From 8c2ba20fa91e726c26fc374f48aa6998a9fcdbbf Mon Sep 17 00:00:00 2001 From: jmillanacosta Date: Fri, 15 Sep 2023 17:20:21 +0200 Subject: [PATCH 01/18] Major rearrangement, from labels to data --- .../workflows/placeholder_create_erm_datasets | 0 .../placeholder_create_erm_literature | 0 Gemfile | 1 + Gemfile.lock | 2 + _config.yml | 10 + _data/erm/ERM00000063.yml | 10 + _data/erm/ERM00000064.yml | 9 + .../erm/ERM00000397.yml | 6 +- .../erm/ERM00000400.yml | 7 +- .../erm/ERM00000403.yml | 7 +- .../erm/ERM00000409.yml | 7 +- _data/erm/ERM00000416.yml | 8 + .../erm/ERM00000421.yml | 7 +- .../erm/ERM00000424.yml | 7 +- .../erm/ERM00000442.yml | 6 +- .../erm/ERM00000445.yml | 7 +- _data/erm/ERM00000582.yml | 7 + _data/erm/ERM00000583.yml | 6 + _data/erm/ERM00000584.yml | 8 + _data/work/10.1186/S13321-022-00614-7.yml | 5 + _data/work/10.3389/FTOX.2022.981701.yml | 5 + _data/work/10.5281/ZENODO.7940162.yml | 5 + _data/work/10.5281/ZENODO.7965603.yml | 5 + _data/work/10.5281/ZENODO.7966134.yml | 5 + _data/work/10.5281/ZENODO.7989699.yml | 5 + _data/work/10.5281/ZENODO.7990086.yml | 5 + _data/work/10.5281/ZENODO.7990214.yml | 5 + _data/work/10.5281/ZENODO.7990251.yml | 5 + _data/work/10.5281/ZENODO.7990302.yml | 5 + _data/work/10.5281/ZENODO.8015080.yml | 5 + _includes/collecttags.html | 19 - _includes/head.html | 5 - _includes/header.html | 1 + _layouts/ontoclass.html | 93 + _layouts/substance.html | 46 +- identifier.markdown | 19 +- log | 67965 ++++++++++++++++ ontology.markdown | 17 + substance/ERM00000063.markdown | 12 - substance/ERM00000064.markdown | 12 - substance/ERM00000416.markdown | 11 - substance/ERM00000582.markdown | 8 - substance/ERM00000583.markdown | 11 - substance/ERM00000584.markdown | 12 - work/10.1186/S13321-022-00614-7.markdown | 7 - work/10.3389/FTOX.2022.981701.markdown | 7 - work/10.5281/ZENODO.7940162.markdown | 7 - work/10.5281/ZENODO.7965603.markdown | 7 - work/10.5281/ZENODO.7966134.markdown | 7 - work/10.5281/ZENODO.7989699.markdown | 7 - work/10.5281/ZENODO.7990086.markdown | 7 - work/10.5281/ZENODO.7990214.markdown | 7 - work/10.5281/ZENODO.7990251.markdown | 7 - work/10.5281/ZENODO.7990302.markdown | 7 - work/10.5281/ZENODO.8015080.markdown | 7 - 55 files changed, 68252 insertions(+), 226 deletions(-) create mode 100644 .github/workflows/placeholder_create_erm_datasets create mode 100644 .github/workflows/placeholder_create_erm_literature create mode 100644 _data/erm/ERM00000063.yml create mode 100644 _data/erm/ERM00000064.yml rename substance/ERM00000397.markdown => _data/erm/ERM00000397.yml (56%) rename substance/ERM00000400.markdown => _data/erm/ERM00000400.yml (61%) rename substance/ERM00000403.markdown => _data/erm/ERM00000403.yml (60%) rename substance/ERM00000409.markdown => _data/erm/ERM00000409.yml (58%) create mode 100644 _data/erm/ERM00000416.yml rename substance/ERM00000421.markdown => _data/erm/ERM00000421.yml (61%) rename substance/ERM00000424.markdown => _data/erm/ERM00000424.yml (60%) rename substance/ERM00000442.markdown => _data/erm/ERM00000442.yml (65%) rename substance/ERM00000445.markdown => _data/erm/ERM00000445.yml (60%) create mode 100644 _data/erm/ERM00000582.yml create mode 100644 _data/erm/ERM00000583.yml create mode 100644 _data/erm/ERM00000584.yml create mode 100644 _data/work/10.1186/S13321-022-00614-7.yml create mode 100644 _data/work/10.3389/FTOX.2022.981701.yml create mode 100644 _data/work/10.5281/ZENODO.7940162.yml create mode 100644 _data/work/10.5281/ZENODO.7965603.yml create mode 100644 _data/work/10.5281/ZENODO.7966134.yml create mode 100644 _data/work/10.5281/ZENODO.7989699.yml create mode 100644 _data/work/10.5281/ZENODO.7990086.yml create mode 100644 _data/work/10.5281/ZENODO.7990214.yml create mode 100644 _data/work/10.5281/ZENODO.7990251.yml create mode 100644 _data/work/10.5281/ZENODO.7990302.yml create mode 100644 _data/work/10.5281/ZENODO.8015080.yml delete mode 100644 _includes/collecttags.html create mode 100644 _layouts/ontoclass.html create mode 100644 log create mode 100644 ontology.markdown delete mode 100644 substance/ERM00000063.markdown delete mode 100644 substance/ERM00000064.markdown delete mode 100644 substance/ERM00000416.markdown delete mode 100644 substance/ERM00000582.markdown delete mode 100644 substance/ERM00000583.markdown delete mode 100644 substance/ERM00000584.markdown delete mode 100644 work/10.1186/S13321-022-00614-7.markdown delete mode 100644 work/10.3389/FTOX.2022.981701.markdown delete mode 100644 work/10.5281/ZENODO.7940162.markdown delete mode 100644 work/10.5281/ZENODO.7965603.markdown delete mode 100644 work/10.5281/ZENODO.7966134.markdown delete mode 100644 work/10.5281/ZENODO.7989699.markdown delete mode 100644 work/10.5281/ZENODO.7990086.markdown delete mode 100644 work/10.5281/ZENODO.7990214.markdown delete mode 100644 work/10.5281/ZENODO.7990251.markdown delete mode 100644 work/10.5281/ZENODO.7990302.markdown delete mode 