm.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "doi2rdm" "1" "2023-09-12" "irdmtools user manual" "version 0.0.48 fb9e58e" +.TH "doi2rdm" "1" "2023-09-12" "irdmtools user manual" "version 0.0.48 0238bfa" .hy .SH NAME .PP diff --git a/man/man1/eprint2rdm.1 b/man/man1/eprint2rdm.1 index c3c4be69..44956c33 100644 --- a/man/man1/eprint2rdm.1 +++ b/man/man1/eprint2rdm.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "eprint2rdm" "1" "2023-09-12" "irdmtools user manual" "version 0.0.48 fb9e58e" +.TH "eprint2rdm" "1" "2023-09-12" "irdmtools user manual" "version 0.0.48 0238bfa" .hy .SH NAME .PP diff --git a/man/man1/eprintrest.1 b/man/man1/eprintrest.1 new file mode 100644 index 00000000..bd3c58f0 --- /dev/null +++ b/man/man1/eprintrest.1 @@ -0,0 +1,101 @@ +.\" Automatically generated by Pandoc 3.1.4 +.\" +.\" Define V font for inline verbatim, using C font in formats +.\" that render this, and otherwise B font. +.ie "\f[CB]x\f[]"x" \{\ +. ftr V B +. ftr VI BI +. ftr VB B +. ftr VBI BI +.\} +.el \{\ +. ftr V CR +. ftr VI CI +. ftr VB CB +. ftr VBI CBI +.\} +.TH "eprintrest" "1" "2023-09-12" "irdmtools user manual" "version 0.0.48 0238bfa" +.hy +.SH NAME +.PP +eprintrest +.SH SYNOPSIS +.PP +eprintrest OPTIONS +.SH DESCRIPTION +.PP +eprintrest is a Caltech Library centric localhost web service that +creates a funcionally similar replica of the EPrints REST API for +EPrints 3.3.x based repositories. +It uses the path to the \[lq]archives\[rq] directory and a MySQL +Database for the repository. +It only supports \[lq]archive\[rq] eprint.eprint_status records and only +the complete XML. +Start up time is slow because it builds the data structures representing +the content in memory. +This makes the response times to request VERY fast compared to the +EPrints REST API. +.PP +NOTE: the rest API does not enforce user permissions, restrictions or +roles. +It is a minimal READ ONLY re-implementation of the EPrints 3.3 REST API! +.PP +The application is configured from the environment. +The following environment variables need to be set. +.TP +REPO_ID +The repository id string (e.g.\ caltechauthors). +Also the name of the database for the repository. +.TP +EPRINT_ARCHIVES_PATH +A path to the \[lq]archives\[rq] directory holding your repository +content (e.g.\ /usr/local/eprints/archives) +.TP +DB_USER +The user name needed to access the MySQL database[1] +.TP +DB_PASSWORD +The password needed to access the MySQL database[2] +.TP +REST_PORT +The localhost port to use for the read only REST API. +.SH OPTIONS +.TP +-help +display help +.TP +-license +display license +.TP +-version +display version +.SH EXAMPLE +.PP +This is an example environment +.IP +.nf +\f[C] +REPO_ID=\[dq]caltechauthors\[dq] +EPRINT_ARCHIVES_PATH=\[dq]/code/eprints3.3/archives\[dq] +REST_PORT=80 +DB_USER=\[dq]eprints\[dq] +DB_PASSWORD=\[dq]something_secret_here\[dq] +\f[R] +.fi +.PP +Running the localhost REST API clone +.IP +.nf +\f[C] +eprintrest +\f[R] +.fi +.SH NOTES +.SS [1] +.PP +MySQL, like this REST service assumes to be running on localhost. +.SS [2] +.PP +MySQL, like this REST service assumes to be running on localhost. +.SH AUTHORS +R. S. Doiel and Tom Morrell. diff --git a/man/man1/people2vocabulary.1 b/man/man1/people2vocabulary.1 index 1fa7339c..279a0d31 100644 --- a/man/man1/people2vocabulary.1 +++ b/man/man1/people2vocabulary.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "people2vocabulary" "1" "2023-09-12" "irdmtools user manual" "version 0.0.48 fb9e58e" +.TH "people2vocabulary" "1" "2023-09-12" "irdmtools user manual" "version 0.0.48 0238bfa" .hy .SH NAME .PP diff --git a/man/man1/rdmutil.1 b/man/man1/rdmutil.1 index d4f1b19d..4ad47226 100644 --- a/man/man1/rdmutil.1 +++ b/man/man1/rdmutil.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "rdmutil" "1" "2023-09-12" "irdmtools user manual" "version 0.0.48 fb9e58e" +.TH "rdmutil" "1" "2023-09-12" "irdmtools user manual" "version 0.0.48 0238bfa" .hy .SH NAME .PP diff --git a/pagefind/fragment/unknown_7cf1198.pf_fragment b/pagefind/fragment/unknown_7cf1198.pf_fragment new file mode 100644 index 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b+{JdglvGN2F0>OP{>c9WluzMpJahm6PxRgh literal 0 HcmV?d00001 diff --git a/pagefind/pagefind-entry.json b/pagefind/pagefind-entry.json index 9df4f931..0b54c005 100644 --- a/pagefind/pagefind-entry.json +++ b/pagefind/pagefind-entry.json @@ -1 +1 @@ -{"version":"0.12.0","languages":{"unknown":{"hash":"unknown_48584b63b23e7dc","wasm":null,"page_count":15}}} \ No newline at end of file +{"version":"0.12.0","languages":{"unknown":{"hash":"unknown_29fa54e2969ebdb","wasm":null,"page_count":16}}} \ No newline at end of file diff --git a/pagefind/pagefind.unknown_29fa54e2969ebdb.pf_meta b/pagefind/pagefind.unknown_29fa54e2969ebdb.pf_meta new file mode 100644 index 0000000000000000000000000000000000000000..3f05825eac42f7caee7737db6f8a8db6f2d51be9 GIT binary patch literal 215 zcmV;|04V<-iwFP!00002|4q-qO@lEE1z?pCkdWLZs>IHpICCIztr9y1gqm^zgt!zC zcgA25HsHiG?Wu{6pPp^K$8y{3zUx*+zszksZru0B{;5Co{Y&2_G4C_O+n~xAFbmua zS~!s`9-gN~;-p?64JuShZ3w>;6*I29UR@6(rJRbaSC^9sn>B(y$RkpS27iN;BNtca zpN(?xWbi-8SmJ^acuJ|&DD7f86$1xlaDxIBTq?rPRMH7!%vbN9>RjNv*VF8Fs^>st RlUC#5a0Ct6^fqS!003dxVoCr2 literal 0 HcmV?d00001 diff --git a/people2vocabulary.1.md b/people2vocabulary.1.md index f43ed7a0..61570649 100644 --- a/people2vocabulary.1.md +++ b/people2vocabulary.1.md @@ -1,4 +1,4 @@ -%people2vocabulary(1) irdmtools user manual | version 0.0.48 fb9e58e +%people2vocabulary(1) irdmtools user manual | version 0.0.48 0238bfa % R. S. Doiel % 2023-09-12 diff --git a/rdmutil.1.md b/rdmutil.1.md index 8f864fed..07dc15e6 100644 --- a/rdmutil.1.md +++ b/rdmutil.1.md @@ -1,4 +1,4 @@ -%rdmutil(1) irdmtools user manual | version 0.0.48 fb9e58e +%rdmutil(1) irdmtools user manual | version 0.0.48 0238bfa % R. S. Doiel and Tom Morrell % 2023-09-12 diff --git a/version.go b/version.go index cbeb84a4..f3535a51 100644 --- a/version.go +++ b/version.go @@ -12,7 +12,7 @@ const ( ReleaseDate = "2023-09-12" // ReleaseHash, the Git hash when version.go was generated - ReleaseHash = "fb9e58e" + ReleaseHash = "0238bfa" LicenseText = ` Redistribution and use in source and binary forms, with or without From 188b576d93c243c2d7cb8e90686ce34c0f8863f0 Mon Sep 17 00:00:00 2001 From: Thomas Morrell Date: Tue, 12 Sep 2023 16:37:51 -0700 Subject: [PATCH 02/11] Complete identifier cleanup --- irdm/fixups.py | 371 +++++++++++------- match_identifiers_with_logs.py | 4 +- migrated_records.csv | 40 -- ...e_identifiers.py => update_from_eprints.py | 49 +-- 4 files changed, 226 insertions(+), 238 deletions(-) rename update_identifiers.py => update_from_eprints.py (84%) diff --git a/irdm/fixups.py b/irdm/fixups.py index 044eb7be..2c131c45 100644 --- a/irdm/fixups.py +++ b/irdm/fixups.py @@ -1,5 +1,5 @@ -'''fixup.py is a module for cleanup output from eprint2rdm and making -it ready for import to RDM with rdmutil''' +"""fixup.py is a module for cleanup output from eprint2rdm and making +it ready for import to RDM with rdmutil""" import os import sys import json @@ -10,35 +10,36 @@ # Roles defined for person_or_org scheme defined_roles = [ - "contactperson", - "datacollector", - "datacurator", - "datamanager", - "distributor", - "editor", - "hostinginstitution", - "producer", - "projectleader", - "projectmanager", - "projectmember", - "registrationagency", - "registrationauthority", - "relatedperson", - "researcher", - "researchgroup", + "contactperson", + "datacollector", + "datacurator", + "datamanager", + "distributor", + "editor", + "hostinginstitution", + "producer", + "projectleader", + "projectmanager", + "projectmember", + "registrationagency", + "registrationauthority", + "relatedperson", + "researcher", + "researchgroup", "rightsholder", "sponsor", "supervisor", "workpackageleader", - "other" + "other", ] # Decide if we're in production or not. Defaut to Not in production. -rdm_url = os.getenv('RDM_URL', None) -in_production = ((rdm_url is not None) and ('caltech.edu' in rdm_url)) +rdm_url = os.getenv("RDM_URL", None) +in_production = (rdm_url is not None) and ("caltech.edu" in rdm_url) + def check_for_doi(doi, production, token=None): - '''Check to see if DOI already exists in our RDM instance''' + """Check to see if DOI already exists in our RDM instance""" # Returns whether or not a DOI has already been added to CaltechAUTHORS if production is True: url = "https://authors.library.caltech.edu/api/records" @@ -46,13 +47,13 @@ def check_for_doi(doi, production, token=None): url = "https://authors.caltechlibrary.dev/api/records" if token: headers = { - "Authorization": "Bearer %s" % token, - "Content-type": "application/json", - } + "Authorization": "Bearer %s" % token, + "Content-type": "application/json", + } else: headers = { - "Content-type": "application/json", - } + "Content-type": "application/json", + } query = f'?q=pids.doi.identifier:"{doi}"&allversions=true' @@ -61,7 +62,7 @@ def