From 9c725b78e8225d18842d66845b65f81aebebb47c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rapha=C3=ABl=20Flores?= <raphael.flores@inrae.fr>
Date: Fri, 28 Jul 2023 11:12:02 +0200
Subject: [PATCH 1/5] Create codemeta.json file.
---
codemeta.json | 149 ++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 149 insertions(+)
create mode 100644 codemeta.json
diff --git a/codemeta.json b/codemeta.json
new file mode 100644
index 00000000..64526ec4
--- /dev/null
+++ b/codemeta.json
@@ -0,0 +1,149 @@
+{
+ "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
+ "@type": "SoftwareSourceCode",
+ "license": "https://spdx.org/licenses/BSD-3-Clause-Attribution",
+ "codeRepository": "https://forgemia.inra.fr/urgi-is/faidare.git",
+ "contIntegration": "https://forgemia.inra.fr/urgi-is/faidare.git",
+ "dateCreated": "2018-11-12",
+ "downloadUrl": "https://forgemia.inra.fr/urgi-is/faidare/-/archive/master/faidare-master.tar.gz",
+ "issueTracker": "https://forgemia.inra.fr/urgi-is/faidare/-/issues",
+ "name": "FAIDARE",
+ "version": "CURRENT",
+ "description": "FAIDARE: FAIR Data-finder for Agronomic Research\n\nIt provides web services (based on the BrAPI standard) and a web interface with easy to use filters to facilitates the access to plant datasets from a federation of sources.",
+ "developmentStatus": "active",
+ "isPartOf": "https://forgemia.inra.fr/urgi-is/data-discovery",
+ "keywords": [
+ "data federation",
+ "agronomy",
+ "genomics"
+ ],
+ "programmingLanguage": [
+ "Java"
+ ],
+ "runtimePlatform": [
+ "JVM"
+ ],
+ "operatingSystem": [
+ "Linux"
+ ],
+ "relatedLink": [
+ "https://urgi.versailles.inrae.fr/faidare/"
+ ],
+ "author": [
+ {
+ "@type": "Person",
+ "givenName": "Jérémy",
+ "familyName": "Destin",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "INRAE-URGI"
+ }
+ },
+ {
+ "@type": "Person",
+ "givenName": "Guillaume",
+ "familyName": "Cornut",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "INRA-URGI"
+ }
+ },
+ {
+ "@type": "Person",
+ "givenName": "Célia",
+ "familyName": "Michotey",
+ "email": "celia.michotey@inrae.fr",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "INRAE-URGI"
+ }
+ },
+ {
+ "@type": "Person",
+ "givenName": "Jean-Baptiste",
+ "familyName": "Nizet",
+ "email": "jb@ninja-squad.fr",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "Ninja Squad"
+ }
+ },
+ {
+ "@type": "Person",
+ "givenName": "Erik",
+ "familyName": "Kimmel",
+ "email": "erik.kimmel@inrae.fr",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "INRAE-URGI"
+ }
+ },
+ {
+ "@type": "Person",
+ "givenName": "Mélanie",
+ "familyName": "Buy",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "INRA-URGI"
+ }
+ },
+ {
+ "@type": "Person",
+ "givenName": "Raphaël",
+ "familyName": "Flores",
+ "email": "raphael.flores@inrae.fr",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "INRAE-URGI"
+ }
+ },
+ {
+ "@type": "Person",
+ "givenName": "Maud",
+ "familyName": "Marty",
+ "email": "maud.marty@inrae.fr",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "INRAE-URGI"
+ }
+ },
+ {
+ "@type": "Person",
+ "givenName": "Cédric",
+ "familyName": "Exbrayat",
+ "email": "cedric@ninja-squad.fr",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "Ninja Squad"
+ }