100644 work/10.5281/ZENODO.8015080.markdown diff --git a/.github/workflows/placeholder_create_erm_datasets b/.github/workflows/placeholder_create_erm_datasets new file mode 100644 index 0000000..e69de29 diff --git a/.github/workflows/placeholder_create_erm_literature b/.github/workflows/placeholder_create_erm_literature new file mode 100644 index 0000000..e69de29 diff --git a/Gemfile b/Gemfile index 317d89c..4cd6edd 100644 --- a/Gemfile +++ b/Gemfile @@ -20,6 +20,7 @@ group :jekyll_plugins do gem 'jekyll-seo-tag' gem 'jekyll-sitemap' gem 'jekyll-paginate' + gem 'jekyll-datapage-generator' end # Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem diff --git a/Gemfile.lock b/Gemfile.lock index 438c75f..ed43e83 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -31,6 +31,7 @@ GEM safe_yaml (~> 1.0) terminal-table (>= 1.8, < 4.0) webrick (~> 1.7) + jekyll-datapage-generator (1.4.0) jekyll-feed (0.17.0) jekyll (>= 3.7, < 5.0) jekyll-mastodon_webfinger (1.0.2) @@ -81,6 +82,7 @@ PLATFORMS DEPENDENCIES http_parser.rb (~> 0.6.0) jekyll (~> 4.3.2) + jekyll-datapage-generator jekyll-feed (~> 0.12) jekyll-mastodon_webfinger (~> 1.0) jekyll-paginate diff --git a/_config.yml b/_config.yml index 4b23f56..544cb3f 100644 --- a/_config.yml +++ b/_config.yml @@ -13,8 +13,18 @@ plugins: - jekyll-seo-tag - jekyll/mastodon_webfinger - jekyll-paginate + - jekyll-datapage-generator feed: tags: true tags: + +### Page generator from _data files + +page_gen: +- data: "erm" + template: "substance" + dir: "substance/ERM/" + name_expr: "record['id'].sub('ERM', '')" + title_expr: "record['title']" \ No newline at end of file diff --git a/_data/erm/ERM00000063.yml b/_data/erm/ERM00000063.yml new file mode 100644 index 0000000..811f502 --- /dev/null +++ b/_data/erm/ERM00000063.yml @@ -0,0 +1,10 @@ +title: "Material: ERM00000063" +type: ChemicalSubstance +id: ERM00000063 +tag: erm:ERM00000063 +chemicalComposition: ZnO +tags: doi:10.3389/FTOX.2022.981701 erm:ERM00000063 +scholarlyArticleDOI: [10.3389/ftox.2022.981701] +datasetDOI: +rdfs:type: owl:Thing +ermid: \ No newline at end of file diff --git a/_data/erm/ERM00000064.yml b/_data/erm/ERM00000064.yml new file mode 100644 index 0000000..c584cbb --- /dev/null +++ b/_data/erm/ERM00000064.yml @@ -0,0 +1,9 @@ +title: "Material: ERM00000064" +type: ChemicalSubstance +id: ERM00000064 +tag: erm:ERM00000064 +tags: erm:ERM00000064 10.3389/ftox.2022.981701 +chemicalComposition: TiO2 +scholarlyArticleDOI: [10.3389/ftox.2022.981701] +datasetDOI: +rdfs:type: owl:Thing \ No newline at end of file diff --git a/substance/ERM00000397.markdown b/_data/erm/ERM00000397.yml similarity index 56% rename from substance/ERM00000397.markdown rename to _data/erm/ERM00000397.yml index b43acb6..b211efb 100644 --- a/substance/ERM00000397.markdown +++ b/_data/erm/ERM00000397.yml @@ -1,7 +1,5 @@ ---- -layout: substance title: "Material: ERM00000397" type: ChemicalSubstance +id: ERM00000397 tag: erm:ERM00000397 -chemicalComposition: CeO2/Co3O4 ---- +rdfs:type: owl:Thing \ No newline at end of file diff --git a/substance/ERM00000400.markdown b/_data/erm/ERM00000400.yml similarity index 61% rename from substance/ERM00000400.markdown rename to _data/erm/ERM00000400.yml index ae5c555..8e4476c 100644 --- a/substance/ERM00000400.markdown +++ b/_data/erm/ERM00000400.yml @@ -1,7 +1,6 @@ ---- -layout: substance title: "Material: ERM00000400" type: ChemicalSubstance -tag: erm:ERM00000400 +id: ERM00000400 chemicalComposition: Ce0.75Zr0.25O2 ---- +rdfs:type: owl:Thing +tag: erm:ERM00000400 \ No newline at end of file diff --git a/substance/ERM00000403.markdown b/_data/erm/ERM00000403.yml similarity index 60% rename from substance/ERM00000403.markdown rename to _data/erm/ERM00000403.yml index 1f814a7..ff9ec06 100644 --- a/substance/ERM00000403.markdown +++ b/_data/erm/ERM00000403.yml @@ -1,7 +1,6 @@ ---- -layout: substance title: "Material: ERM00000403" type: ChemicalSubstance -tag: erm:ERM00000403 +id: ERM00000403 chemicalComposition: Ce0.1Zr0.9O2 ---- +rdfs:type: owl:Thing +tag: erm:ERM00000403 \ No newline at end of file diff --git a/substance/ERM00000409.markdown b/_data/erm/ERM00000409.yml similarity index 58% rename from substance/ERM00000409.markdown rename to _data/erm/ERM00000409.yml index 0d6b85f..f689139 100644 --- a/substance/ERM00000409.markdown +++ b/_data/erm/ERM00000409.yml @@ -1,7 +1,6 @@ ---- -layout: substance title: "Material: ERM00000409" type: ChemicalSubstance -tag: erm:ERM00000409 +id: ERM00000409 chemicalComposition: Fe3O4 ---- +rdfs:type: owl:Thing +tag: erm:ERM00000409 \ No newline at end of file diff --git a/_data/erm/ERM00000416.yml b/_data/erm/ERM00000416.yml new file mode 100644 index 0000000..2f4cbca --- /dev/null +++ b/_data/erm/ERM00000416.yml @@ -0,0 +1,8 @@ +layout: substance +title: "Material: ERM00000416" +id: ERM00000416 +tags: doi:10.5281/ZENODO.7940162 ERM00000416 +chemicalComposition: ZnO +datasetDOI: 