check_for_doi(doi, production, token=None): except Exception as err: return False, err if response.status_code != 200: - print(f'error {response.text}', file = sys.stderr) + print(f"error {response.text}", file=sys.stderr) return False, None records = response.json() if records["hits"]["total"] > 0: @@ -69,8 +70,8 @@ def check_for_doi(doi, production, token=None): return False, None -def get_dict_path(obj, args = None): - '''look up path in dict recursively, return value if found''' +def get_dict_path(obj, args=None): + """look up path in dict recursively, return value if found""" if args is None: return None if len(args) == 0: @@ -82,70 +83,80 @@ def get_dict_path(obj, args = None): return get_dict_path(obj[arg], args[1:]) return None -def normalize_doi(doi = None): - '''vet and normalize DOI''' + +def normalize_doi(doi=None): + """vet and normalize DOI""" if doi is not None and idutils.is_doi(doi): return idutils.normalize_doi(doi) return None -def normalize_pmcid(pmcid = None): - '''normalize PCM ids to just the id, trim from URL if needed.''' + +def normalize_pmcid(pmcid=None): + """normalize PCM ids to just the id, trim from URL if needed.""" if pmcid is not None: if idutils.is_url(pmcid): if idutils.is_doi(pmcid): return None _u = urlparse(pmcid) - pmcid = os.path.basename(_u.path.rstrip('/')).lower() + pmcid = os.path.basename(_u.path.rstrip("/")).lower() return pmcid.upper() + def trim_prefixes(text, prefixes): - '''trim prefixes from string''' + """trim prefixes from string""" for prefix in prefixes: if text.startswith(prefix): - return text[len(prefix):] + return text[len(prefix) :] return text + def trim_suffixes(text, suffixes): - '''trim suffixes from string''' + """trim suffixes from string""" for suffix in suffixes: if text.endswith(suffix): - return text[0:(len(suffix)*-1)] + return text[0 : (len(suffix) * -1)] return text -def normalize_arxiv(arxiv = None): - '''vet and normalize an arxiv''' - arxiv = trim_prefixes(arxiv, ['http://arxiv.org/abs/', 'https://arxiv.org/abs/']) + +def normalize_arxiv(arxiv=None): + """vet and normalize an arxiv""" + arxiv = trim_prefixes(arxiv, ["http://arxiv.org/abs/", "https://arxiv.org/abs/"]) if idutils.is_doi(arxiv): return None if idutils.is_arxiv(arxiv): return idutils.normalize_arxiv(arxiv) return None -def normalize_ads(ads = None): - '''vet and normalize an ads id''' - ads = trim_prefixes(ads, ['https://ui.adsabs.harvard.edu/abs/']) - ads = trim_suffixes(ads, ['/abstract']) + +def normalize_ads(ads=None): + """vet and normalize an ads id""" + ads = trim_prefixes(ads, ["https://ui.adsabs.harvard.edu/abs/"]) + ads = trim_suffixes(ads, ["/abstract"]) if idutils.is_ads(ads): return idutils.normalize_ads(ads) return None -def normalize_pub(pub_url = None, doi = None): - '''vet and normalize a publication url, uses whitelist matching''' + +def normalize_pub(pub_url=None, doi=None): + """vet and normalize a publication url, uses whitelist matching""" if idutils.is_url(pub_url): _u = urlparse(pub_url) - if 'hostname' in _u: - if _u.hostname in [ 'rdcu.be', 'geoscienceworld', 'ieeexplore.ieee.org' ]: - if _u.hostname == 'ieeexplore.ieee.org' and \ - (doi is not None and doi.startswith('10.1364/')): + if "hostname" in _u: + if _u.hostname in ["rdcu.be", "geoscienceworld", "ieeexplore.ieee.org"]: + if _u.hostname == "ieeexplore.ieee.org" and ( + doi is not None and doi.startswith("10.1364/") + ): return pub_url - elif _u.netloc in [ 'rdcu.be', 'geoscienceworld', 'ieeexplore.ieee.org' ]: - if _u.netloc == 'ieeexplore.ieee.org' and \ - (doi is not None and doi.startswith('10.1364/')): + elif _u.netloc in ["rdcu.be", "geoscienceworld", "ieeexplore.ieee.org"]: + if _u.netloc == "ieeexplore.ieee.org" and ( + doi is not None and doi.startswith("10.1364/") + ): return pub_url return None + # fixup_record takes the simplfied record and prepares a -# draft record structure for import using rdmutil. +# draft record structure for import using rdmutil. # # This include things like crosswalking vocabularies to map from an # existing Caltech Library EPrints repository to @@ -154,18 +165,18 @@ def normalize_pub(pub_url = None, doi = None): # Where possible these adjustments should be ported back # into eprinttools' simple.go and crosswalk.go. # -def fixup_record(record,reload=False,token=None): - """fixup_record accepts a dict of simple record and files returns a -normlzied record dict that is a for migration into Invenio-RDM.""" +def fixup_record(record, reload=False, token=None): + """fixup_record accepts a dict of simple record and files returns a + normlzied record dict that is a for migration into Invenio-RDM.""" record_id = get_dict_path(record, ["pid", "id"]) - #FIXME: sort out how these fields should be structured then + # FIXME: sort out how these fields should be structured then # update the eprinttools simple.go and crosswalk.go to reflect # correction and remove this code. if "access" in record: del record["access"] if "metadata" in record: # Fixup resource type mapping from EPrints to Invenio-RDM types - resource_type = get_dict_path(record, [ "metadata", "resource_type", "id" ]) + resource_type = get_dict_path(record, ["metadata", "resource_type", "id"]) if resource_type is not None: if resource_type == "book_section": record["metadata"]["resource_type"]["id"] = "publication-section" @@ -181,25 +192,33 @@ def fixup_record(record,reload=False,token=None): if "dates" in record["metadata"]: date_list = [] for entry in record["metadata"]["dates"]: - if "type" in entry and "id" in entry["type"] and \ - (entry["type"]["id"] == "created" or \ - entry["type"]["id"] == "updated"): + if ( + "type" in entry + and "id" in entry["type"] + and ( + entry["type"]["id"] == "created" + or entry["type"]["id"] == "updated" + ) + ): date_list.append(entry) record["metadata"]["dates"] = date_list if "funding" in record["metadata"]: for i, funder in enumerate(record["metadata"]["funding"]): if "award" in funder and not "title" in funder["award"]: - funder["award"]["title"] = { "en": " " } + funder["award"]["title"] = {"en": " "} record["metadata"]["funding"][i] = funder # Fixup name in creators and contributors if "creators" in record["metadata"]: for i, creator in enumerate(record["metadata"]["creators"]): - if "person_or_org" in creator and not 'name' in creator["person_or_org"]: + if ( + "person_or_org" in creator + and not "name" in creator["person_or_org"] + ): person = creator["person_or_org"] - family_name = person.get('family_name', None) - given_name = person.get('given_name', None) + family_name = person.get("family_name", None) + given_name = person.get("given_name", None) if family_name is not None and given_name is not None: - person['name'] = f'{family_name}, {given_name}' + person["name"] = f"{family_name}, {given_name}" record["metadata"]["creators"][i]["person_or_org"] = person # Fix up contributor roles, FIXME: since we don't have a mapping, # undefined roles get mapped to "other" @@ -207,7 +226,7 @@ def fixup_record(record,reload=False,token=None): for i, contributor in enumerate(record["metadata"]["contributors"]): # FIXME: This is a temporary mapping of role until we get Caltech Library # roles implemented properly. - role_id = get_dict_path(contributor, [ "role", "id"]) + role_id = get_dict_path(contributor, ["role", "id"]) if not role_id in defined_roles: record["metadata"]["contributors"][i]["role"]["id"] = "other" # Fixup alternative title types @@ -216,37 +235,46 @@ def fixup_record(record,reload=False,token=None): if not "type" in title: title["type"] = { "id": "alternative-title", - "title": { - "en": "Alternative Title" - } + "title": {"en": "Alternative Title"}, } record["metadata"]["additional_titles"][i] = title if "contributors" in record["metadata"]: for i, contributor in enumerate(record["metadata"]["contributors"]): - if "person_or_org" in contributor and not 'name' in contributor['person_or_org']: - person = contributor['person_or_org'] - if 'family_name' in person: - person['name'] = f'{person["family_name"]}, {person["given_name"]}' + if ( + "person_or_org" in contributor + and not "name" in contributor["person_or_org"] + ): + person = contributor["person_or_org"] + if "family_name" in person: + person[ + "name" + ] = f'{person["family_name"]}, {person["given_name"]}' record["metadata"]["contributors"][i]["person_or_org"] = person else: - print(json.dumps(record, indent = 4)) - print(f'ERROR: (id: {record_id}) contributor missing family name') + print(json.dumps(record, indent=4)) + print( + f"ERROR: (id: {record_id}) contributor missing family name" + ) sys.exit(1) # Map the eprintid to the identifier list - if "pid" in record and "id" in record["pid"] and \ - "eprint" in record["pid"] and record["pid"]["eprint"] == "eprintid": + if ( + "pid" in record + and "id" in record["pid"] + and "eprint" in record["pid"] + and record["pid"]["eprint"] == "eprintid" + ): eprintid = record["pid"]["id"] if "metadata" in record and "identifier" in