+ },
+ {
+ "@type": "Person",
+ "givenName": "Thomas",
+ "familyName": "Letellier",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "INRA-URGI"
+ }
+ },
+ {
+ "@type": "Person",
+ "givenName": "Cyril",
+ "familyName": "Pommier",
+ "email": "cyril.pommier@inrae.fr",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "INRAE-URGI"
+ }
+ },
+ {
+ "@type": "Person",
+ "givenName": "Bilal",
+ "familyName": "El-Houdaigui",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "INRA-URGI"
+ }
+ }
+ ]
+}
\ No newline at end of file
--
GitLab
From c05ed298ef707b54c50d639cf4d17f44531653be Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rapha=C3=ABl=20Flores?= <raphael.flores@inrae.fr>
Date: Fri, 28 Jul 2023 11:13:36 +0200
Subject: [PATCH 2/5] Fix contIntegration
---
codemeta.json | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/codemeta.json b/codemeta.json
index 64526ec4..6efc154d 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -3,7 +3,7 @@
"@type": "SoftwareSourceCode",
"license": "https://spdx.org/licenses/BSD-3-Clause-Attribution",
"codeRepository": "https://forgemia.inra.fr/urgi-is/faidare.git",
- "contIntegration": "https://forgemia.inra.fr/urgi-is/faidare.git",
+ "contIntegration": "https://forgemia.inra.fr/urgi-is/data-discovery/-/pipelines",
"dateCreated": "2018-11-12",
"downloadUrl": "https://forgemia.inra.fr/urgi-is/faidare/-/archive/master/faidare-master.tar.gz",
"issueTracker": "https://forgemia.inra.fr/urgi-is/faidare/-/issues",
--
GitLab
From d85dded85422efc86aabdb0d838f1cdd886a57d2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rapha=C3=ABl=20Flores?= <raphael.flores@inrae.fr>
Date: Tue, 10 Sep 2024 10:11:58 +0200
Subject: [PATCH 3/5] Add Najwa in contributors
---
codemeta.json | 11 ++++++++++-
1 file changed, 10 insertions(+), 1 deletion(-)
diff --git a/codemeta.json b/codemeta.json
index 6efc154d..73dbec1d 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -144,6 +144,15 @@
"@type": "Organization",
"name": "INRA-URGI"
}
+ },
+ {
+ "@type": "Person",
+ "givenName": "Najwa",
+ "familyName": "Lakmouri",
+ "affiliation": {
+ "@type": "Organization",
+ "name": "INRA-URGI"
+ }
}
]
-}
\ No newline at end of file
+}
--
GitLab
From 0ec9054b1b00f2470dce8e873b094d5bd0481e2a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rapha=C3=ABl=20Flores?= <raphael.flores@inrae.fr>
Date: Tue, 10 Sep 2024 10:23:27 +0200
Subject: [PATCH 4/5] Update to codemeta v3.
---
codemeta.json | 318 ++++++++++++++++++++++++++------------------------
1 file changed, 163 insertions(+), 155 deletions(-)
diff --git a/codemeta.json b/codemeta.json
index 73dbec1d..1109400c 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -1,158 +1,166 @@
{
- "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
- "@type": "SoftwareSourceCode",
- "license": "https://spdx.org/licenses/BSD-3-Clause-Attribution",
- "codeRepository": "https://forgemia.inra.fr/urgi-is/faidare.git",
- "contIntegration": "https://forgemia.inra.fr/urgi-is/data-discovery/-/pipelines",
- "dateCreated": "2018-11-12",
- "downloadUrl": "https://forgemia.inra.fr/urgi-is/faidare/-/archive/master/faidare-master.tar.gz",
- "issueTracker": "https://forgemia.inra.fr/urgi-is/faidare/-/issues",
- "name": "FAIDARE",