10.5281/ZENODO.7940162 +rdfs:type: owl:Thing +tag: erm:ERM00000416 \ No newline at end of file diff --git a/substance/ERM00000421.markdown b/_data/erm/ERM00000421.yml similarity index 61% rename from substance/ERM00000421.markdown rename to _data/erm/ERM00000421.yml index af92a1d..a6fd39d 100644 --- a/substance/ERM00000421.markdown +++ b/_data/erm/ERM00000421.yml @@ -1,7 +1,6 @@ ---- -layout: substance title: "Material: ERM00000421" type: ChemicalSubstance -tag: erm:ERM00000421 +id: ERM00000421 chemicalComposition: Ce0.75Zr0.25O2 ---- +rdfs:type: owl:Thing +tag: erm:ERM00000421 \ No newline at end of file diff --git a/substance/ERM00000424.markdown b/_data/erm/ERM00000424.yml similarity index 60% rename from substance/ERM00000424.markdown rename to _data/erm/ERM00000424.yml index baa7e2a..6a9d700 100644 --- a/substance/ERM00000424.markdown +++ b/_data/erm/ERM00000424.yml @@ -1,7 +1,6 @@ ---- -layout: substance title: "Material: ERM00000424" type: ChemicalSubstance -tag: erm:ERM00000424 +id: ERM00000424 chemicalComposition: Ce0.1Zr0.9O2 ---- +rdfs:type: owl:Thing +tag: erm:ERM00000424 \ No newline at end of file diff --git a/substance/ERM00000442.markdown b/_data/erm/ERM00000442.yml similarity index 65% rename from substance/ERM00000442.markdown rename to _data/erm/ERM00000442.yml index 36e73f7..3ac4dbb 100644 --- a/substance/ERM00000442.markdown +++ b/_data/erm/ERM00000442.yml @@ -1,7 +1,7 @@ ---- layout: substance title: "Material: ERM00000442" type: ChemicalSubstance -tag: erm:ERM00000442 +id: ERM00000442 chemicalComposition: Ce0.75Zr0.25O2 ---- +rdfs:type: owl:Thing +tag: erm:ERM00000442 \ No newline at end of file diff --git a/substance/ERM00000445.markdown b/_data/erm/ERM00000445.yml similarity index 60% rename from substance/ERM00000445.markdown rename to _data/erm/ERM00000445.yml index 033eda7..5a54515 100644 --- a/substance/ERM00000445.markdown +++ b/_data/erm/ERM00000445.yml @@ -1,7 +1,6 @@ ---- -layout: substance title: "Material: ERM00000445" type: ChemicalSubstance -tag: erm:ERM00000445 +id: ERM00000445 chemicalComposition: Ce0.1Zr0.9O2 ---- +rdfs:type: owl:Thing +tag: erm:ERM00000445 \ No newline at end of file diff --git a/_data/erm/ERM00000582.yml b/_data/erm/ERM00000582.yml new file mode 100644 index 0000000..c009e75 --- /dev/null +++ b/_data/erm/ERM00000582.yml @@ -0,0 +1,7 @@ +title: "Material: ERM00000582" +type: ChemicalSubstance +id: ERM00000582 +chemicalSubstance: Au +datasetDOI: [10.5281/ZENODO.7990251] +rdfs:type: owl:Thing +tag: erm:ERM00000582 \ No newline at end of file diff --git a/_data/erm/ERM00000583.yml b/_data/erm/ERM00000583.yml new file mode 100644 index 0000000..d0c8f24 --- /dev/null +++ b/_data/erm/ERM00000583.yml @@ -0,0 +1,6 @@ +title: "Material: ERM00000583" +id: ERM00000583 +chemicalComposition: Fe3O4 +datasetDOI: [10.5281/ZENODO.7990302] +rdfs:type: owl:Thing +tag: erm:ERM00000583 \ No newline at end of file diff --git a/_data/erm/ERM00000584.yml b/_data/erm/ERM00000584.yml new file mode 100644 index 0000000..dfb0006 --- /dev/null +++ b/_data/erm/ERM00000584.yml @@ -0,0 +1,8 @@ +title: "Material: ERM00000584" +type: ChemicalSubstance +id: ERM00000584 +chemicalComposition: ZnO +tags: doi:10.5281/ZENODO.7990214 +datasetDOI: [10.5281/ZENODO.7990214] +rdfs:type: owl:Thing +tag: erm:ERM00000584 \ No newline at end of file diff --git a/_data/work/10.1186/S13321-022-00614-7.yml b/_data/work/10.1186/S13321-022-00614-7.yml new file mode 100644 index 0000000..ae0fe5b --- /dev/null +++ b/_data/work/10.1186/S13321-022-00614-7.yml @@ -0,0 +1,5 @@ +title: "Work: European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials" +type: ScholarlyArticle +tag: doi:10.1186/S13321-022-00614-7 +doi: doi:10.1186/S13321-022-00614-7 +uri: https://doi.org/doi:10.1186/S13321-022-00614-7 diff --git a/_data/work/10.3389/FTOX.2022.981701.yml b/_data/work/10.3389/FTOX.2022.981701.yml new file mode 100644 index 0000000..e6292bb --- /dev/null +++ b/_data/work/10.3389/FTOX.2022.981701.yml @@ -0,0 +1,5 @@ +title: "Work: The alamar blue assay in the context of safety testing of nanomaterials" +type: ScholarlyArticle +tag: doi:10.3389/FTOX.2022.981701 +doi: doi:10.3389/FTOX.2022.981701 +uri: https://doi.org/doi:10.3389/FTOX.2022.981701 diff --git a/_data/work/10.5281/ZENODO.7940162.yml b/_data/work/10.5281/ZENODO.7940162.yml new file mode 100644 index 0000000..a0ce393 --- /dev/null +++ b/_data/work/10.5281/ZENODO.7940162.yml @@ -0,0 +1,5 @@ +title: "Work: Physico-chemical characterization of sterilized ZnO nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7940162 +doi: 10.5281/ZENODO.7940162 +uri: https://doi.org/10.5281/ZENODO.7940162 diff --git a/_data/work/10.5281/ZENODO.7965603.yml b/_data/work/10.5281/ZENODO.7965603.yml new file mode 100644 index 0000000..6198792 --- /dev/null +++ b/_data/work/10.5281/ZENODO.7965603.yml @@ -0,0 +1,5 @@ +title: "Work: Physico-chemical characterization of sterilized Ce0.1Zr0.9O2 nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7965603 +doi: doi:10.5281/ZENODO.7965603 +uri: https://doi.org/doi:10.5281/ZENODO.7965603 diff --git a/_data/work/10.5281/ZENODO.7966134.yml b/_data/work/10.5281/ZENODO.7966134.yml new file mode 100644 index 0000000..5092b69 --- /dev/null +++ b/_data/work/10.5281/ZENODO.7966134.yml @@ -0,0 +1,5 @@ +title: "Work: Physico-chemical characterization of sterilized Ce0.75Zr0.25O2 nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7966134 +doi: doi:10.5281/ZENODO.7966134 +uri: https://doi.org/doi:10.5281/ZENODO.7966134 diff --git a/_data/work/10.5281/ZENODO.7989699.yml b/_data/work/10.5281/ZENODO.7989699.yml new file mode 100644 index 0000000..a1be2f5 --- /dev/null +++ b/_data/work/10.5281/ZENODO.7989699.yml @@ -0,0 +1,5 @@ +title: "Work: Physico-chemical characterization of CeO2/Co3O4 nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7989699 +doi: doi:10.5281/ZENODO.7989699 +uri: https://doi.org/doi:10.5281/ZENODO.7989699 diff --git a/_data/work/10.5281/ZENODO.7990086.yml b/_data/work/10.5281/ZENODO.7990086.yml new file mode 100644 index 0000000..9137ce2 --- /dev/null +++ b/_data/work/10.5281/ZENODO.7990086.yml @@ -0,0 +1,5 @@ +title: "Work: Physico-chemical characterization of Fe3O4 nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7990086 +doi: doi:10.5281/ZENODO.7990086 +uri: https://doi.org/doi:10.5281/ZENODO.7990086 diff --git a/_data/work/10.5281/ZENODO.7990214.yml b/_data/work/10.5281/ZENODO.7990214.yml new file mode 100644 index 0000000..d686cc3 --- /dev/null +++ b/_data/work/10.5281/ZENODO.7990214.yml @@ -0,0 +1,5 @@ +title: "Work: Physico-chemical characterization of sterile ZnO nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7990214 +doi: doi:10.5281/ZENODO.7990214 +uri: https://doi.org/doi:10.5281/ZENODO.7990214 diff --git a/_data/work/10.5281/ZENODO.7990251.yml b/_data/work/10.5281/ZENODO.7990251.yml new file mode 100644 index 0000000..903a273 --- /dev/null +++ b/_data/work/10.5281/ZENODO.7990251.yml @@ -0,0 +1,5 @@ +title: "Work: Physico-chemical characterization of sterile citrated stabilized Au nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7990251 +doi: doi:10.5281/ZENODO.7990251 +uri: https://doi.org/doi:10.5281/ZENODO.7990251 diff --git a/_data/work/10.5281/ZENODO.7990302.yml b/_data/work/10.5281/ZENODO.7990302.yml new file mode 100644 index 0000000..daea4c4 --- /dev/null +++ b/_data/work/10.5281/ZENODO.7990302.yml @@ -0,0 +1,5 @@ +title: "Work: Physico-chemical characterization of sterile Fe3O4 nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7990302 +doi: 10.5281/ZENODO.7990302 +uri: https://doi.org/10.5281/ZENODO.7990302 diff --git a/_data/work/10.5281/ZENODO.8015080.yml b/_data/work/10.5281/ZENODO.8015080.yml new file mode 100644 index 0000000..3d3a5f2 --- /dev/null +++ b/_data/work/10.5281/ZENODO.8015080.yml @@ -0,0 +1,5 @@ +title: "Work: Ontology IRIs for the JRC representative industrial nanomaterials" +type: Report +tag: doi:10.5281/ZENODO.8015080 +doi: doi:10.5281/ZENODO.8015080 +uri: https://doi.org/doi:10.5281/ZENODO.8015080 diff --git a/_includes/collecttags.html b/_includes/collecttags.html deleted file mode 100644 index 7a3092e..0000000 --- a/_includes/collecttags.html +++ /dev/null @@ -1,19 +0,0 @@ - -{% assign rawtags = "" %} -{% for post in site.posts %} - {% assign ttags = post.tags | join:'|' | append:'|' %} - {% assign rawtags = rawtags | append:ttags %} -{% endfor %} -{% assign rawtags = rawtags | split:'|' | sort %} - -{% assign site.tags = "" %} -{% for tag in rawtags %} - {% if tag != "" %} - {% if tags == "" %} - {% assign tags = tag | split:'|' %} - {% endif %} - {% unless tags contains tag %} - {% assign tags = tags | join:'|' | append:'|' | append:tag | split:'|' %} - {% endunless %} - {% endif %} -{% endfor %} diff --git a/_includes/head.html b/_includes/head.html index 1a62f76..e22765f 100644 --- a/_includes/head.html +++ b/_includes/head.html @@ -5,11 +5,6 @@ {%- seo -%} - {%- feed_meta -%} - - {% if site.tags != "" %} - {% include collecttags.html %} - {% endif %} diff --git a/_includes/header.html b/_includes/header.html index 81bdfcc..8ebd3fe 100644 --- a/_includes/header.html +++ b/_includes/header.html @@ -24,6 +24,7 @@ {% elsif my_page.title contains "Molecule:" %} {% elsif my_page.title contains "Material:" %} {% elsif my_page.title contains "Work:" %} + {% elsif my_page.title contains "class" %} {% elsif my_page.title %} {{ my_page.title | escape }} {% endif %} diff --git a/_layouts/ontoclass.html b/_layouts/ontoclass.html new file mode 100644 index 0000000..eabcb81 --- /dev/null +++ b/_layouts/ontoclass.html @@ -0,0 +1,93 @@ +--- +layout: base +--- + + +{% assign title_parts = page.title | split: ':' %} +{% assign clean_title = title_parts[1] | strip %} +{% assign down_title = clean_title | downcase %} + +{% assign substance_split = page.tag | split:':' %} +{% assign substance = substance_split[1] %} + +
+