record["metadata"]: - record["metadata"]["identifier"].append({ - "scheme": "eprintid", "identifier": f"{eprintid}" - }) + record["metadata"]["identifier"].append( + {"scheme": "eprintid", "identifier": f"{eprintid}"} + ) # Setup an empty .files attribute for use with rdmutil upload_files - if 'files' in record: - record["files"] = { "enabled": True, "order": [] } + if "files" in record: + record["files"] = {"enabled": True, "order": []} else: - record["files"] = { "enabled": False, "order": [] } + record["files"] = {"enabled": False, "order": []} # Normalize DOI, issue #39 - doi = normalize_doi(get_dict_path(record, ['pids', 'doi', 'identifier'])) + doi = normalize_doi(get_dict_path(record, ["pids", "doi", "identifier"])) if doi is not None: if not reload: # See if DOI already exists in CaltechAUTHORS, if so move it to metadata identifiers. @@ -254,33 +282,35 @@ def fixup_record(record,reload=False,token=None): if err is not None: return rec, err if has_doi: - del record['pids']['doi'] + del record["pids"]["doi"] if "metadata" not in record: record["metadata"] = {} if "identifiers" not in record["metadata"]: record["metadata"]["identifiers"] = [] - record["metadata"]["identifiers"].append({ "scheme": "doi", "identifier": f"{doi}" }) + record["metadata"]["identifiers"].append( + {"scheme": "doi", "identifier": f"{doi}"} + ) doi = None - #Mark system DOIs - #if doi.startswith('10.7907'): + # Mark system DOIs + # if doi.startswith('10.7907'): # record['pids']['doi']['provider'] = 'datacite' # record['pids']['doi']['client'] = 'datacite' # Make sure records DOI isn't in related identifiers - identifiers = get_dict_path(record, [ 'metadata', 'related_identifiers']) + identifiers = get_dict_path(record, ["metadata", "related_identifiers"]) added_identifiers = [] if identifiers is not None: keep_identifiers = [] for identifier in identifiers: - scheme = get_dict_path(identifier, ['scheme']) - id_val = get_dict_path(identifier, ['identifier']) - relation = get_dict_path(identifier,["relation_type","id"]) + scheme = get_dict_path(identifier, ["scheme"]) + id_val = get_dict_path(identifier, ["identifier"]) + relation = get_dict_path(identifier, ["relation_type", "id"]) if idutils.is_doi(id_val): normalized = normalize_doi(id_val) if normalized != doi: if id_val not in added_identifiers: - identifier['identifier'] = id_val - identifier['scheme'] = 'doi' + identifier["identifier"] = id_val + identifier["scheme"] = "doi" added_identifiers.append(id_val) keep_identifiers.append(identifier) else: @@ -294,97 +324,138 @@ def fixup_record(record,reload=False,token=None): identifier["identifier"] = normalized added_identifiers.append(normalized) keep_identifiers.append(identifier) - record['metadata']['related_identifiers'] = keep_identifiers + record["metadata"]["related_identifiers"] = keep_identifiers # Run through related URLs, if DOI then normalize DOI, if DOI match # pids.doi.identifier then discard related url value, issue #39 - identifiers = get_dict_path(record, [ 'metadata', 'identifiers']) + identifiers = get_dict_path(record, ["metadata", "identifiers"]) if identifiers is not None: + keep_identifiers = [] # Find a PMCID in the indenitifiers ro compare with pmc id ... pmcid = None for identifier in identifiers: - scheme = get_dict_path(identifier, ['scheme']) - if scheme == 'pmcid': - pmcid = normalize_pmcid(get_dict_path(identifier, ['identifier'])) - keep_identifiers = [] + scheme = get_dict_path(identifier, ["scheme"]) + if scheme == "pmcid": + # We have two or more values, add to related + if pmcid: + related_pmcid = normalize_pmcid( + get_dict_path(identifier, ["identifier"]) + ) + record["metadata"]["related_identifiers"].append( + { + "scheme": "pmcid", + "identifier": related_pmcid, + "relation_type": {"id": "isvariantformof"}, + } + ) + # Haven't seen a pmcid yet + else: + pmcid = normalize_pmcid(get_dict_path(identifier, ["identifier"])) + keep_identifiers.append({"scheme": "pmcid", "identifier": pmcid}) for identifier in identifiers: - scheme = get_dict_path(identifier, ['scheme']) - id_val = get_dict_path(identifier, ['identifier']) + scheme = get_dict_path(identifier, ["scheme"]) + id_val = get_dict_path(identifier, ["identifier"]) if scheme is not None: - if scheme == 'doi': - related_doi = normalize_doi(get_dict_path(identifier, ['identifier'])) + if scheme == "doi": + related_doi = normalize_doi( + get_dict_path(identifier, ["identifier"]) + ) if related_doi is not None: if related_doi != doi: - keep_identifiers.append({"scheme": "doi", "identifier": related_doi}) + keep_identifiers.append( + {"scheme": "doi", "identifier": related_doi} + ) if doi is None: doi = related_doi - elif scheme == 'pmcid': - related_pmcid = normalize_pmcid(get_dict_path(identifier, [ 'identifier'])) - if related_pmcid is not None: - keep_identifiers.append({"scheme":"pmcid", "identifier": related_pmcid}) - elif scheme == 'pmc': - related_pmcid = normalize_pmcid(get_dict_path(identifier, ['identifier'])) + elif scheme == "pmc": + related_pmcid = normalize_pmcid( + get_dict_path(identifier, ["identifier"]) + ) if related_pmcid is not None: if related_pmcid != pmcid: - keep_identifiers.append({"scheme": "pmcid", "identifier": related_pmcid}) - elif scheme == 'arxiv': - related_arxiv = normalize_arxiv(get_dict_path(identifier, ['identifier'])) + # Extra pmcid values go in related identifiers + record["metadata"]["related_identifiers"].append( + { + "scheme": "pmcid", + "identifier": related_pmcid, + "relation_type": {"id": "isvariantformof"}, + } + ) + elif scheme == "arxiv": + related_arxiv = normalize_arxiv( + get_dict_path(identifier, ["identifier"]) + ) if related_arxiv is not None: - keep_identifiers.append({"scheme": "arxiv", "identifier": related_arxiv}) - elif scheme == 'ads': - related_ads = normalize_ads(get_dict_path(identifier, ['identifier'])) + keep_identifiers.append( + {"scheme": "arxiv", "identifier": related_arxiv} + ) + elif scheme == "ads": + related_ads = normalize_ads( + get_dict_path(identifier, ["identifier"]) + ) if related_ads is not None: - keep_identifiers.append({"scheme": "ads", "identifier": related_ads}) - elif scheme == 'pub': - related_pub = normalize_pub(get_dict_path(identifier, ['identifier']), doi) + keep_identifiers.append( + {"scheme": "ads", "identifier": related_ads} + ) + elif scheme == "pub": + related_pub = normalize_pub( + get_dict_path(identifier, ["identifier"]), doi + ) if related_pub is not None: - keep_identifiers.append({"scheme": "url", "identifier": related_pub}) - elif scheme == 'eprintid': - keep_identifiers.append({"scheme": "eprintid", "identifier": id_val}) - elif scheme == 'resolverid': - keep_identifiers.append({"scheme": "resolverid", "identifier": id_val}) + keep_identifiers.append( + {"scheme": "url", "identifier": related_pub} + ) + elif scheme == "eprintid": + keep_identifiers.append( + {"scheme": "eprintid", "identifier": id_val} + ) + elif scheme == "resolverid": + keep_identifiers.append( + {"scheme": "resolverid", "identifier": id_val} + ) else: if id_val is not None and id_val.strip() != "": - if idutils.is_url(identifier['identifier']): - keep_identifiers.append({"scheme":"url", "identifier": id_val}) + if idutils.is_url(identifier["identifier"]): + keep_identifiers.append( + {"scheme": "url", "identifier": id_val} + ) else: keep_identifiers.append({"scheme": scheme, "identifier": id_val}) if len(keep_identifiers) > 0: - record['metadata']['identifiers'] = keep_identifiers + record["metadata"]["identifiers"] = keep_identifiers else: - del record['metadata']['identifiers'] - + del record["metadata"]["identifiers"] + # Clean up caltech groups - groups = get_dict_path(record, [ 'custom_fields', 'caltech:groups']) + groups = get_dict_path(record, ["custom_fields", "caltech:groups"]) new = [] if groups: for group in groups: - if group['id'] == "Institute-for-Quantum-Information-and-Matter": - new.append({'id':'IQIM'}) - elif group['id'] == 'Owens-Valley-Radio-Observatory-(OVRO)': - new.append({'id':'Owens-Valley-Radio-Observatory'}) - elif group['id'] == 'Library-System-Papers-and-Publications': - new.append({'id':'Caltech-Library'}) + if group["id"] == "Institute-for-Quantum-Information-and-Matter": + new.append({"id": "IQIM"}) + elif group["id"] == "Owens-Valley-Radio-Observatory-(OVRO)": + new.append({"id": "Owens-Valley-Radio-Observatory"}) + elif group["id"] == "Library-System-Papers-and-Publications": + new.append({"id": "Caltech-Library"}) else: new.append(group) - record['custom_fields']['caltech:groups'] = new + record["custom_fields"]["caltech:groups"] = new # Remove .custom_fields["caltech:internal_note"] if it exist. if "custom_fields" in record and "caltech:internal_note" in record["custom_fields"]: del record["custom_fields"]["caltech:internal_note"] # Check to see if pids object is empty - pids = record.get('pids', None) + pids = record.get("pids", None) if pids is not None: - doi = pids.get('doi', {}) - doi_identifier = doi.get('identifier') + doi = pids.get("doi", {}) + doi_identifier = doi.get("identifier") if doi_identifier == "": - del pids['doi'] + del pids["doi"] if len(pids) == 0: - del record['pids'] + del record["pids"] # Remove eprint revision version number if is makes it through from - if 'metadata' in record and 'version' in record['metadata']: - del record['metadata']['version'] + if "metadata" in record and "version" in record["metadata"]: + del record["metadata"]["version"] # FIXME: Need to make sure we don't have duplicate related identifiers ..., # pmcid seem to have duplicates in some case. return record, None - diff --git a/match_identifiers_with_logs.py b/match_identifiers_with_logs.py index f3c2f65d..517875e4 100644 --- a/match_identifiers_with_logs.py +++ b/match_identifiers_with_logs.py @@ -1,5 +1,5 @@ import glob,sys -from update_identifiers import update_identifiers +from update_from_eprints import update_from_eprints logs = glob.glob('logs/*.log') mapping = {} @@ -21,7 +21,7 @@ for idv in ids: idv = idv.strip('\n') if idv in mapping: - update_identifiers(mapping[idv],idv,reload) + update_from_eprints(mapping[idv],idv,reload) with open('migrated_records.csv','a') as outfile: print(f"{mapping[idv]},{idv},public",file=outfile) print(idv + ',' + mapping[idv]) diff --git a/migrated_records.csv b/migrated_records.csv index d5d04717..38297ca1 100644 --- a/migrated_records.csv +++ b/migrated_records.csv @@ -135450,8 +135450,6 @@ eprintid,rdmid,record_status 122008,5nfwv-cna88,public 122276,ddt7k-74524,public 122426,gk8zt-p6252,public -19,f8d3n-r8v05,public -111440,vzr2z-cvj59,public 120695,d5pvp-0hp41,public 120697,2ybre-3g121,public 120698,4nvz3-n9t72,public @@ -135493,16 +135491,6 @@ eprintid,rdmid,record_status 121931,5hzgb-dp771,public 122478,j0vpp-a6b96,public 122397,hsvrt-31d55,public -105918,a7kkt-w2v79,public -44072,q8bd2-ktj03,public -100493,a6x6t-yfr73,public -43624,0wes0-5dg92,public -44222,gtfhn-53976,public -82287,e4mb2-pxv70,public -83078,asx3k-p9q34,public -83718,72t40-dkx78,public -83283,my3wd-7zq33,public -78687,y52z8-p2409,public 122477,hce37-9wp32,public 121809,c5gn3-cb856,public 121349,ckkk0-9et64,public @@ -135540,31 +135528,3 @@ eprintid,rdmid,record_status 122575,xhesv-wv708,public 122556,y6fck-maq35,public 122558,862gc-y4k77,public -37817,x01sa-v8665,public -101933,w4rpn-gm294,public -98954,v2tra-3gp34,public -55879,gb6gh-qbd38,public -102847,dqhe3-4k349,public -116166,2r0th-av040,public -108081,n456j-wgq95,public -106739,74cpm-pe049,public -99630,zscnk-xce70,public -74714,57pcw-w6930,public -94608,j0dkf-09y90,public -110311,73pzr-wrc40,public -122210,degbr-djc54,public -119325,h2ec9-3qs83,public -70204,67s3z-2px14,public -75231,a9mrs-hpw87,public -108641,r8qh8-y4065,public -90052,xfj8b-gky84,public -85532,6t6nv-52n04,public -45157,kmm22-n7586,public -91895,4xjbk-5nh74,public -90151,nxx3z-pcj85,public -86494,xqxz7-q9s24,public -65777,sa235-14m40,public -116205,y0ebs-b6g15,public -39274,6yhr2-fr809,public -1884,4wg6f-wm239,public -42811,h2b6f-vvm23,public diff --git a/update_identifiers.py b/update_from_eprints.py similarity index 84% rename from update_identifiers.py rename to update_from_eprints.py index 5d28ce2f..fe5ac68d 100755 --- a/update_identifiers.py +++ b/update_from_eprints.py @@ -111,52 +111,10 @@ def pairtree(txt): def update_record(config, rec, rdmutil, rdm_id): - """update draft record handling versioning if needed""" - url = "https://authors.library.caltech.edu/" - - headers = { - "Authorization": "Bearer %s" % config['RDMTOK'], - "Content-type": "application/json", - } - # Get existing metadata - existing = requests.get( - url + "/api/records/" + rdm_id, - headers=headers, - ) - existing = existing.json() - - # We want to update the pids section - if 'pids' in rec: - existing['pids'] = rec['pids'] - - #And add any missed identifiers - rec = rec['metadata'] - new_ids = [] - for idv in rec["identifiers"]: - new_ids.append(idv["identifier"]) - - identifiers = rec["identifiers"] - if "identifiers" in existing: - for idv in existing["identifiers"]: - if idv["identifier"] not in new_ids: - identifiers.append(idv) - existing["metadata"]["identifiers"] = identifiers - - new_related = [] - if "related_identifiers" in rec: - for idv in rec["related_identifiers"]: - new_related.append(idv["identifier"]) - - related_identifiers = rec["related_identifiers"] - if "related_identifiers" in existing: - for idv in existing["related_identifiers"]: - if idv["identifier"] not in new_related: - related_identifiers.append(idv) - existing["metadata"]["related_identifiers"] = related_identifiers caltechdata_edit( rdm_id, - metadata=existing, + metadata=rec, token=config['RDMTOK'], production=True, publish=True, @@ -193,7 +151,6 @@ def fix_record(config, eprintid, rdm_id,reload=False): print( f"{eprintid}, {rdm_id}, failed ({eprintid}): rdmutil new_record, fixup_record failed {err}" ) - #print(json.dumps(rec)) update_record(config, rec, rdmutil, rdm_id) return None @@ -264,12 +221,12 @@ def get_eprint_ids(): eprint_ids.append(eprint_id.strip()) return eprint_ids -def update_identifiers(eprintid,rdm_id,reload=False): +def update_from_eprints(eprintid,rdm_id,reload=False): config, is_ok = check_environment() if is_ok: err = fix_record(config, eprintid, rdm_id,reload) if err is not None: - print(f"Aborting update_identifiers, {err}", file=sys.stderr) + print(f"Aborting update_from_eprints, {err}", file=sys.stderr) sys.exit(1) From 89c170100daa328f80c7c49ec389f4d4a50ca5aa Mon Sep 17 00:00:00 2001 From: Thomas Morrell Date: Wed, 13 Sep 2023 09:24:24 -0700 Subject: [PATCH 03/11] Add missing records --- check_transferred_records.py | 20 +- get_missing_identifiers.py | 2 +- migrated_records.csv | 3 + missing_records.txt | 2345 ++++++++++++++++++++++++++++++++++ 4 files changed, 2365 insertions(+), 5 deletions(-) create mode 100644 missing_records.txt diff --git a/check_transferred_records.py b/check_transferred_records.py index cc7a99cd..f25bec21 100644 --- a/check_transferred_records.py +++ b/check_transferred_records.py @@ -12,12 +12,24 @@ reader = csv.DictReader(f) for row in reader: status = row['record_status'] - if status != 'restricted-duplicate': + if status == 'public': eprintid = row['eprintid'] if eprintid not in all_rdm_records: all_rdm_records.append(eprintid) - if eprintid not in eprint_mapping: - eprint_mapping[row['eprintid']] = row['rdmid'] else: - eprint_mapping[row['eprintid']] = [eprint_mapping[row['eprintid']] ,row['rdmid']] + print('duplicate', eprintid, row['rdmid']) + #if eprintid not in eprint_mapping: + # eprint_mapping[row['eprintid']] = row['rdmid'] + #else: + # eprint_mapping[row['eprintid']] = [eprint_mapping[row['eprintid']] ,row['rdmid']] print("Number of RDM records: ",len(all_rdm_records)) + +print('Missing Eprints records:') +count = 0 + +for record in eprints_records: + if record not in all_rdm_records: + print(record) + count += 1 + +print('Number of missing records: ',count) diff --git a/get_missing_identifiers.py b/get_missing_identifiers.py index cffa416c..24d7b3c6 100644 --- a/get_missing_identifiers.py +++ b/get_missing_identifiers.py @@ -4,7 +4,7 @@ url = "https://authors.library.caltech.edu/api/records" -query = '?q=NOT%20_exists_%3Ametadata.identifiers%20%2Bcreated%3A%5B2023-01-01%20TO%202023-08-28%5D' +query = '?q=NOT%20metadata.identifiers.scheme%3A"eprintid"%20%2Bcreated%3A%5B2023-01-01%20TO%202023-08-28%5D&f=access_status%3Aopen' response = requests.get(f"{url}{query}") total = response.json()["hits"]["total"] diff --git a/migrated_records.csv b/migrated_records.csv index 38297ca1..046b7352 100644 --- a/migrated_records.csv +++ b/migrated_records.csv @@ -135528,3 +135528,6 @@ eprintid,rdmid,record_status 122575,xhesv-wv708,public 122556,y6fck-maq35,public 122558,862gc-y4k77,public +122502,sneaq-f9v10,public 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+121137 +121138 +121173 +121176 +121177 +121216 +121448 +121455 +121457 +121652 +121700 +121949 +121983 +121988 +122024 +122105 +122181 +122210 +122218 +122350 +122358 From 7af291fd70b7017a4a62027bac8e9d2c1e47b403 Mon Sep 17 00:00:00 2001 From: Thomas Morrell Date: Wed, 13 Sep 2023 09:50:42 -0700 Subject: [PATCH 04/11] In progress migration --- eprints_to_rdm.py | 4 ++- migrated_records.csv | 75 ++++++++++++++++++++++++++++++++++++++++++++ missing_records.txt | 2 -- 3 files changed, 78 insertions(+), 3 deletions(-) diff --git a/eprints_to_rdm.py b/eprints_to_rdm.py index 3a44c0ba..01029fa0 100755 --- a/eprints_to_rdm.py +++ b/eprints_to_rdm.py @@ -182,7 +182,7 @@ def get_file_list(config, eprintid, rec, security): if content: content = content_mapping[content] format_des = metadata.get('format_des', None) - if format_desc: + if format_des: content = content + format_des if _security is not None and security == _security: file_url = file['file_id'] @@ -421,6 +421,8 @@ def migrate_record(config, eprintid): return err # sys.exit(1) print(f'{obj.eprintid}, {rdm_id}, {restriction}') print(f'{obj.eprintid}, {root_rdm_id}, migrated') + with