- "version": "CURRENT",
- "description": "FAIDARE: FAIR Data-finder for Agronomic Research\n\nIt provides web services (based on the BrAPI standard) and a web interface with easy to use filters to facilitates the access to plant datasets from a federation of sources.",
- "developmentStatus": "active",
- "isPartOf": "https://forgemia.inra.fr/urgi-is/data-discovery",
- "keywords": [
- "data federation",
- "agronomy",
- "genomics"
- ],
- "programmingLanguage": [
- "Java"
- ],
- "runtimePlatform": [
- "JVM"
- ],
- "operatingSystem": [
- "Linux"
- ],
- "relatedLink": [
- "https://urgi.versailles.inrae.fr/faidare/"
- ],
- "author": [
- {
- "@type": "Person",
- "givenName": "Jérémy",
- "familyName": "Destin",
- "affiliation": {
- "@type": "Organization",
- "name": "INRAE-URGI"
- }
- },
- {
- "@type": "Person",
- "givenName": "Guillaume",
- "familyName": "Cornut",
- "affiliation": {
- "@type": "Organization",
- "name": "INRA-URGI"
- }
- },
- {
- "@type": "Person",
- "givenName": "Célia",
- "familyName": "Michotey",
- "email": "celia.michotey@inrae.fr",
- "affiliation": {
- "@type": "Organization",
- "name": "INRAE-URGI"
- }
- },
- {
- "@type": "Person",
- "givenName": "Jean-Baptiste",
- "familyName": "Nizet",
- "email": "jb@ninja-squad.fr",
- "affiliation": {
- "@type": "Organization",
- "name": "Ninja Squad"
- }
- },
- {
- "@type": "Person",
- "givenName": "Erik",
- "familyName": "Kimmel",
- "email": "erik.kimmel@inrae.fr",
- "affiliation": {
- "@type": "Organization",
- "name": "INRAE-URGI"
- }
- },
- {
- "@type": "Person",
- "givenName": "Mélanie",
- "familyName": "Buy",
- "affiliation": {
- "@type": "Organization",
- "name": "INRA-URGI"
- }
- },
- {
- "@type": "Person",
- "givenName": "Raphaël",
- "familyName": "Flores",
- "email": "raphael.flores@inrae.fr",
- "affiliation": {
- "@type": "Organization",
- "name": "INRAE-URGI"
- }
- },
- {
- "@type": "Person",
- "givenName": "Maud",
- "familyName": "Marty",
- "email": "maud.marty@inrae.fr",
- "affiliation": {
- "@type": "Organization",
- "name": "INRAE-URGI"
- }
- },
- {
- "@type": "Person",
- "givenName": "Cédric",
- "familyName": "Exbrayat",
- "email": "cedric@ninja-squad.fr",
- "affiliation": {
- "@type": "Organization",
- "name": "Ninja Squad"
- }
- },
- {
- "@type": "Person",
- "givenName": "Thomas",
- "familyName": "Letellier",
- "affiliation": {
- "@type": "Organization",
- "name": "INRA-URGI"
- }
- },
- {
- "@type": "Person",
- "givenName": "Cyril",
- "familyName": "Pommier",
- "email": "cyril.pommier@inrae.fr",
- "affiliation": {
- "@type": "Organization",
- "name": "INRAE-URGI"
- }
- },
- {
- "@type": "Person",
- "givenName": "Bilal",
- "familyName": "El-Houdaigui",
- "affiliation": {
- "@type": "Organization",
- "name": "INRA-URGI"
- }
+ "@context": "https://w3id.org/codemeta/3.0",
+ "type": "SoftwareSourceCode",
+ "author": [
+ {
+ "id": "_:author_1",
+ "type": "Person",
+ "affiliation": {
+ "type": "Organization",
+ "name": "INRAE-URGI"
},
- {
- "@type": "Person",
- "givenName": "Najwa",
- "familyName": "Lakmouri",
- "affiliation": {
- "@type": "Organization",
- "name": "INRA-URGI"
- }
- }
- ]
+ "familyName": "Destin",
+ "givenName": "Jérémy"
+ },
+ {
+ "id": "_:author_2",
+ "type": "Person",
+ "affiliation": {
