Merge branch 'main' of https://github.com/IPK-BIT/miappe-wizard

IPK-BIT · Feb 22, 2024 · aff2113 · aff2113
2 parents 9aa6163 + f9f172f
commit aff2113
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Showing 10 changed files with 310 additions and 89 deletions.
diff --git a/config/breedfides/wizard.config.js b/config/breedfides/wizard.config.js
@@ -16,6 +16,17 @@ window.config = {
                 address : 'Corrensstraße 3, 06646 Seeland',
                 affiliation : 'IPK Gatersleben'
             }
+        },
+        {
+            type: 'comment',
+            isaMapping: {
+                entity: 'investigation',
+                attribute: 'comments'
+            },
+            values: {
+                name: 'Study Country',
+                value: 'Germany'
+            }
         }
     ],
 
@@ -62,8 +73,8 @@ window.config = {
                     { "label":"Light intensity", "explanation":"Intensity of total light" },
                     { "label":"Range in peak light intensity", "explanation":"Range in peak light intensity for the whole experiment." },
                     { "label":"Fraction of outside light intercepted by growth facility components and surrounding structures", "explanation":"Fraction of outside light intercepted by growth facility components and surrounding structures." },
-                    { "label":"Type of lamps used", "explanation":"Nature of the light source for controlled environments. XEO: 00137" },
-                    { "label":"R/FR ratio", "explanation":"Red light to far red light ratio. XEO:00036" },
+                    { "label":"Type of lamps used", "explanation":"Nature of the light source for controlled environments. XEO: 00137" }
+/*                    { "label":"R/FR ratio", "explanation":"Red light to far red light ratio. XEO:00036" },
                     { "label":"Daily UV-A radiation", "explanation":"Intensity of UVA radiation (320-400 nm); XEO:00037" },
                     { "label":"Daily UV-B radiation", "explanation":"Intensity of UVB radiation (290-320 nm); XEO:00038" },
                     { "label":"Total daily irradiance", "explanation":"Intensity of total light (XEO:00034) averaged over the experiment." },
@@ -98,7 +109,7 @@ window.config = {
                     { "label":"Matrix potential", "explanation":"Range in water potential for soil." },
                     { "label":"Watering regimen", "explanation":"The treatment involving an exposure to watering frequencies." },
                     { "label":"Composition of nutrient solutions used for irrigation", "explanation":"For all nutrients, including micronutrients, the ontology term with concentration." },
-                    { "label":"Electrical conductivity", "explanation":"A conductivity quality inhering in a bearer by virtue of the bearer's ability to convey electricity." }
+                    { "label":"Electrical conductivity", "explanation":"A conductivity quality inhering in a bearer by virtue of the bearer's ability to convey electricity." } */
                 ]
             },
             {

diff --git a/config/breedfides/wizard.steps.config.js b/config/breedfides/wizard.steps.config.js
@@ -1,6 +1,6 @@
 window.steps = [
     {
-        title: 'Please provide the Title and Description of your Plant Phenotyping Project and when you submitted and published the Dataset.',
+        title: 'Please provide a Title and Description of your Dataset and which Institution or Organisation is responsible for.',
         fields: [
             {
                 label: 'Project Title',
@@ -21,50 +21,39 @@ window.steps = [
                 explanation: 'DM-4'
             },
             {
-                label: 'Submission Date',
-                type: 'date',
+                label: 'Institution',
+                type: 'text',
                 isaMapping: {
                     entity: 'investigation',
-                    attribute: 'submissionDate'
+                    attribute: 'comments',
+                    commentName: 'Study Contact Institution'
                 },
-                explanation: 'DM-5'
+                explanation: 'DM-16'
             },
             {
-                label: 'Public Release Date',
-                type: 'date',
-                isaMapping: {
-                    entity: 'investigation',
-                    attribute: 'publicReleaseDate'
-                },
-                explanation: 'DM-6'
-            }
-        ]
-    },
-   /* {
-        title: 'What is the submission date of your plant phenotyping project?',
-        fields: [
-            {
-                label: 'Submission Date',
-                type: 'date',
+                label: 'Institution Address',
+                type: 'text',
                 isaMapping: {
                     entity: 'investigation',
-                    attribute: 'submissionDate'
+                    attribute: 'comments',
+                    commentName: 'Study Contact Institution'
                 },
-                explanation: 'DM-5'
+                explanation: 'DM-16'
             },
             {
-                label: 'Public Release Date',
-                type: 'date',
+                label: 'Country (PREFILL)',
+                type: 'text',
                 isaMapping: {
                     entity: 'investigation',
-                    attribute: 'publicReleaseDate'
+                    attribute: 'comments',
+                    commentName: 'Study Country'
                 },
-                explanation: 'DM-6'
+                explanation: 'DM-17'
             }
         ]
-    },*/
+    },
     {
-        title: 'Please provide the Authors of your Dataset and define their Contribution.',
+        title: 'Please provide all Authors of your Dataset and define their Contribution.',
         fields: [
             {
                // label: 'Project title',
@@ -78,36 +67,11 @@ window.steps = [
                     showComments: false
                 }
             }
-        ]
-    },
-    {
-        title: 'Please provide the responsible Institute for the whole Plant Phenotyping Project.',
-        fields: [
-            {
-                label: 'Contact address',
-                type: 'text',
-                isaMapping: {
-                    entity: 'investigation',
-                    attribute: 'comments',
-                    commentName: 'Study Contact Institution'
-                },
-                explanation: 'DM-16'
-            },
-            {
-                label: 'Country',
-                type: 'text',
-                isaMapping: {
-                    entity: 'investigation',
-                    attribute: 'comments',
-                    commentName: 'Study Country'
-                },
-                explanation: 'DM-17'
-            }
         ],
         hook: 'addStudy'
     },
     {
-        title: 'Please provide is the Title of your Experiment and the responsible Institution',
+        title: 'Please provide the Title and Location of your Study',
         fields: [
             {
                 label: 'Study title',
@@ -119,53 +83,48 @@ window.steps = [
                 }
             },
             {
-                label: 'Contact address',
+                label: 'Location',
                 type: 'text',
                 isaMapping: {
                     entity: 'study',
                     attribute: 'comments',
-                    commentName: 'Study Contact Institution'
+                    commentName: 'Study Experimental Site'
                 },
-                explanation: 'DM-16'
+                explanation: 'DM-18'
             },
             {
-                label: 'Country',
+                label: 'Location Latitude',
                 type: 'text',
                 isaMapping: {
                     entity: 'study',
                     attribute: 'comments',
-                    commentName: 'Study Country'
+                    commentName: 'Study Latitude'
                 },
-                explanation: 'DM-17'
-            }
-        ]
-    },
-  /*  {
-        title: 'Please provide contact address of your institute.',
-        fields: [
+                explanation: 'DM-19'
+            },
             {
-                label: 'Contact address',
+                label: 'Location Longitude',
                 type: 'text',
-                explanation: 'DM-16',
                 isaMapping: {
                     entity: 'study',
                     attribute: 'comments',
-                    commentName: 'Study Contact Institution'
-                }
+                    commentName: 'Study Longitude'
+                },
+                explanation: 'DM-20'
             },
             {
                 label: 'Country',
                 type: 'text',
-                explanation: 'DM-17',
                 isaMapping: {
                     entity: 'study',
                     attribute: 'comments',
                     commentName: 'Study Country'
-                }
+                },
+                explanation: 'DM-17'
             }
         ]
-    },*/
-    {
+    },
+ /*   {
         title: 'Please provide a link to the data file of the study.',
         fields: [
             {
@@ -194,9 +153,16 @@ window.steps = [
             protocolDescription: 'How the plants were grown up.',
             protocolParameters: ['Light intensity', 'Air temperature']
         }
-    },
+    },*/
     {
         title: 'Please provide a brief summary of the Growth Conditions.',
+        hook: 'addProtocol',
+        hookParameters: {
+            protocolName: 'Growth',
+            protocolVersion: 'MIAPPE v1.1',
+            protocolDescription: 'How the plants were grown up.',
+            protocolParameters: ['Light intensity', 'Air temperature']
+        },
         fields: [
             {
                 label: 'Growth description',