open('migrated_records.csv','a') as outfile: + print(f"{obj.eprintid},{rdm_id},public",file=outfile) sys.stdout.flush() return None diff --git a/migrated_records.csv b/migrated_records.csv index 046b7352..833b0f1d 100644 --- a/migrated_records.csv +++ b/migrated_records.csv @@ -135531,3 +135531,78 @@ eprintid,rdmid,record_status 122502,sneaq-f9v10,public 122422,b399m-w3c59,public 78687,y52z8-p2409,public +176, mvhgr-qkt66, public +279,8jkb9-v1q69,public +535,wvcwj-0fx78,public +552,hgcq6-gjx82,public +785,464dn-zy612,public +876,rprm5-ka839,public +929,65fxp-8t742,public +976,expg6-ep752,public +992,5emmx-ybq38,public +1434,v2hr4-kya24,public +1480,5517q-nf413,public +1608,59dpj-58d58,public +1632,fcn9b-c3e17,public +1739,4pex3-vr798,public +1853,51a9m-dcm55,public +1884,edmxd-gda68,public +1995,hx545-eh615,public +2063,2hn96-37618,public +2094,w3arp-2ws06,public +2227,vrwkw-an486,public +2386,ccakd-phh08,public +2461,qp8b5-khw19,public +2514,06j8s-x9106,public +2631,6acnt-ee187,public +2653,mppty-w7t10,public +2778,1bfpr-55j46,public +2861,h3mpa-fvf21,public +2873,xra7s-0fx85,public +2990,w4jzz-k1e89,public +3001,m4cz0-x2030,public +3136,zq1f0-2k797,public +3172,mmsyw-gce91,public +3487,92y2s-74173,public +3980,qghxn-hm551,public +3986,c90ss-8xr37,public +4115,ks9mt-6db05,public +4134,qqpf0-eg361,public +4159,1s8q3-1bh63,public +4523,9wche-sra06,public +4586,anran-2jm51,public +4662,sr4a6-1f023,public +4806,5x52v-e1p03,public +4865,d6cgg-aw541,public +4874,p5aj0-3hz85,public +4936,j1whe-wye58,public +4947,29v21-20j45,public +4957,b5gx3-p7p56,public +4983,dzbfp-40995,public +5124,9wrpm-sv054,public +5128,5n9c8-0re85,public +5244,4mz2v-yp161,public +5299,s9vz1-mjd18,public +5354,s4khe-y4y25,public +5355,c01y1-fkd86,public +5356,kbd2a-bd486,public +5439,b93ka-zt125,public +5525,d2nyq-97676,public +5586,e0mvw-3xb52,public +5618,f24hj-5z112,public +5752,ewvs6-15n29,public +6275,xkxb6-m7x34,public +6299,20zma-84305,public +6300,91p93-qxk69,public +6301,7cj0m-r7p68,public +6302,bfxny-pmm86,public +6387,yywhb-vrx54,public +6420,m5fxm-5v613,public +6424,z4yt7-gxm35,public +6487,pjaj4-36h15,public +6491,0te3k-ss181,public +6509,pkary-5qk26,public +6532,9c5ha-vdq85,public +6587,c4eny-3ay82,public +6758,41jdm-39h72,public +6815,eg2np-pwr70,public diff --git a/missing_records.txt b/missing_records.txt index bac39d0b..856f572e 100644 --- a/missing_records.txt +++ b/missing_records.txt @@ -1,5 +1,3 @@ -176 -279 535 552 785 From 81e3fc75b4c9f6c1ffbe2fccb3ad2df710fcfcea Mon Sep 17 00:00:00 2001 From: Thomas Morrell Date: Wed, 13 Sep 2023 10:02:27 -0700 Subject: [PATCH 05/11] Update to current status --- migrated_records.csv | 28 ++++++++++++- missing_records.txt | 99 +------------------------------------------- 2 files changed, 27 insertions(+), 100 deletions(-) diff --git a/migrated_records.csv b/migrated_records.csv index 833b0f1d..f9d170bb 100644 --- a/migrated_records.csv +++ b/migrated_records.csv @@ -135530,8 +135530,7 @@ eprintid,rdmid,record_status 122558,862gc-y4k77,public 122502,sneaq-f9v10,public 122422,b399m-w3c59,public -78687,y52z8-p2409,public -176, mvhgr-qkt66, public +176,mvhgr-qkt66,public 279,8jkb9-v1q69,public 535,wvcwj-0fx78,public 552,hgcq6-gjx82,public @@ -135606,3 +135605,28 @@ eprintid,rdmid,record_status 6587,c4eny-3ay82,public 6758,41jdm-39h72,public 6815,eg2np-pwr70,public +6855,wg56b-4pa74,public +6993,hpzfj-8c316,public +7067,990rs-1kv04,public +7177,cgjzf-ns258,public +7208,422xf-1np28,public +7327,nkwat-xx774,public +7464,wts8p-vnw55,public +7596,zmvts-36w09,public +8710,5anjz-s4v17,public +8835,p0gc5-d0w45,public +8908,6hfep-vtc08,public +8996,49zrs-cj069,public +9057,y68n8-0ex38,public +9061,7msch-gmw37,public +9335,35v6c-z8531,public +9404,yayps-tds62,public +9693,hckdg-rf028,public +9694,hhajh-69k65,public +9935,5q6ne-w7952,public +9943,jse7w-d2396,public +9971,ypccs-26768,public +10257,qnbd7-3b550,public +10278,nj2d1-djc15,public +10344,9qgbv-tey36,public +10386,tag51-0hv59,public diff --git a/missing_records.txt b/missing_records.txt index 856f572e..ba496f45 100644 --- a/missing_records.txt +++ b/missing_records.txt @@ -1,132 +1,34 @@ -535 -552 -785 854 -876 -929 941 944 965 966 967 968 -976 -992 1048 -1434 -1480 1506 -1608 -1632 -1739 -1853 -1884 -1995 -2063 -2094 -2227 -2386 -2461 -2514 -2631 -2653 -2778 -2861 -2873 -2990 -3001 -3136 -3172 3358 -3487 -3980 -3986 -4115 -4134 -4159 4452 -4523 -4586 -4662 4691 -4806 -4865 4868 -4874 -4936 -4947 -4957 -4983 -5124 -5128 -5244 -5299 5329 -5354 -5355 -5356 -5439 -5525 -5586 -5618 -5752 5881 -6275 -6299 -6300 -6301 -6302 -6387 -6420 -6424 -6487 -6491 -6509 -6532 -6587 -6758 -6815 -6855 -6993 -7067 7163 -7177 -7208 7215 7306 -7327 -7464 7506 -7596 7654 7655 7682 7705 8643 -8710 -8835 8851 -8908 -8996 -9057 -9061 -9335 -9404 9518 9602 9686 -9693 -9694 9763 -9935 -9943 -9971 10079 -10257 -10278 10343 -10344 -10386 10423 10493 10569 @@ -2341,3 +2243,4 @@ 122218 122350 122358 + From 436b9ed05be51585cd6391669305f6c5a8719c9a Mon Sep 17 00:00:00 2001 From: "R. S. Doiel" Date: Thu, 14 Sep 2023 09:47:14 -0700 Subject: [PATCH 06/11] fix: irdmtools issue #53 --- CITATION.cff | 2 +- about.md | 4 ++-- codemeta.json | 4 ++-- doi2rdm.1.md | 4 ++-- eprint2rdm.1.md | 4 ++-- eprint2rdm.go | 33 +++++++++++++++------------------ eprintrest.1.md | 4 ++-- installer.sh | 2 +- man/man1/doi2rdm.1 | 2 +- man/man1/eprint2rdm.1 | 2 +- man/man1/eprintrest.1 | 2 +- man/man1/people2vocabulary.1 | 2 +- man/man1/rdmutil.1 | 2 +- people2vocabulary.1.md | 4 ++-- rdmutil.1.md | 4 ++-- version.go | 6 +++--- 16 files changed, 39 insertions(+), 42 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 58da891c..b40e7be3 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -14,7 +14,7 @@ authors: repository-code: "https://github.com/caltechlibrary/irdmtools" -version: 0.0.48 +version: 0.0.49 license-url: "https://caltechlibrary.github.io/irdmtools/LICENSE" keywords: [ "institutional repository", "data management", "Invenio", "Invenio-RDM" ] diff --git a/about.md b/about.md index e2023ebe..d35473ec 100644 --- a/about.md +++ b/about.md @@ -14,7 +14,7 @@ authors: orcid: "https://orcid.org/0000-0001-9266-5146" repository-code: "https://github.com/caltechlibrary/irdmtools" -version: 0.0.48 +version: 0.0.49 license-url: "https://caltechlibrary.github.io/irdmtools/LICENSE" keywords: [ "institutional repository", "data management", "Invenio", "Invenio-RDM" ] @@ -24,7 +24,7 @@ management", "Invenio", "Invenio-RDM" ] About this software =================== -## irdmtools 0.0.48 +## irdmtools 0.0.49 ### Authors diff --git a/codemeta.json b/codemeta.json index 2d33c66e..7f3533a0 100644 --- a/codemeta.json +++ b/codemeta.json @@ -4,10 +4,10 @@ "license": "https://caltechlibrary.github.io/irdmtools/LICENSE", "codeRepository": "https://github.com/caltechlibrary/irdmtools", "dateCreated": "2022-10-27", - "dateRelease": "2023-09-12", + "dateRelease": "2023-09-14", "issueTracker": "https://github.com/caltechlibrary/irdmtools/issues", "name": "irdmtools", - "version": "0.0.48", + "version": "0.0.49", "description": "Tools for working with institutional repositories and data management systems. Current implementation targets Invenio-RDM.", "applicationCategory": "library science", "releaseNotes": "This is a proof of concept", diff --git a/doi2rdm.1.md b/doi2rdm.1.md index 4ca7b598..0f5f2085 100644 --- a/doi2rdm.1.md +++ b/doi2rdm.1.md @@ -1,6 +1,6 @@ -%doi2rdm(1) irdmtools user manual | version 0.0.48 0238bfa +%doi2rdm(1) irdmtools user manual | version 0.0.49 21ad7b1 % R. S. Doiel and Tom Morrell -% 2023-09-12 +% 2023-09-14 # NAME diff --git a/eprint2rdm.1.md b/eprint2rdm.1.md index 6f6e760d..30c85be0 100644 --- a/eprint2rdm.1.md +++ b/eprint2rdm.1.md @@ -1,6 +1,6 @@ -%eprint2rdm(1) irdmtools user manual | version 0.0.48 0238bfa +%eprint2rdm(1) irdmtools user manual | version 0.0.49 21ad7b1 % R. S. Doiel and Tom Morrell -% 2023-09-12 +% 2023-09-14 # NAME diff --git a/eprint2rdm.go b/eprint2rdm.go index cf5e1a0b..6798f223 100644 --- a/eprint2rdm.go +++ b/eprint2rdm.go @@ -359,18 +359,13 @@ func customFieldsMetadataFromEPrint(eprint *eprinttools.EPrint, rec *simplified. // instread of simplified.go because I need to gaurantee duplicate subjects don't get added // as part of the merging of keywords and subjects from EPrints. if eprint.Keywords != "" || (eprint.Subjects != nil && eprint.Subjects.Length() > 0) { - if rec.Metadata.Subjects == nil { - rec.Metadata.Subjects = []*simplified.Subject{} - } - subjectsTest := map[string]bool{} + subjectStrings := []string{} if eprint.Keywords != "" { keywords := strings.Split(eprint.Keywords, ";") for _, keyword := range keywords { - if _, duplicate := subjectsTest[keyword]; ! duplicate { - subjectsTest[keyword] = true - rec.Metadata.Subjects = append(rec.Metadata.Subjects, &simplified.Subject{ - Subject: strings.TrimSpace(keyword), - }) + val := strings.TrimSpace(keyword) + if val != "" && val != "cls" { + subjectStrings = append(subjectStrings, val) } } } @@ -378,19 +373,21 @@ func customFieldsMetadataFromEPrint(eprint *eprinttools.EPrint, rec *simplified. subject := eprint.Subjects.IndexOf(i) //NOTE: irdmtools issue #51, ignore cls as a subject, this was an EPrints-ism // needed for Caltech Library only. - if subject.Value != "" && subject.Value != "cls" { - if _, duplicate := subjectsTest[subject.Value]; ! duplicate { - subjectsTest[subject.Value] = true - rec.Metadata.Subjects = append(rec.Metadata.Subjects, &simplified.Subject{ - Subject: strings.TrimSpace(subject.Value), - }) + val := strings.TrimSpace(subject.Value) + if val != "" && val != "cls" { + subjectStrings = append(subjectStrings, val) + } + } + if len(subjectStrings) > 0 { + duplicates := map[string]bool{} + for _, subject := range subjectStrings { + if _, duplicate := duplicates[subject]; ! duplicate { + AddSubject(rec, subject) } + duplicates[subject] = true } } } - - // FIXME: Handle non-subject keyswords - return nil } diff --git a/eprintrest.1.md b/eprintrest.1.md index 6838b4c8..8bc0c076 100644 --- a/eprintrest.1.md +++ b/eprintrest.1.md @@ -1,6 +1,6 @@ -%eprintrest(1) irdmtools user manual | version 0.0.48 0238bfa +%eprintrest(1) irdmtools user manual | version 0.0.49 21ad7b1 % R. S. Doiel and Tom Morrell -% 2023-09-12 +% 2023-09-14 # NAME diff --git a/installer.sh b/installer.sh index 78f04d08..ee4b8a67 100755 --- a/installer.sh +++ b/installer.sh @@ -4,7 +4,7 @@ # Set the package name and version to install # PACKAGE="irdmtools" -VERSION="0.0.48" +VERSION="0.0.49" GIT_GROUP="caltechlibrary" RELEASE="https://github.com/$GIT_GROUP/$PACKAGE/releases/tag/v$VERSION" diff --git a/man/man1/doi2rdm.1 b/man/man1/doi2rdm.1 index 88040c2b..4598c21e 100644 --- a/man/man1/doi2rdm.1 +++ b/man/man1/doi2rdm.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "doi2rdm" "1" "2023-09-12" "irdmtools user manual" "version 0.0.48 0238bfa" +.TH "doi2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 21ad7b1" .hy .SH NAME .PP diff --git a/man/man1/eprint2rdm.1 b/man/man1/eprint2rdm.1 index 44956c33..fca18dd1 100644 --- a/man/man1/eprint2rdm.1 +++ b/man/man1/eprint2rdm.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "eprint2rdm" "1" "2023-09-12" "irdmtools user manual" "version 0.0.48 0238bfa" +.TH "eprint2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 21ad7b1" .hy .SH NAME .PP diff --git a/man/man1/eprintrest.1 b/man/man1/eprintrest.1 index bd3c58f0..fb6141a0 100644 --- a/man/man1/eprintrest.1 +++ b/man/man1/eprintrest.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "eprintrest" "1" "2023-09-12" "irdmtools user manual" "version 0.0.48 0238bfa" +.TH "eprintrest" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 21ad7b1" .hy .SH NAME .PP diff --git a/man/man1/people2vocabulary.1 b/man/man1/people2vocabulary.1 index 279a0d31..9f427861 100644 --- a/man/man1/people2vocabulary.1 +++ b/man/man1/people2vocabulary.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "people2vocabulary" "1" "2023-09-12" "irdmtools user manual" "version 0.0.48 0238bfa" +.TH "people2vocabulary" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 21ad7b1" .hy .SH NAME .PP diff --git a/man/man1/rdmutil.1 b/man/man1/rdmutil.1 index 4ad47226..24c4d6c1 100644 --- a/man/man1/rdmutil.1 +++ b/man/man1/rdmutil.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "rdmutil" "1" "2023-09-12" "irdmtools user manual" "version 0.0.48 0238bfa" +.TH "rdmutil" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 21ad7b1" .hy .SH NAME .PP diff --git a/people2vocabulary.1.md b/people2vocabulary.1.md index 61570649..f22c23d5 100644 --- a/people2vocabulary.1.md +++ b/people2vocabulary.1.md @@ -1,6 +1,6 @@ -%people2vocabulary(1) irdmtools user manual | version 0.0.48 0238bfa +%people2vocabulary(1) irdmtools user manual | version 0.0.49 21ad7b1 % R. S. Doiel -% 2023-09-12 +% 2023-09-14 # NAME diff --git a/rdmutil.1.md b/rdmutil.1.md index 07dc15e6..f0b4b82b 100644 --- a/rdmutil.1.md +++ b/rdmutil.1.md @@ -1,6 +1,6 @@ -%rdmutil(1) irdmtools user manual | version 0.0.48 0238bfa +%rdmutil(1) irdmtools user manual | version 0.0.49 21ad7b1 % R. S. Doiel and Tom Morrell -% 2023-09-12 +% 2023-09-14 # NAME diff --git a/version.go b/version.go index f3535a51..e16b6822 100644 --- a/version.go +++ b/version.go @@ -6,13 +6,13 @@ import ( const ( // Version number of release - Version = "0.0.48" + Version = "0.0.49" // ReleaseDate, the date version.go was generated - ReleaseDate = "2023-09-12" + ReleaseDate = "2023-09-14" // ReleaseHash, the Git hash when version.go was generated - ReleaseHash = "0238bfa" + ReleaseHash = "21ad7b1" LicenseText = ` Redistribution and use in source and binary forms, with or without From 894e4c9b0d3e5a32b5bc9a08b3a49411853473ad Mon Sep 17 00:00:00 2001 From: "R. S. Doiel" Date: Thu, 14 Sep 2023 09:47:21 -0700 Subject: [PATCH 07/11] Quick Save --- about.html | 2 +- doi2rdm.1.md | 2 +- eprint2rdm.1.md | 2 +- eprintrest.1.md | 2 +- man/man1/doi2rdm.1 | 2 +- man/man1/eprint2rdm.1 | 2 +- man/man1/eprintrest.1 | 2 +- man/man1/people2vocabulary.1 | 2 +- man/man1/rdmutil.1 | 2 +- pagefind/fragment/unknown_bc9d25d.pf_fragment | Bin 0 -> 447 bytes pagefind/index/unknown_b221bfd.pf_index | Bin 0 -> 17900 bytes pagefind/pagefind-entry.json | 2 +- .../pagefind.unknown_b5c993ddd607e7d.pf_meta | Bin 0 -> 212 bytes people2vocabulary.1.md | 2 +- rdmutil.1.md | 2 +- version.go | 2 +- 16 files changed, 13 insertions(+), 13 deletions(-) create mode 100644 pagefind/fragment/unknown_bc9d25d.pf_fragment create mode 100644 pagefind/index/unknown_b221bfd.pf_index create mode 100644 pagefind/pagefind.unknown_b5c993ddd607e7d.pf_meta diff --git a/about.html b/about.html index 97adbf65..9745ba01 100644 --- a/about.html +++ b/about.html @@ -24,7 +24,7 @@

    About this software

    -

    irdmtools 0.0.48

    +

    irdmtools 0.0.49

    Authors

    • R. S. Doiel
      • diff --git a/doi2rdm.1.md b/doi2rdm.1.md index 0f5f2085..0c94887d 100644 --- a/doi2rdm.1.md +++ b/doi2rdm.1.md @@ -1,4 +1,4 @@ -%doi2rdm(1) irdmtools user manual | version 0.0.49 21ad7b1 +%doi2rdm(1) irdmtools user manual | version 0.0.49 436b9ed % R. S. Doiel and Tom Morrell % 2023-09-14 diff --git a/eprint2rdm.1.md b/eprint2rdm.1.md index 30c85be0..c949b963 100644 --- a/eprint2rdm.1.md +++ b/eprint2rdm.1.md @@ -1,4 +1,4 @@ -%eprint2rdm(1) irdmtools user manual | version 0.0.49 21ad7b1 +%eprint2rdm(1) irdmtools user manual | version 0.0.49 436b9ed % R. S. Doiel and Tom Morrell % 2023-09-14 diff --git a/eprintrest.1.md b/eprintrest.1.md index 8bc0c076..acfc785d 100644 --- a/eprintrest.1.md +++ b/eprintrest.1.md @@ -1,4 +1,4 @@ -%eprintrest(1) irdmtools user manual | version 0.0.49 21ad7b1 +%eprintrest(1) irdmtools user manual | version 0.0.49 436b9ed % R. S. Doiel and Tom Morrell % 2023-09-14 diff --git a/man/man1/doi2rdm.1 b/man/man1/doi2rdm.1 index 4598c21e..ea71a96f 100644 --- a/man/man1/doi2rdm.1 +++ b/man/man1/doi2rdm.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "doi2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 21ad7b1" +.TH "doi2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 436b9ed" .hy .SH NAME .PP diff --git a/man/man1/eprint2rdm.1 b/man/man1/eprint2rdm.1 index fca18dd1..21d46889 100644 --- a/man/man1/eprint2rdm.1 +++ b/man/man1/eprint2rdm.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "eprint2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 21ad7b1" +.TH "eprint2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 436b9ed" .hy .SH NAME .PP diff --git a/man/man1/eprintrest.1 b/man/man1/eprintrest.1 index fb6141a0..557a0017 100644 --- a/man/man1/eprintrest.1 +++ b/man/man1/eprintrest.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "eprintrest" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 21ad7b1" +.TH "eprintrest" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 436b9ed" .hy .SH NAME .PP diff --git a/man/man1/people2vocabulary.1 b/man/man1/people2vocabulary.1 index 9f427861..7860abc0 100644 --- a/man/man1/people2vocabulary.1 +++ b/man/man1/people2vocabulary.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "people2vocabulary" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 21ad7b1" +.TH "people2vocabulary" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 436b9ed" .hy .SH NAME .PP diff --git a/man/man1/rdmutil.1 b/man/man1/rdmutil.1 index 24c4d6c1..7f34bdc9 100644 --- a/man/man1/rdmutil.1 +++ b/man/man1/rdmutil.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "rdmutil" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 21ad7b1" +.TH "rdmutil" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 436b9ed" .hy .SH NAME .PP diff --git a/pagefind/fragment/unknown_bc9d25d.pf_fragment b/pagefind/fragment/unknown_bc9d25d.pf_fragment new file mode 100644 index 0000000000000000000000000000000000000000..9588e2b13a6abe05c004b11384da2aa44e2817ea GIT binary patch literal 447 zcmV;w0YLsAiwFP!00002|CLg~ZWBQa{S|A^VYUS#K_rl>G%A6Fw%JM?tI4jjYcV?x z9uFa^^6z+;KqbV5+sw25Y`^EdZ*fPld2H(DsmKzFSyB2eXLX(Sp_mjkN5!ayUkxy5 zM+p+|^xy>@kTktAhXfby!o7a$;3{j!k{oOtR1U70FgSSN9@Z>^!9H{26xwDT^FDd) zj_{GYm^eDPL6#Qbjzv+1!hw9p0tc3_6k9luc0e&HX;$Ls0|@RpkRU7Gi=6@=46e=w!v?