+ "type": "Organization",
+ "name": "INRA-URGI"
+ },
+ "familyName": "Cornut",
+ "givenName": "Guillaume"
+ },
+ {
+ "id": "_:author_3",
+ "type": "Person",
+ "affiliation": {
+ "type": "Organization",
+ "name": "INRAE-URGI"
+ },
+ "email": "celia.michotey@inrae.fr",
+ "familyName": "Michotey",
+ "givenName": "Célia"
+ },
+ {
+ "id": "_:author_4",
+ "type": "Person",
+ "affiliation": {
+ "type": "Organization",
+ "name": "Ninja Squad"
+ },
+ "email": "jb@ninja-squad.fr",
+ "familyName": "Nizet",
+ "givenName": "Jean-Baptiste"
+ },
+ {
+ "id": "_:author_5",
+ "type": "Person",
+ "affiliation": {
+ "type": "Organization",
+ "name": "INRAE-URGI"
+ },
+ "email": "erik.kimmel@inrae.fr",
+ "familyName": "Kimmel",
+ "givenName": "Erik"
+ },
+ {
+ "id": "_:author_6",
+ "type": "Person",
+ "affiliation": {
+ "type": "Organization",
+ "name": "INRA-URGI"
+ },
+ "familyName": "Buy",
+ "givenName": "Mélanie"
+ },
+ {
+ "id": "_:author_7",
+ "type": "Person",
+ "affiliation": {
+ "type": "Organization",
+ "name": "INRAE-URGI"
+ },
+ "email": "raphael.flores@inrae.fr",
+ "familyName": "Flores",
+ "givenName": "Raphaël"
+ },
+ {
+ "id": "_:author_8",
+ "type": "Person",
+ "affiliation": {
+ "type": "Organization",
+ "name": "INRAE-URGI"
+ },
+ "email": "maud.marty@inrae.fr",
+ "familyName": "Marty",
+ "givenName": "Maud"
+ },
+ {
+ "id": "_:author_9",
+ "type": "Person",
+ "affiliation": {
+ "type": "Organization",
+ "name": "Ninja Squad"
+ },
+ "email": "cedric@ninja-squad.fr",
+ "familyName": "Exbrayat",
+ "givenName": "Cédric"
+ },
+ {
+ "id": "_:author_10",
+ "type": "Person",
+ "affiliation": {
+ "type": "Organization",
+ "name": "INRA-URGI"
+ },
+ "familyName": "Letellier",
+ "givenName": "Thomas"
+ },
+ {
+ "id": "_:author_11",
+ "type": "Person",
+ "affiliation": {
+ "type": "Organization",
+ "name": "INRAE-URGI"
+ },
+ "email": "cyril.pommier@inrae.fr",
+ "familyName": "Pommier",
+ "givenName": "Cyril"
+ },
+ {
+ "id": "_:author_12",
+ "type": "Person",
+ "affiliation": {
+ "type": "Organization",
+ "name": "INRA-URGI"
+ },
+ "familyName": "El-Houdaigui",
+ "givenName": "Bilal"
+ },
+ {
+ "id": "_:author_13",
+ "type": "Person",
+ "affiliation": {
+ "type": "Organization",
+ "name": "INRA-URGI"
+ },
+ "familyName": "Lakmouri",
+ "givenName": "Najwa"
+ }
+ ],
+ "codeRepository": "https://forgemia.inra.fr/urgi-is/faidare.git",
+ "dateCreated": "2018-11-12",
+ "description": "FAIDARE: FAIR Data-finder for Agronomic Research\n\nIt provides web services (based on the BrAPI standard) and a web interface with easy to use filters to facilitates the access to plant datasets from a federation of sources.",
+ "downloadUrl": "https://forgemia.inra.fr/urgi-is/faidare/-/archive/master/faidare-master.tar.gz",
+ "isPartOf": "https://forgemia.inra.fr/urgi-is/data-discovery",
+ "keywords": [
+ "data federation",
+ "agronomy",
+ "genomics"
+ ],
+ "license": "https://spdx.org/licenses/BSD-3-Clause-Attribution",
+ "name": "FAIDARE",
+ "operatingSystem": "Linux",
+ "programmingLanguage": "Java",
+ "relatedLink": "https://urgi.versailles.inrae.fr/faidare/",
+ "runtimePlatform": "JVM",
+ "version": "CURRENT",
+ "codemeta:contIntegration": {
+ "id": "https://forgemia.inra.fr/urgi-is/faidare/-/pipelines?page=1&scope=all&ref=master"
