From 5f408e63343fbf02fb0337b536b7600d39acf2a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ren=C3=A9=20H=C3=A4nsel?= Date: Tue, 23 Jan 2024 16:19:05 +0100 Subject: [PATCH 1/2] cleanup --- docs/_config.yml | 68 ------------------------------------------------ 1 file changed, 68 deletions(-) delete mode 100644 docs/_config.yml diff --git a/docs/_config.yml b/docs/_config.yml deleted file mode 100644 index c143739902..0000000000 --- a/docs/_config.yml +++ /dev/null @@ -1,68 +0,0 @@ -remote_theme: zendesk/jekyll-theme-zendesk-garden@main - -plugins: -- jekyll-remote-theme # add this line to the plugins list if you already have one - - -title: Local Data Hub Documentation -permalink: pretty - -search_enabled: true -auto_page_title: true - -mermaid_enabled: true -mermaid_theme: forest - -sidebar: - - label: User Guide - children: - - label: User - children: - - Registrierung in SEEK - - Profil bearbeiten - - label: LDH - children: - - Projekt beitreten - - Projekt erstellen - - label: ISA Struktur erstellen - children: - - Investigation erstellen - - Studie erstellen - - Erstellen eines Assays - - Erstellen einer Modellierungsanalyse - - ISA Übersicht - - Publikation hinzufügen - - Investigation, Studie oder assay zitierfähig machen - - Spezielle Benutzerrollen - - Projekt Dashboard - - label: ISA Nutzung für NFDI4Health - children: - - ISA Best Practice - - label: Admin Guide - children: - - label: Einrichten - children: - - LDH Einrichtung mittels Docker Skript - - LDH als Entwicklungssystem - - LDH in einer Produktivumgebung - - Verwendung in Docker - - Solr einrichten - - label: Verwalten - children: - - Admin panel - - -highlighter: rouge -markdown: kramdown -kramdown: - input: GFM - auto_ids: true - hard_wrap: false - syntax_highlighter: rouge - -defaults: - - scope: - path: '' - type: 'pages' - values: - layout: default From 711b6e7314a13027b8504d2f45eafde9d888e908 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ren=C3=A9=20H=C3=A4nsel?= Date: Wed, 24 Jan 2024 17:52:36 +0100 Subject: [PATCH 2/2] updating sample attribute type for Design centers --- db/seeds/018_MDS_3_3_Project_gen.seeds.rb | 2 +- db/seeds/019_MDS_3_3_Study_gen.seeds.rb | 2 +- db/seeds/020_MDS_3_3_Investigation_gen.seeds.rb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/db/seeds/018_MDS_3_3_Project_gen.seeds.rb b/db/seeds/018_MDS_3_3_Project_gen.seeds.rb index cbdf67cde5..792e372f53 100644 --- a/db/seeds/018_MDS_3_3_Project_gen.seeds.rb +++ b/db/seeds/018_MDS_3_3_Project_gen.seeds.rb @@ -445,7 +445,7 @@ def create_sample_controlled_vocab_terms_attributes(array) emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_groupsOfDiseases_Project', sample_attribute_type: SampleAttributeType.where(title:'Linked Extended Metadata').first , linked_extended_metadata_type: ExtendedMetadataType.where(title:'Design_groupsOfDiseases_Project', supported_type:'ExtendedMetadata').first, label: 'Groups of diseases or conditions(*)' ) emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_mortalityData_Project', sample_attribute_type: @cv_type, sample_controlled_vocab:Design_mortalityData_Project_cv, description:'Indication whether mortality data are collected in the Project.', label:'Collects mortality data?') emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_administrativeInformation_Project', sample_attribute_type: SampleAttributeType.where(title:'Linked Extended Metadata').first , linked_extended_metadata_type: ExtendedMetadataType.where(title:'Design_administrativeInformation_Project', supported_type:'ExtendedMetadata').first, label: 'Administrative information about the Project' ) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_centers_Project', sample_attribute_type: @cv_list_type, sample_controlled_vocab:Design_centers_Project_cv, description:'Specification whether the Project is conducted at only one or at more than one Project center.', label:'Mono- or multicentric?') + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_centers_Project', sample_attribute_type: @cv_type, sample_controlled_vocab:Design_centers_Project_cv, description:'Specification whether the Project is conducted at only one or at more than one Project center.', label:'Mono- or multicentric?') emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_centersNumber_Project', sample_attribute_type: @int_type, sample_controlled_vocab: nil, description: 'Number of centers involved in the Project.', label: 'Number of centers') emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_dataProviders_Project', sample_attribute_type: @cv_type, sample_controlled_vocab:Design_dataProviders_Project_cv, description:'Specification whether the Project involves only one or more than one data provider.', label:'One or more data providers?') emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_dataProvidersNumber_Project', sample_attribute_type: @int_type, sample_controlled_vocab: nil, description: 'Number of data providers involved in the Project.', label: 'Number of data providers') diff --git a/db/seeds/019_MDS_3_3_Study_gen.seeds.rb b/db/seeds/019_MDS_3_3_Study_gen.seeds.rb index de663b56d1..0d1d4b876f 100644 --- a/db/seeds/019_MDS_3_3_Study_gen.seeds.rb +++ b/db/seeds/019_MDS_3_3_Study_gen.seeds.rb @@ -445,7 +445,7 @@ def