diff --git a/config/miappe/wizard.config.js b/config/miappe/wizard.config.js
@@ -16,6 +16,46 @@ window.config = {
                 address : 'Corrensstraße 3, 06646 Seeland',
                 affiliation : 'IPK Gatersleben'
             }
+        },
+        {
+            type: 'comment',
+            isaMapping: {
+                entity: 'investigation',
+                attribute: 'comments'
+            },
+            values: {
+                name: 'Study Country',
+                value: 'Germany'
+            }
+        },
+        {
+            type: 'comment',
+            isaMapping: {
+                entity: 'study',
+                attribute: 'comments',
+                studyIndex: 0
+            },
+            values: {
+                name: 'Study Country',
+                value: 'Germany'
+            }
+        },
+        {
+            type: 'value',
+            isaMapping: {
+                entity: 'investigation',
+                attribute: 'title'
+            },
+            value: 'Prefilled investigation title ...'
+        },
+        {
+            type: 'value',
+            isaMapping: {
+                entity: 'study',
+                attribute: 'description',
+                studyIndex: 0
+            },
+            value: 'Prefilled study description ...'
         }
     ],
 

diff --git a/config/miappe/wizard.steps.config.js b/config/miappe/wizard.steps.config.js
@@ -137,6 +137,15 @@ window.steps = [
                     commentName: 'Study Country'
                 },
                 explanation: 'DM-17'
+            },
+            {
+                label: 'ROR ID of your institute',
+                type: 'ror',
+                isaMapping: {
+                    entity: 'study',
+                    attribute: 'comments',
+                    commentName: 'Study Contact Institution ROR'
+                }
             }
         ]
     },

diff --git a/src/components/isa/generic/PersonOrcid.svelte b/src/components/isa/generic/PersonOrcid.svelte
@@ -117,11 +117,12 @@ onMount(() => {
         padding: 0;
         margin: 0;
         font-size: 100%;
-        color: darkslateblue;
+        color: black;
+        font-weight: 500;
     }
     section {
         margin-top: 10px;
-        border: 1px solid rgb(200,200,200);
+        border: 1px solid rgb(0,0,0);
         /*background: rgb(235,235,235);*/
         padding: 10px;
     }

diff --git a/src/components/isa/generic/PersonRoles.svelte b/src/components/isa/generic/PersonRoles.svelte
@@ -101,11 +101,12 @@ h5 {
     padding: 0;
     margin: 0;
     font-size: 100%;
-    color: darkslateblue;
+    color: black;
+    font-weight: 500;
 }
 section {
     margin-top: 10px;
-    border: 1px solid rgb(200,200,200);
+    border: 1px solid rgb(0,0,0);
     /*background: rgb(235,235,235);*/
     padding: 10px;
 }
@@ -146,7 +147,7 @@ div.role label {
 
 div.role input {
     position: absolute;
-    top: 0px;
+    top: 2px;
     left: 7px;
 }