{{ clean_title }}

+ +

{{ page.tag }}

+ +{% if page.chemicalComposition %}

Chemical composition: {{ page.chemicalComposition }}

{% endif %} + +

Blog posts

+ +
+ + + +
+ {{ content }} +
+ +{% if page.tags.size > 0 %} + + +{% endif %} diff --git a/_layouts/substance.html b/_layouts/substance.html index eabcb81..f93039a 100644 --- a/_layouts/substance.html +++ b/_layouts/substance.html @@ -31,6 +31,27 @@

Blog posts

{% endfor %} + +{% assign datasets = page.datasetDOI %} +{% if datasets.size > 0 %} +

Datasets

+ +{% endif %} + +{% assign journalArticles = page.journalArticleDOI | split: ' ' %} +{% if journalArticles.size > 0 %} +

Datasets

+ +{% endif %} + - -
- {{ content }} -
-{% if page.tags.size > 0 %} + +{% assign scholarlyArticles = page.scholarlyArticleDOI | split: ' ' %} +{% if scholarlyArticles.size > 0 %} + + + + + + + + + + + + + + + + + + +
ERM IDOntology classCURIEChemical CompositionIn DatasetSame As
+ + + + + From e323290f5181b6975b03a65e92ea84c6c56ce905 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 17 Oct 2023 00:05:42 +0200 Subject: [PATCH 07/18] Fixed the link --- _layouts/home.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_layouts/home.html b/_layouts/home.html index 019f4ce..d5562e6 100644 --- a/_layouts/home.html +++ b/_layouts/home.html @@ -3,7 +3,7 @@ --- This database provides information about materials with an European Registry of Materials (ERM) -identifier. The About page provides more information. +identifier. The About page provides more information.

