From 5f3fccd9e09e96838f9fb3618aef3096b2c15ef2 Mon Sep 17 00:00:00 2001
From: Matt Jones <gitcode@magisa.org>
Date: Wed, 4 Sep 2019 17:07:57 -0800
Subject: [PATCH] Add a codemeta.json file and a bibtext citation.

The codemeta.json file is included in the HTML of the generated book, and the Bobtex entry is made available through a 'Copy Bibtex' button.
---
 README.md            |  14 +++++-
 docs/_output.yml     |   3 ++
 docs/codemeta.json   | 108 +++++++++++++++++++++++++++++++++++++++++++
 docs/javascript.html |  17 +++++++
 docs/style.css       |  15 ++++++
 5 files changed, 156 insertions(+), 1 deletion(-)
 create mode 100644 docs/codemeta.json
 create mode 100644 docs/javascript.html
 create mode 100644 docs/style.css

diff --git a/README.md b/README.md
index 1d2e6fa7..8b502b8b 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,19 @@
 
 *Cite as*:
 
-[Matthew B. Jones](https://orcid.org/0000-0003-0077-4738),  [Margaret O'Brien](https://orcid.org/0000-0002-1693-8322), [Bryce Mecum](https://orcid.org/0000-0002-0381-3766), [Carl Boettiger](https://orcid.org/0000-0002-1642-628X), [Mark Schildhauer](https://orcid.org/0000-0003-0632-7576), [Mitchell Maier](https://orcid.org/0000-0001-6955-0535), [Timothy Whiteaker](https://orcid.org/0000-0002-1940-4158), [Stevan Earl](https://orcid.org/0000-0002-4465-452X), [Steven Chong](https://orcid.org/0000-0003-1264-1166). 2019. **Ecological Metadata Language version 2.2.0.** KNB Data Repository. [doi:10.5063/F11834T2](https://doi.org/10.5063/F11834T2)
+[Matthew B. Jones](https://orcid.org/0000-0003-0077-4738),  [Margaret O'Brien](https://orcid.org/0000-0002-1693-8322), [Bryce Mecum](https://orcid.org/0000-0002-0381-3766), [Carl Boettiger](https://orcid.org/0000-0002-1642-628X), [Mark Schildhauer](https://orcid.org/0000-0003-0632-7576), [Mitchell Maier](https://orcid.org/0000-0001-6955-0535), [Timothy Whiteaker](https://orcid.org/0000-0002-1940-4158), [Stevan Earl](https://orcid.org/0000-0002-4465-452X), [Steven Chong](https://orcid.org/0000-0003-1264-1166). 2019. **Ecological Metadata Language version 2.2.0.** KNB Data Repository. [doi:10.5063/F11834T2](https://doi.org/10.5063/F11834T2) <button id="bibtext-button">Copy Bibtex</button>
+
+<input type="text" id="placeholder"/>
+<span id="bibtex">
+&#x0040;article{EML_2019,
+  title={Ecological Metadata Language version 2.2.0},
+  url={https://eml.ecoinformatics.org},
+  DOI={10.5063/f11834t2},
+  publisher={KNB Data Repository}, 
+  author={Jones, Matthew and O’Brien, Margaret and Mecum, Bryce and Boettiger, Carl and Schildhauer, Mark and Maier, Mitchell and Whiteaker, Timothy and Earl, Stevan and Chong, Steven},
+  year={2019}
+}
+</span>
 
 The Ecological Metadata Language (EML) defines a comprehensive vocabulary and a readable XML markup syntax for documenting research data.  It is in widespread use in the earth and environmental sciences, and increasingly in other research disciplines as well.  EML is a community-maintained specification, and evolves to meet the data documentation needs of researchers who want to openly document, preserve, and share data and outputs.  EML includes modules for identifying and citing data packages, for describing the spatial, temporal, taxonomic, and thematic extent of data, for describing research methods and protocols, for describing the structure and content of data within sometimes complex packages of data, and for precisely annotating data with semantic vocabularies. EML includes metadata fields to fully detail data papers that are published in journals specializing in scientific data sharing and preservation.
 