=)5>rY? zE_nYAF5OFW+E_VhD_GsHMs#{cHjColc4!*|L&~+0$uKSZ{By!u$^S?>j6`r=O~@Js8RY008SO(J24` literal 0 HcmV?d00001 diff --git a/pagefind/index/unknown_b221bfd.pf_index b/pagefind/index/unknown_b221bfd.pf_index new file mode 100644 index 0000000000000000000000000000000000000000..913a60444f3bf86d0cb3c06828604f94fd0d9564 GIT binary patch literal 17900 zcmV(=K-s?^iwFP!00002|BZbIcwEKRwr)|eWXlC(&!J<$Hr=w^=)IfXt61$`tybFR zEh==4BzMz`=_R4}-UA^d^pFHX3IS3`2qC@KFaP_VxhvZw-}8SYA-dDcnN!|#X116} zM_rkGsw0(54P6`VY*TaQ%-e0qjvESXqHW054@r2v?P{CDe}-(+ka+F3+%~6e&fK;{ zvYg0e7IwDHUoam<8;8vtbGv!QCfnxpqNX*Y;_YWU+uBB~KV-VumbWpQFk7Q}vk4`eHfozYw+)p%Yc4ZaqWSq8 zt(j*Nb6t_CHZ^z7+;)yY!W$&K#dh->LyqV3g<3*;obW{(&7G(7;}FFr+I7TN+R%#E zD&7_x^bU5MHM^UAZD+08&G@r@*wzi1JW84q#M^`gH?zt1_JJX$=4omFOEx*5 zT{I7w88$V4PW<;w{5`K7LvKLW!?tq)iu+7XEYf-HWury&=g&idz?!|yVw*^;v2~+O zlg(_?WiGSc$P}}+In@l|++2ZIcgJA~KP#C+-rD-%dV`af!n)Pj zB`&q2m?$N3Q6(ys*=K`rLo>6!B*^JA(0W#V7V-@u_jsVl`hTD+IA!P#t~f7mu)@9V^W&^B9huXryXJ|6`8AxhNgbVrg8-iu*I4!%v{zk(WVX{8cVQCQQj|yyS}wzV+U|oAYzd0X zmJ3VCNR}}tqd7;2_cQMK|JdeXlQ9MH=Ck87v0Yg#Zaz`ro^pYDYYCaYh-)^P16^i* z%OUkA2Fs4{9<-f_95!^s9HLC&1Mv$ek*n>q89{;kDvshc>kS!$g$!&kWDc?6Qd2hf znkURp&9BT~ZT)f_(JzXBtN8awutvh7gaZ;@Xd9MI!T~+T+%4Wa;x~$4<+|dSciZMs zvlK`0S@Rq5Dz;^45{P&s@v`Dwij~A>50*0+Xe-v~dTd@kwT8!I7TCQvJk1g*FP<;nmf{@?aRbh{ z>10%GGbfvZ`NV+RHHtSwGfxrkTJdfb?@sZa5bsOky)53p#h)nt;o`3r|MwCUBv>uM zD-wKDf}hxii@}@n<~qgn1Rrc+# z9QabOk!iMh1cSc^Z0Q5ij4?af)>YFm$2pi?r+5wGEfjBw^6Ll0dkPz$FXRWYVLZ5? zkaxv@m}{lve-Wd|Uom|1D-mZGJT&FQ9yMgKOX=ot{r*vUQ3dEmp3nD3e2*!t0p zFq1i^Pr}!1!>ZDvLOIXW^Adg9)7Gw?Txg)jQr3s}%BH4|)dQ!cT)-M%`rHq~uuou6{ z=GIHg4mw7%iepgzVUEPGOUZ6MLv_?fxSBK3x=TbM5af2|D%2=NqpC7M_*`P^SDO>e zfcXW)hj?ET-xGha1fB#_B$y|`5(&GoTV_zaU3r|Z(D@$CR&vU#w!_p*ID{!>6$>z| zR`8BeDKSXSW44fB2P`u5g9*q$t%{EJAda?@Nm5ebwC`yS$DCb4PnoQ_aRkEU4)dUS z8YfM>d6XpHa1M_o^!D`KFZcH3)?uwOMOXeRKZDoXtSOk`ZbKrknf=$V2o;0s0 zNxX&@Dish!t)nf_LZuSrD4%g8kH<->R7#o7Y9$tn*Gq68##c)$D}z2>d!L8xsaCoR zC9S#|E$LU8N?W}hF!5(L(^*QC29spP?6^9_r91*eSFIFspkoT8L8n+}(SKhelck<9 zOcLnhjy^^1et?az7g1`IB)GW^N6pqs(YuLvK4m7BJf#G*gr)DaDU|M36&;Fa!6`OHBG+L; 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S. Doiel % 2023-09-14 diff --git a/rdmutil.1.md b/rdmutil.1.md index f0b4b82b..e0707a3c 100644 --- a/rdmutil.1.md +++ b/rdmutil.1.md @@ -1,4 +1,4 @@ -%rdmutil(1) irdmtools user manual | version 0.0.49 21ad7b1 +%rdmutil(1) irdmtools user manual | version 0.0.49 436b9ed % R. S. Doiel and Tom Morrell % 2023-09-14 diff --git a/version.go b/version.go index e16b6822..d53a9439 100644 --- a/version.go +++ b/version.go @@ -12,7 +12,7 @@ const ( ReleaseDate = "2023-09-14" // ReleaseHash, the Git hash when version.go was generated - ReleaseHash = "21ad7b1" + ReleaseHash = "436b9ed" LicenseText = ` Redistribution and use in source and binary forms, with or without From 6fc184a5b7305caaf9eaefec1dba2fa29ea2b570 Mon Sep 17 00:00:00 2001 From: "R. S. Doiel" Date: Thu, 14 Sep 2023 09:47:41 -0700 Subject: [PATCH 08/11] fix: irdmtools issue #53 --- doi2rdm.1.md | 2 +- eprint2rdm.1.md | 2 +- eprintrest.1.md | 2 +- man/man1/doi2rdm.1 | 2 +- man/man1/eprint2rdm.1 | 2 +- man/man1/eprintrest.1 | 2 +- man/man1/people2vocabulary.1 | 2 +- man/man1/rdmutil.1 | 2 +- people2vocabulary.1.md | 2 +- rdmutil.1.md | 2 +- version.go | 2 +- 11 files changed, 11 insertions(+), 11 deletions(-) diff --git a/doi2rdm.1.md b/doi2rdm.1.md index 0c94887d..72aedeec 100644 --- a/doi2rdm.1.md +++ b/doi2rdm.1.md @@ -1,4 +1,4 @@ -%doi2rdm(1) irdmtools user manual | version 0.0.49 436b9ed +%doi2rdm(1) irdmtools user manual | version 0.0.49 6b95911 % R. S. Doiel and Tom Morrell % 2023-09-14 diff --git a/eprint2rdm.1.md b/eprint2rdm.1.md index c949b963..84fff5f0 100644 --- a/eprint2rdm.1.md +++ b/eprint2rdm.1.md @@ -1,4 +1,4 @@ -%eprint2rdm(1) irdmtools user manual | version 0.0.49 436b9ed +%eprint2rdm(1) irdmtools user manual | version 0.0.49 6b95911 % R. S. Doiel and Tom Morrell % 2023-09-14 diff --git a/eprintrest.1.md b/eprintrest.1.md index acfc785d..4a40e7dc 100644 --- a/eprintrest.1.md +++ b/eprintrest.1.md @@ -1,4 +1,4 @@ -%eprintrest(1) irdmtools user manual | version 0.0.49 436b9ed +%eprintrest(1) irdmtools user manual | version 0.0.49 6b95911 % R. S. Doiel and Tom Morrell % 2023-09-14 diff --git a/man/man1/doi2rdm.1 b/man/man1/doi2rdm.1 index ea71a96f..1084f9d8 100644 --- a/man/man1/doi2rdm.1 +++ b/man/man1/doi2rdm.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "doi2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 436b9ed" +.TH "doi2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6b95911" .hy .SH NAME .PP diff --git a/man/man1/eprint2rdm.1 b/man/man1/eprint2rdm.1 index 21d46889..5b39e310 100644 --- a/man/man1/eprint2rdm.1 +++ b/man/man1/eprint2rdm.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "eprint2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 436b9ed" +.TH "eprint2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6b95911" .hy .SH NAME .PP diff --git a/man/man1/eprintrest.1 b/man/man1/eprintrest.1 index 557a0017..b8976da5 100644 --- a/man/man1/eprintrest.1 +++ b/man/man1/eprintrest.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "eprintrest" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 436b9ed" +.TH "eprintrest" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6b95911" .hy .SH NAME .PP diff --git a/man/man1/people2vocabulary.1 b/man/man1/people2vocabulary.1 index 7860abc0..3d1fe9cc 100644 --- a/man/man1/people2vocabulary.1 +++ b/man/man1/people2vocabulary.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "people2vocabulary" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 436b9ed" +.TH "people2vocabulary" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6b95911" .hy .SH NAME .PP diff --git a/man/man1/rdmutil.1 b/man/man1/rdmutil.1 index 7f34bdc9..9d06958a 100644 --- a/man/man1/rdmutil.1 +++ b/man/man1/rdmutil.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "rdmutil" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 436b9ed" +.TH "rdmutil" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6b95911" .hy .SH NAME .PP diff --git a/people2vocabulary.1.md b/people2vocabulary.1.md index a0e8a78c..e747d2fb 100644 --- a/people2vocabulary.1.md +++ b/people2vocabulary.1.md @@ -1,4 +1,4 @@ -%people2vocabulary(1) irdmtools user manual | version 0.0.49 436b9ed +%people2vocabulary(1) irdmtools user manual | version 0.0.49 6b95911 % R. S. Doiel % 2023-09-14 diff --git a/rdmutil.1.md b/rdmutil.1.md index e0707a3c..9194543b 100644 --- a/rdmutil.1.md +++ b/rdmutil.1.md @@ -1,4 +1,4 @@ -%rdmutil(1) irdmtools user manual | version 0.0.49 436b9ed +%rdmutil(1) irdmtools user manual | version 0.0.49 6b95911 % R. S. Doiel and Tom Morrell % 2023-09-14 diff --git a/version.go b/version.go index d53a9439..a58a217b 100644 --- a/version.go +++ b/version.go @@ -12,7 +12,7 @@ const ( ReleaseDate = "2023-09-14" // ReleaseHash, the Git hash when version.go was generated - ReleaseHash = "436b9ed" + ReleaseHash = "6b95911" LicenseText = ` Redistribution and use in source and binary forms, with or without From 265a46b14d886aea1ce4a58dc1ed6e597607af4b Mon Sep 17 00:00:00 2001 From: "R. S. Doiel" Date: Thu, 14 Sep 2023 09:47:48 -0700 Subject: [PATCH 09/11] Quick Save --- doi2rdm.1.md | 2 +- eprint2rdm.1.md | 2 +- eprintrest.1.md | 2 +- man/man1/doi2rdm.1 | 2 +- man/man1/eprint2rdm.1 | 2 +- man/man1/eprintrest.1 | 2 +- man/man1/people2vocabulary.1 | 2 +- man/man1/rdmutil.1 | 2 +- people2vocabulary.1.md | 2 +- rdmutil.1.md | 2 +- version.go | 2 +- 11 files changed, 11 insertions(+), 11 deletions(-) diff --git a/doi2rdm.1.md b/doi2rdm.1.md index 72aedeec..8c200d51 100644 --- a/doi2rdm.1.md +++ b/doi2rdm.1.md @@ -1,4 +1,4 @@ -%doi2rdm(1) irdmtools user manual | version 0.0.49 6b95911 +%doi2rdm(1) irdmtools user manual | version 0.0.49 6fc184a % R. S. Doiel and Tom Morrell % 2023-09-14 diff --git a/eprint2rdm.1.md b/eprint2rdm.1.md index 84fff5f0..086f9c12 100644 --- a/eprint2rdm.1.md +++ b/eprint2rdm.1.md @@ -1,4 +1,4 @@ -%eprint2rdm(1) irdmtools user manual | version 0.0.49 6b95911 +%eprint2rdm(1) irdmtools user manual | version 0.0.49 6fc184a % R. S. Doiel and Tom Morrell % 2023-09-14 diff --git a/eprintrest.1.md b/eprintrest.1.md index 4a40e7dc..170d2432 100644 --- a/eprintrest.1.md +++ b/eprintrest.1.md @@ -1,4 +1,4 @@ -%eprintrest(1) irdmtools user manual | version 0.0.49 6b95911 +%eprintrest(1) irdmtools user manual | version 0.0.49 6fc184a % R. S. Doiel and Tom Morrell % 2023-09-14 diff --git a/man/man1/doi2rdm.1 b/man/man1/doi2rdm.1 index 1084f9d8..5ee0140c 100644 --- a/man/man1/doi2rdm.1 +++ b/man/man1/doi2rdm.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "doi2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6b95911" +.TH "doi2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6fc184a" .hy .SH NAME .PP diff --git a/man/man1/eprint2rdm.1 b/man/man1/eprint2rdm.1 index 5b39e310..656eb316 100644 --- a/man/man1/eprint2rdm.1 +++ b/man/man1/eprint2rdm.