News

From fc209a10bd08d134775159d45f6b0f20cfeeceaf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Javier=20Mill=C3=A1n=20Acosta?= <83466805+jmillanacosta@users.noreply.github.com> Date: Tue, 9 Jan 2024 16:06:19 +0100 Subject: [PATCH 08/18] Includes ERM: namespace when populating list --- ontology.markdown | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ontology.markdown b/ontology.markdown index 3f64c7c..130f1a7 100644 --- a/ontology.markdown +++ b/ontology.markdown @@ -17,7 +17,7 @@ permalink: /enmo/ {% assign erm = erm_hash[1] %} {% if enmo.curie == erm.a %}
  • - {{ erm.id }} + {{ erm.id | replace: 'ERM', 'erm:ERM'}}
    • {% endif %} @@ -27,4 +27,4 @@ permalink: /enmo/ {% endfor %} - \ No newline at end of file + From ba858d2ffe90076121f44091f200c86ce69ba8ec Mon Sep 17 00:00:00 2001 From: jmillanacosta Date: Tue, 9 Jan 2024 16:33:01 +0100 Subject: [PATCH 09/18] Added ERM namespaces, fixed hrefs --- identifier.markdown | 2 +- ontology.markdown | 2 +- tags.markdown | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/identifier.markdown b/identifier.markdown index bef0e8b..546d289 100644 --- a/identifier.markdown +++ b/identifier.markdown @@ -10,7 +10,7 @@ permalink: /identifiers/ {% assign erm = erm_hash[1] %}
  • - {{ erm.id }} + {{ erm.id | replace: 'ERM', 'erm:ERM' }}
    • {% endfor %} diff --git a/ontology.markdown b/ontology.markdown index 130f1a7..a621dab 100644 --- a/ontology.markdown +++ b/ontology.markdown @@ -1,6 +1,6 @@ --- layout: page -title: ENMO - ontology +title: eNM Ontology permalink: /enmo/ ---
    diff --git a/tags.markdown b/tags.markdown index ebe0863..3356caa 100644 --- a/tags.markdown +++ b/tags.markdown @@ -11,7 +11,7 @@ permalink: /tags/ {% assign tag_name = tag[0] %} {% if tag_name contains "erm:" %} - {{ tag | first }} + {{ tag | first }} {% endif %} {% endfor %} From 3c162dc85452b3b2f3722e0bad4f7c0d8989d292 Mon Sep 17 00:00:00 2001 From: jmillanacosta Date: Tue, 9 Jan 2024 16:33:41 +0100 Subject: [PATCH 10/18] Added new ontology terms as placeholders --- _data/enmo/CHEBI:23367.yml | 4 + _data/enmo/npo:NPO_1486.yml | 4 + _data/enmo/npo:NPO_1542.yml | 3 +- _data/enmo/npo:NPO_707.yml | 4 + .../{owl:thing.yml => obo:BFO_0000040.yml} | 2 +- _data/erm/ERM00000064.yml | 2 +- _data/erm/ERM00000397.yml | 2 +- _data/erm/ERM00000416.yml | 2 +- _data/erm/ERM00000424.yml | 2 +- _data/erm/ERM00000445.yml | 2 +- _data/erm/ERM00000582.yml | 2 +- _data/erm/ERM00000583.yml | 2 +- _data/erm/ERM00000584.yml | 2 +- _layouts/ontoclass.html | 93 ------------------- 14 files changed, 23 insertions(+), 103 deletions(-) create mode 100644 _data/enmo/CHEBI:23367.yml create mode 100644 _data/enmo/npo:NPO_1486.yml create mode 100644 _data/enmo/npo:NPO_707.yml rename _data/enmo/{owl:thing.yml => obo:BFO_0000040.yml} (71%) delete mode 100644 _layouts/ontoclass.html diff --git a/_data/enmo/CHEBI:23367.yml b/_data/enmo/CHEBI:23367.yml new file mode 100644 index 0000000..48f46bb --- /dev/null +++ b/_data/enmo/CHEBI:23367.yml @@ -0,0 +1,4 @@ +label: molecular entity +URI: http://purl.obolibrary.org/obo/CHEBI_23367 +curie: CHEBI:23367 +a: obo:BFO_0000040 \ No newline at end of file diff --git a/_data/enmo/npo:NPO_1486.yml b/_data/enmo/npo:NPO_1486.yml new file mode 100644 index 0000000..fae26f0 --- /dev/null +++ b/_data/enmo/npo:NPO_1486.yml @@ -0,0 +1,4 @@ +label: titanium oxide nanoparticle +URI: http://purl.bioontology.org/ontology/npo#NPO_1486 +curie: npo:NPO_1486 +a: npo:NPO_707 \ No newline at end of file diff --git a/_data/enmo/npo:NPO_1542.yml b/_data/enmo/npo:NPO_1542.yml index edc6675..ca382ad 100644 --- a/_data/enmo/npo:NPO_1542.yml +++ b/_data/enmo/npo:NPO_1542.yml @@ -1,3 +1,4 @@ label: zinc oxide nanoparticle URI: http://purl.bioontology.org/ontology/npo#NPO_1542 -curie: npo:NPO_1542 \ No newline at end of file +curie: npo:NPO_1542 +a: npo:NPO_707 \ No newline at end of file diff --git a/_data/enmo/npo:NPO_707.yml b/_data/enmo/npo:NPO_707.yml new file mode 100644 index 0000000..f84e240 --- /dev/null +++ b/_data/enmo/npo:NPO_707.yml @@ -0,0 +1,4 @@ +label: nanoparticle +URI: http://purl.bioontology.org/ontology/npo#NPO_707 +curie: npo:NPO_707 +a: CHEBI_23367 \ No newline at end of file diff --git a/_data/enmo/owl:thing.yml b/_data/enmo/obo:BFO_0000040.yml similarity index 71% rename from _data/enmo/owl:thing.yml rename to _data/enmo/obo:BFO_0000040.yml index dd4f52e..3b9208c 100644 --- a/_data/enmo/owl:thing.yml +++ b/_data/enmo/obo:BFO_0000040.yml @@ -1,3 +1,3 @@ -label: Thing +label: material entity URI: http://www.w3.org/2002/07/owl#Thing curie: owl:Thing \ No newline at end of file diff --git a/_data/erm/ERM00000064.yml b/_data/erm/ERM00000064.yml index bdf8766..7b35300 100644 --- a/_data/erm/ERM00000064.yml +++ b/_data/erm/ERM00000064.yml @@ -6,7 +6,7 @@ tags: erm:ERM00000064 10.3389/ftox.2022.981701 chemicalComposition: TiO2 scholarlyArticleDOI: [10.3389/ftox.2022.981701] datasetDOI: -a: owl:Thing +a: npo:NPO_1486 otherLinks: - url: https://joint-research-centre.ec.europa.eu/system/files/2016-06/JRC%2520Nanomaterials%2520Repository-List%2520of%2520Representative%2520Nanomaterials-201606.pdf title: EUROPEAN COMMISSION JOINT RESEARCH CENTRE JRC NANOMATERIALS REPOSITORY - List of Representative Nanomaterials diff --git a/_data/erm/ERM00000397.yml b/_data/erm/ERM00000397.yml index 9db12f4..b47078f 100644 --- a/_data/erm/ERM00000397.yml +++ b/_data/erm/ERM00000397.yml @@ -2,4 +2,4 @@ title: "Material: ERM00000397" type: ChemicalSubstance id: ERM00000397 tag: erm:ERM00000397 -a: owl:Thing \ No newline at end of file +a: CHEBI:23367 \ No newline at end of file diff --git a/_data/erm/ERM00000416.yml b/_data/erm/ERM00000416.yml index 146cdc3..51b049f 100644 --- a/_data/erm/ERM00000416.yml +++ b/_data/erm/ERM00000416.yml @@ -4,5 +4,5 @@ id: ERM00000416 tags: doi:10.5281/ZENODO.7940162 ERM00000416 chemicalComposition: ZnO datasetDOI: 10.5281/ZENODO.7940162 -a: owl:Thing +a: npo:NPO_1542 tag: erm:ERM00000416 \ No newline at end of file diff --git a/_data/erm/ERM00000424.yml b/_data/erm/ERM00000424.yml index a96a84e..c42f1a9 100644 --- a/_data/erm/ERM00000424.yml +++ b/_data/erm/ERM00000424.yml @@ -2,5 +2,5 @@ title: "Material: ERM00000424" type: ChemicalSubstance id: ERM00000424 chemicalComposition: Ce0.1Zr0.9O2 -a: owl:Thing +a: CHEBI:23367 tag: erm:ERM00000424 \ No newline at end of file diff --git a/_data/erm/ERM00000445.yml b/_data/erm/ERM00000445.yml index cc4e167..43836f2 100644 --- a/_data/erm/ERM00000445.yml +++ b/_data/erm/ERM00000445.yml @@ -2,5 +2,5 @@ title: "Material: ERM00000445" type: ChemicalSubstance id: ERM00000445 chemicalComposition: Ce0.1Zr0.9O2 -a: owl:Thing +a: CHEBI:23367 tag: erm:ERM00000445 \ No newline at end of file diff --git a/_data/erm/ERM00000582.yml b/_data/erm/ERM00000582.yml index fa24023..7338b18 100644 --- a/_data/erm/ERM00000582.yml +++ b/_data/erm/ERM00000582.yml @@ -3,6 +3,6 @@ type: ChemicalSubstance id: ERM00000582 chemicalSubstance: Au datasetDOI: [10.5281/ZENODO.7990251] -a: owl:Thing +a: CHEBI:23367 tag: erm:ERM00000582 sameAs: [RiskGONE NM 18] \ No newline at end of file diff --git a/_data/erm/ERM00000583.yml b/_data/erm/ERM00000583.yml index 42ac2fb..ea6150a 100644 --- a/_data/erm/ERM00000583.yml +++ b/_data/erm/ERM00000583.yml @@ -2,6 +2,6 @@ title: "Material: ERM00000583" id: ERM00000583 chemicalComposition: Fe3O4 datasetDOI: [10.5281/ZENODO.7990302] -a: owl:Thing +a: CHEBI:23367 tag: erm:ERM00000583 sameAs: [RiskGONE NM 19] \ No newline at end of file diff --git a/_data/erm/ERM00000584.yml b/_data/erm/ERM00000584.yml index 7d0bad3..703ff72 100644 --- a/_data/erm/ERM00000584.yml +++ b/_data/erm/ERM00000584.yml @@ -4,6 +4,6 @@ id: ERM00000584 chemicalComposition: ZnO tags: doi:10.5281/ZENODO.7990214 datasetDOI: [10.5281/ZENODO.7990214] -a: owl:Thing +a: npo:NPO_1542 tag: erm:ERM00000584 sameAs: [RiskGONE NM 20] \ No newline at end of file diff --git a/_layouts/ontoclass.html b/_layouts/ontoclass.html deleted file mode 100644 index eabcb81..0000000 --- a/_layouts/ontoclass.html +++ /dev/null @@ -1,93 +0,0 @@ ---- -layout: base ---- - - -{% assign title_parts = page.title | split: ':' %} -{% assign clean_title = title_parts[1] | strip %} -{% assign down_title = clean_title | downcase %} - -{% assign substance_split = page.tag | split:':' %} -{% assign substance = substance_split[1] %} - -
    -