diff --git a/docs/_output.yml b/docs/_output.yml
index c14cc3e4..2088ffd2 100755
--- a/docs/_output.yml
+++ b/docs/_output.yml
@@ -5,3 +5,6 @@ bookdown::gitbook:
       collapse: section
       before: |
         <li><a href="./">EML Specification</a></li>
+  includes:
+    after_body: javascript.html
+    in_header: codemeta.json
diff --git a/docs/codemeta.json b/docs/codemeta.json
new file mode 100644
index 00000000..76b54593
--- /dev/null
+++ b/docs/codemeta.json
@@ -0,0 +1,108 @@
+<script type='application/ld+json'>
+{
+    "@context": [
+        "https://doi.org/10.5063/schema/codemeta-2.0",
+        "http://schema.org"
+    ],
+    "@type": "SoftwareSourceCode",
+	"@id": "https://doi.org/10.5063/F11834T2",
+    "name": "Ecological Metadata Language version 2.2.0",
+    "url": "https://eml.ecoinformatics.org",
+    "sameAs": "doi:10.5063/F11834T2",
+    "version": "2.2.0",
+    "license": "https://spdx.org/licenses/GPL-2.0-or-later.html",
+    "identifier": {
+        "@type": ["PropertyValue", "datacite:ResourceIdentifier"],
+        "datacite:usesIdentifierScheme": {
+            "@id": "datacite:doi"
+        },
+        "propertyID": "DOI",
+        "url": "https://doi.org/10.5063/F11834T2",
+        "value": "10.5063/F11834T2"
+    },
+    "programmingLanguage": {
+        "@type": "ComputerLanguage",
+        "name": "XML"
+    },
+    "creator": [
+		{
+	        "@id": "https://orcid.org/0000-0003-0077-4738",
+	        "@type": "Person",
+	        "name": "Matthew B. Jones",
+	        "givenName": "Matthew",
+	        "familyName": "Jones",
+	        "url": "https://orcid.org/0000-0003-0077-4738"
+    	},
+		{
+			"@id": "https://orcid.org/0000-0002-1693-8322",
+			"@type": "Person",
+			"name": "Margaret O’Brien",
+			"givenName": "Margaret",
+			"familyName": "O’Brien",
+			"url": "https://orcid.org/0000-0002-1693-8322"
+		},
+		{
+	        "@id": "https://orcid.org/0000-0002-0381-3766",
+	        "@type": "Person",
+	        "name": "Bryce Mecum",
+	        "givenName": "Bryce",
+	        "familyName": "Mecum",
+	        "url": "https://orcid.org/0000-0002-0381-3766"
+    	},
+		{
+	        "@id": "https://orcid.org/0000-0002-1642-628X",
+	        "@type": "Person",
+	        "name": "Carl Boettiger",
+	        "givenName": "Carl",
+	        "familyName": "Boettiger",
+	        "url": "https://orcid.org/0000-0002-1642-628X"
+    	},
+		{
+	        "@id": "https://orcid.org/0000-0003-0632-7576",
+	        "@type": "Person",
+	        "name": "Mark Schildhauer",
+	        "givenName": "Mark",
+	        "familyName": "Schildhauer",
+	        "url": "https://orcid.org/0000-0003-0632-7576"
+    	},
+		{
+	        "@id": "https://orcid.org/0000-0001-6955-0535",
+	        "@type": "Person",
+	        "name": "Mitchell",
+	        "givenName": "Mitchell Maier",
+	        "familyName": "Maier",
+	        "url": "https://orcid.org/0000-0001-6955-0535"
+    	},
+		{
+	        "@id": "https://orcid.org/0000-0002-1940-4158",
+	        "@type": "Person",
+	        "name": "Timothy Whiteaker",
+	        "givenName": "Timothy",
+	        "familyName": "Whiteaker",
+	        "url": "https://orcid.org/0000-0002-1940-4158"
+    	},
+		{
+	        "@id": "https://orcid.org/0000-0002-4465-452X",
+	        "@type": "Person",
+	        "name": "Stevan Earl",
+	        "givenName": "Stevan",
+	        "familyName": "Earl",
+	        "url": "https://orcid.org/0000-0002-4465-452X"
+    	},
+		{
+	        "@id": "https://orcid.org/0000-0003-1264-1166",
+	        "@type": "Person",
+	        "name": "Steven Chong",
+	        "givenName": "Steven",
+	        "familyName": "Chong",
+	        "url": "https://orcid.org/0000-0003-1264-1166"
+    	}
+	],
+	"copyrightYear": "2019",
+    "datePublished": "2019",
+    "isAccessibleForFree": true,
+    "keywords": ["metadata", "xml", "specification", "ecology", "environmental science", "earth science", "EML"],
+    "codeRepository": "https://github.com/NCEAS/eml",
+    "issueTracker": "https://github.com/NCEAS/eml/issues"
+}
+</script>
diff --git a/docs/javascript.html b/docs/javascript.html
new file mode 100644
index 00000000..cef4459f
--- /dev/null
+++ b/docs/javascript.html
@@ -0,0 +1,17 @@
+<script type="text/javascript">
+document.body.addEventListener('click', copy);
+
+function copy(e) {
+  // copy data to placeholder - Don't use .innerText, use .textContent
+  placeholder.value = bibtex.textContent;
+  if (placeholder.select) {
+    placeholder.select();
+    try {
+      // copy text
+      document.execCommand('copy');
+    } catch (err) {
+      alert('Use Ctrl/Cmd+C to copy');
+    }
+  }
+}
+</script>
diff --git a/docs/style.css b/docs/style.css
new file mode 100644
index 00000000..588c789f
--- /dev/null
+++ b/docs/style.css
@@ -0,0 +1,15 @@
+#placeholder {
+    position: absolute;
+    opacity: 0;
+    white-space: pre;
+}
+
+#bibtex {
+    position: absolute;
+    opacity: 0;
+    white-space: pre;
+}
+
+#bibtex-button {
+    color: red;
+}