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "eprint2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6b95911" +.TH "eprint2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6fc184a" .hy .SH NAME .PP diff --git a/man/man1/eprintrest.1 b/man/man1/eprintrest.1 index b8976da5..e2ee2a90 100644 --- a/man/man1/eprintrest.1 +++ b/man/man1/eprintrest.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "eprintrest" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6b95911" +.TH "eprintrest" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6fc184a" .hy .SH NAME .PP diff --git a/man/man1/people2vocabulary.1 b/man/man1/people2vocabulary.1 index 3d1fe9cc..6c55040e 100644 --- a/man/man1/people2vocabulary.1 +++ b/man/man1/people2vocabulary.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "people2vocabulary" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6b95911" +.TH "people2vocabulary" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6fc184a" .hy .SH NAME .PP diff --git a/man/man1/rdmutil.1 b/man/man1/rdmutil.1 index 9d06958a..53626ea1 100644 --- a/man/man1/rdmutil.1 +++ b/man/man1/rdmutil.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "rdmutil" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6b95911" +.TH "rdmutil" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6fc184a" .hy .SH NAME .PP diff --git a/people2vocabulary.1.md b/people2vocabulary.1.md index e747d2fb..8669de9d 100644 --- a/people2vocabulary.1.md +++ b/people2vocabulary.1.md @@ -1,4 +1,4 @@ -%people2vocabulary(1) irdmtools user manual | version 0.0.49 6b95911 +%people2vocabulary(1) irdmtools user manual | version 0.0.49 6fc184a % R. S. Doiel % 2023-09-14 diff --git a/rdmutil.1.md b/rdmutil.1.md index 9194543b..f3d83897 100644 --- a/rdmutil.1.md +++ b/rdmutil.1.md @@ -1,4 +1,4 @@ -%rdmutil(1) irdmtools user manual | version 0.0.49 6b95911 +%rdmutil(1) irdmtools user manual | version 0.0.49 6fc184a % R. S. Doiel and Tom Morrell % 2023-09-14 diff --git a/version.go b/version.go index a58a217b..80a79ef3 100644 --- a/version.go +++ b/version.go @@ -12,7 +12,7 @@ const ( ReleaseDate = "2023-09-14" // ReleaseHash, the Git hash when version.go was generated - ReleaseHash = "6b95911" + ReleaseHash = "6fc184a" LicenseText = ` Redistribution and use in source and binary forms, with or without From a3f1768e242b553b1634eaabea0cdf2d50a8ed48 Mon Sep 17 00:00:00 2001 From: "R. S. Doiel" Date: Thu, 14 Sep 2023 09:54:16 -0700 Subject: [PATCH 10/11] release v0.0.49 --- doi2rdm.1.md | 2 +- eprint2rdm.1.md | 2 +- eprintrest.1.md | 2 +- man/man1/doi2rdm.1 | 2 +- man/man1/eprint2rdm.1 | 2 +- man/man1/eprintrest.1 | 2 +- man/man1/people2vocabulary.1 | 2 +- man/man1/rdmutil.1 | 2 +- people2vocabulary.1.md | 2 +- rdmutil.1.md | 2 +- version.go | 2 +- 11 files changed, 11 insertions(+), 11 deletions(-) diff --git a/doi2rdm.1.md b/doi2rdm.1.md index 8c200d51..0e92f983 100644 --- a/doi2rdm.1.md +++ b/doi2rdm.1.md @@ -1,4 +1,4 @@ -%doi2rdm(1) irdmtools user manual | version 0.0.49 6fc184a +%doi2rdm(1) irdmtools user manual | version 0.0.49 265a46b % R. S. Doiel and Tom Morrell % 2023-09-14 diff --git a/eprint2rdm.1.md b/eprint2rdm.1.md index 086f9c12..c5c016bc 100644 --- a/eprint2rdm.1.md +++ b/eprint2rdm.1.md @@ -1,4 +1,4 @@ -%eprint2rdm(1) irdmtools user manual | version 0.0.49 6fc184a +%eprint2rdm(1) irdmtools user manual | version 0.0.49 265a46b % R. S. Doiel and Tom Morrell % 2023-09-14 diff --git a/eprintrest.1.md b/eprintrest.1.md index 170d2432..dbd71838 100644 --- a/eprintrest.1.md +++ b/eprintrest.1.md @@ -1,4 +1,4 @@ -%eprintrest(1) irdmtools user manual | version 0.0.49 6fc184a +%eprintrest(1) irdmtools user manual | version 0.0.49 265a46b % R. S. Doiel and Tom Morrell % 2023-09-14 diff --git a/man/man1/doi2rdm.1 b/man/man1/doi2rdm.1 index 5ee0140c..7ebf201e 100644 --- a/man/man1/doi2rdm.1 +++ b/man/man1/doi2rdm.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "doi2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6fc184a" +.TH "doi2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 265a46b" .hy .SH NAME .PP diff --git a/man/man1/eprint2rdm.1 b/man/man1/eprint2rdm.1 index 656eb316..398a5310 100644 --- a/man/man1/eprint2rdm.1 +++ b/man/man1/eprint2rdm.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "eprint2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6fc184a" +.TH "eprint2rdm" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 265a46b" .hy .SH NAME .PP diff --git a/man/man1/eprintrest.1 b/man/man1/eprintrest.1 index e2ee2a90..2b55dac5 100644 --- a/man/man1/eprintrest.1 +++ b/man/man1/eprintrest.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "eprintrest" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6fc184a" +.TH "eprintrest" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 265a46b" .hy .SH NAME .PP diff --git a/man/man1/people2vocabulary.1 b/man/man1/people2vocabulary.1 index 6c55040e..b4e181ed 100644 --- a/man/man1/people2vocabulary.1 +++ b/man/man1/people2vocabulary.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "people2vocabulary" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6fc184a" +.TH "people2vocabulary" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 265a46b" .hy .SH NAME .PP diff --git a/man/man1/rdmutil.1 b/man/man1/rdmutil.1 index 53626ea1..798e0dd3 100644 --- a/man/man1/rdmutil.1 +++ b/man/man1/rdmutil.1 @@ -14,7 +14,7 @@ . ftr VB CB . ftr VBI CBI .\} -.TH "rdmutil" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 6fc184a" +.TH "rdmutil" "1" "2023-09-14" "irdmtools user manual" "version 0.0.49 265a46b" .hy .SH NAME .PP diff --git a/people2vocabulary.1.md b/people2vocabulary.1.md index 8669de9d..0c264191 100644 --- a/people2vocabulary.1.md +++ b/people2vocabulary.1.md @@ -1,4 +1,4 @@ -%people2vocabulary(1) irdmtools user manual | version 0.0.49 6fc184a +%people2vocabulary(1) irdmtools user manual | version 0.0.49 265a46b % R. S. Doiel % 2023-09-14 diff --git a/rdmutil.1.md b/rdmutil.1.md index f3d83897..51a431e0 100644 --- a/rdmutil.1.md +++ b/rdmutil.1.md @@ -1,4 +1,4 @@ -%rdmutil(1) irdmtools user manual | version 0.0.49 6fc184a +%rdmutil(1) irdmtools user manual | version 0.0.49 265a46b % R. S. Doiel and Tom Morrell % 2023-09-14 diff --git a/version.go b/version.go index 80a79ef3..f6d07195 100644 --- a/version.go +++ b/version.go @@ -12,7 +12,7 @@ const ( ReleaseDate = "2023-09-14" // ReleaseHash, the Git hash when version.go was generated - ReleaseHash = "6fc184a" + ReleaseHash = "265a46b" LicenseText = ` Redistribution and use in source and binary forms, with or without From 8575da6fca927427fe7060c1d1dbdbffdb1601b1 Mon Sep 17 00:00:00 2001 From: Thomas Morrell Date: Thu, 14 Sep 2023 09:59:23 -0700 Subject: [PATCH 11/11] Additional group fix --- irdm/fixups.py | 2 ++ migrated_records.csv | 47 ++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 49 insertions(+) diff --git a/irdm/fixups.py b/irdm/fixups.py index 2c131c45..5d6d987a 100644 --- a/irdm/fixups.py +++ b/irdm/fixups.py @@ -437,6 +437,8 @@ def fixup_record(record, reload=False, token=None): new.append({"id": "Owens-Valley-Radio-Observatory"}) elif group["id"] == "Library-System-Papers-and-Publications": new.append({"id": "Caltech-Library"}) + elif group["id"] == 'Koch-Laboratory-(KLAB)': + new.append({"id": "Koch-Laboratory"}) else: new.append(group) record["custom_fields"]["caltech:groups"] = new diff --git a/migrated_records.csv b/migrated_records.csv index f9d170bb..c6299732 100644 --- a/migrated_records.csv +++ b/migrated_records.csv @@ -135630,3 +135630,50 @@ eprintid,rdmid,record_status 10278,nj2d1-djc15,public 10344,9qgbv-tey36,public 10386,tag51-0hv59,public +10571,4xdnv-yr859,public +10787,0sn8a-9ss32,public +10791,zf6yv-wyz65,public +10953,5f28q-aks55,public +10954,s6dv5-0wv41,public +10956,xdmxy-2qw19,public +11003,ft4cg-ez334,public +11148,513m7-kn635,public +11149,29emd-eth25,public +11151,emats-q3e25,public +11177,24czq-28a81,public +11179,gd51h-cye59,public +11182,81bdh-qk895,public +11194,7grp1-gkr73,public +11218,cejm8-hbf89,public +11169,y7g3c-w5g95,public +11117,grqbc-bx868,public +11220,qea1q-7ay26,public +11233,e0tpv-t9h46,public +11234,543fd-mbf50,public +11249,m8pmd-y0042,public +11250,8ytb3-2x127,public +11343,pm25q-m5n08,public +11352,fagpg-d9b74,public +11355,1b2hx-7tx89,public +11369,bjzqg-cry21,public +11383,p6pdb-vsk02,public +11452,8d0mt-avg30,public +11515,8mxw1-cbc17,public +11590,21sze-z2340,public +11657,v18jb-xb789,public +11693,eanx2-5zy62,public +11735,t882t-h4867,public +11770,bb7ve-k0486,public +11827,cn5d6-ez857,public +11954,3b91s-8jv08,public +11999,qg4xz-jnv92,public +12016,gf9rc-wfb95,public +12154,h73fj-4t355,public +12202,61vhr-z0s35,public +12369,bywz9-are23,public +12393,w9880-ger04,public +12407,6f9kb-hsf29,public +12474,zz44n-yby19,public +12491,5e3b0-rbc22,public +12591,300h0-18998,public +12613,r20n5-8mz88,public