create_sample_controlled_vocab_terms_attributes(array) emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_groupsOfDiseases_Study', sample_attribute_type: SampleAttributeType.where(title:'Linked Extended Metadata').first , linked_extended_metadata_type: ExtendedMetadataType.where(title:'Design_groupsOfDiseases_Study', supported_type:'ExtendedMetadata').first, label: 'Groups of diseases or conditions(*)' ) emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_mortalityData_Study', sample_attribute_type: @cv_type, sample_controlled_vocab:Design_mortalityData_Study_cv, description:'Indication whether mortality data are collected in the Study.', label:'Collects mortality data?') emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_administrativeInformation_Study', sample_attribute_type: SampleAttributeType.where(title:'Linked Extended Metadata').first , linked_extended_metadata_type: ExtendedMetadataType.where(title:'Design_administrativeInformation_Study', supported_type:'ExtendedMetadata').first, label: 'Administrative information about the Study' ) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_centers_Study', sample_attribute_type: @cv_list_type, sample_controlled_vocab:Design_centers_Study_cv, description:'Specification whether the Study is conducted at only one or at more than one Study center.', label:'Mono- or multicentric?') + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_centers_Study', sample_attribute_type: @cv_type, sample_controlled_vocab:Design_centers_Study_cv, description:'Specification whether the Study is conducted at only one or at more than one Study center.', label:'Mono- or multicentric?') emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_centersNumber_Study', sample_attribute_type: @int_type, sample_controlled_vocab: nil, description: 'Number of centers involved in the Study.', label: 'Number of centers') emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_dataProviders_Study', sample_attribute_type: @cv_type, sample_controlled_vocab:Design_dataProviders_Study_cv, description:'Specification whether the Study involves only one or more than one data provider.', label:'One or more data providers?') emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_dataProvidersNumber_Study', sample_attribute_type: @int_type, sample_controlled_vocab: nil, description: 'Number of data providers involved in the Study.', label: 'Number of data providers') diff --git a/db/seeds/020_MDS_3_3_Investigation_gen.seeds.rb b/db/seeds/020_MDS_3_3_Investigation_gen.seeds.rb index 6d07172904..53505655c2 100644 --- a/db/seeds/020_MDS_3_3_Investigation_gen.seeds.rb +++ b/db/seeds/020_MDS_3_3_Investigation_gen.seeds.rb @@ -445,7 +445,7 @@ def create_sample_controlled_vocab_terms_attributes(array) emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_groupsOfDiseases_Investigation', sample_attribute_type: SampleAttributeType.where(title:'Linked Extended Metadata').first , linked_extended_metadata_type: ExtendedMetadataType.where(title:'Design_groupsOfDiseases_Investigation', supported_type:'ExtendedMetadata').first, label: 'Groups of diseases or conditions(*)' ) emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_mortalityData_Investigation', sample_attribute_type: @cv_type, sample_controlled_vocab:Design_mortalityData_Investigation_cv, description:'Indication whether mortality data are collected in the Investigation.', label:'Collects mortality data?') emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_administrativeInformation_Investigation', sample_attribute_type: SampleAttributeType.where(title:'Linked Extended Metadata').first , linked_extended_metadata_type: ExtendedMetadataType.where(title:'Design_administrativeInformation_Investigation', supported_type:'ExtendedMetadata').first, label: 'Administrative information about the Investigation' ) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_centers_Investigation', sample_attribute_type: @cv_list_type, sample_controlled_vocab:Design_centers_Investigation_cv, description:'Specification whether the Investigation is conducted at only one or at more than one Investigation center.', label:'Mono- or multicentric?') + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_centers_Investigation', sample_attribute_type: @cv_type, sample_controlled_vocab:Design_centers_Investigation_cv, description:'Specification whether the Investigation is conducted at only one or at more than one Investigation center.', label:'Mono- or multicentric?') emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_centersNumber_Investigation', sample_attribute_type: @int_type, sample_controlled_vocab: nil, description: 'Number of centers involved in the Investigation.', label: 'Number of centers') emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_dataProviders_Investigation', sample_attribute_type: @cv_type, sample_controlled_vocab:Design_dataProviders_Investigation_cv, description:'Specification whether the Investigation involves only one or more than one data provider.', label:'One or more data providers?') emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Design_dataProvidersNumber_Investigation', sample_attribute_type: @int_type, sample_controlled_vocab: nil, description: 'Number of data providers involved in the Investigation.', label: 'Number of data providers')