+ },
+ "continuousIntegration": "https://forgemia.inra.fr/urgi-is/faidare/-/pipelines?page=1&scope=all&ref=master",
+ "developmentStatus": "active",
+ "issueTracker": "https://forgemia.inra.fr/urgi-is/faidare/-/issues"
}
--
GitLab
From 3bbd61a8831d454f0911299a4f8b4cdbfa069956 Mon Sep 17 00:00:00 2001
From: Cyril Pommier <cyril.pommier@inra.fr>
Date: Wed, 11 Sep 2024 10:13:42 +0200
Subject: [PATCH 5/5] Add hal citation and authors positions
---
codemeta.json | 40 +++++++++++++++++++++++++++-------------
1 file changed, 27 insertions(+), 13 deletions(-)
diff --git a/codemeta.json b/codemeta.json
index 1109400c..24adb29e 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -10,7 +10,8 @@
"name": "INRAE-URGI"
},
"familyName": "Destin",
- "givenName": "Jérémy"
+ "givenName": "Jérémy",
+ "position": 7
},
{
"id": "_:author_2",
@@ -20,7 +21,8 @@
"name": "INRA-URGI"
},
"familyName": "Cornut",
- "givenName": "Guillaume"
+ "givenName": "Guillaume",
+ "position": 6
},
{
"id": "_:author_3",
@@ -31,7 +33,8 @@
},
"email": "celia.michotey@inrae.fr",
"familyName": "Michotey",
- "givenName": "Célia"
+ "givenName": "Célia",
+ "position": 2
},
{
"id": "_:author_4",
@@ -42,7 +45,8 @@
},
"email": "jb@ninja-squad.fr",
"familyName": "Nizet",
- "givenName": "Jean-Baptiste"
+ "givenName": "Jean-Baptiste",
+ "position": 5
},
{
"id": "_:author_5",
@@ -53,7 +57,8 @@
},
"email": "erik.kimmel@inrae.fr",
"familyName": "Kimmel",
- "givenName": "Erik"
+ "givenName": "Erik",
+ "position": 11
},
{
"id": "_:author_6",
@@ -63,7 +68,8 @@
"name": "INRA-URGI"
},
"familyName": "Buy",
- "givenName": "Mélanie"
+ "givenName": "Mélanie",
+ "position": 13
},
{
"id": "_:author_7",
@@ -74,7 +80,8 @@
},
"email": "raphael.flores@inrae.fr",
"familyName": "Flores",
- "givenName": "Raphaël"
+ "givenName": "Raphaël",
+ "position": 3
},
{
"id": "_:author_8",
@@ -85,7 +92,8 @@
},
"email": "maud.marty@inrae.fr",
"familyName": "Marty",
- "givenName": "Maud"
+ "givenName": "Maud",
+ "position": 9
},
{
"id": "_:author_9",
@@ -96,7 +104,8 @@
},
"email": "cedric@ninja-squad.fr",
"familyName": "Exbrayat",
- "givenName": "Cédric"
+ "givenName": "Cédric",
+ "position": 4
},
{
"id": "_:author_10",
@@ -106,7 +115,8 @@
"name": "INRA-URGI"
},
"familyName": "Letellier",
- "givenName": "Thomas"
+ "givenName": "Thomas",
+ "position": 10
},
{
"id": "_:author_11",
@@ -117,7 +127,8 @@
},
"email": "cyril.pommier@inrae.fr",
"familyName": "Pommier",
- "givenName": "Cyril"
+ "givenName": "Cyril",
+ "position": 1
},
{
"id": "_:author_12",
@@ -127,7 +138,8 @@
"name": "INRA-URGI"
},
"familyName": "El-Houdaigui",
- "givenName": "Bilal"
+ "givenName": "Bilal",
+ "position": 8
},
{
"id": "_:author_13",
@@ -137,9 +149,11 @@
"name": "INRA-URGI"
},
"familyName": "Lakmouri",
- "givenName": "Najwa"
+ "givenName": "Najwa",
+ "position": 12
}
],
+ "citation": "https://hal.inrae.fr/hal-04638310",
"codeRepository": "https://forgemia.inra.fr/urgi-is/faidare.git",
"dateCreated": "2018-11-12",
"description": "FAIDARE: FAIR Data-finder for Agronomic Research\n\nIt provides web services (based on the BrAPI standard) and a web interface with easy to use filters to facilitates the access to plant datasets from a federation of sources.",
--
GitLab