    {{ clean_title }}

    - -

    {{ page.tag }}

    - -{% if page.chemicalComposition %}

    Chemical composition: {{ page.chemicalComposition }}

    {% endif %} - -

    Blog posts

    -
      -{% for post in site.tags[page.tag] %} - {% if post.lang %} -
    • - {% else %} -
    • - {% endif %} - {{ post.title }} ({{ post.date | date_to_string }})
      - {{ post.description }} - -
      • -{% endfor %} -
    -
    - - - -
    - {{ content }} -
    - -{% if page.tags.size > 0 %} - - -{% endif %} From 6a285b4fc5376858285573788cecc26be6bd1132 Mon Sep 17 00:00:00 2001 From: jmillanacosta Date: Tue, 9 Jan 2024 16:34:03 +0100 Subject: [PATCH 11/18] Changed ignore rules for nanomiles data --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 74a9223..1059128 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,4 @@ _site/ # Ignore folders generated by Bundler .bundle/ vendor/ +_data/nanomiles/data.tsv From 56ec26bb6a86997244e95f59855d3cc1657118bd Mon Sep 17 00:00:00 2001 From: jmillanacosta Date: Tue, 9 Jan 2024 16:36:24 +0100 Subject: [PATCH 12/18] Fixed wrong data --- _data/enmo/obo:BFO_0000040.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_data/enmo/obo:BFO_0000040.yml b/_data/enmo/obo:BFO_0000040.yml index 3b9208c..5e8b30e 100644 --- a/_data/enmo/obo:BFO_0000040.yml +++ b/_data/enmo/obo:BFO_0000040.yml @@ -1,3 +1,3 @@ label: material entity -URI: http://www.w3.org/2002/07/owl#Thing -curie: owl:Thing \ No newline at end of file +URI: http://purl.obolibrary.org/obo/BFO_0000040 +curie: obo:BFO_0000040 \ No newline at end of file From 92880c82a8e11676a16a03ba7f09b0139f02ce3f Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 9 Jan 2024 19:56:24 +0100 Subject: [PATCH 13/18] Restored the work pages --- work/10.1186/S13321-022-00614-7.markdown | 7 +++++++ work/10.3389/FTOX.2022.981701.markdown | 7 +++++++ work/10.5281/ZENODO.7940162.markdown | 7 +++++++ work/10.5281/ZENODO.7965603.markdown | 7 +++++++ work/10.5281/ZENODO.7966134.markdown | 7 +++++++ work/10.5281/ZENODO.7989699.markdown | 7 +++++++ work/10.5281/ZENODO.7990086.markdown | 7 +++++++ work/10.5281/ZENODO.7990214.markdown | 7 +++++++ work/10.5281/ZENODO.7990251.markdown | 7 +++++++ work/10.5281/ZENODO.7990302.markdown | 7 +++++++ work/10.5281/ZENODO.8015080.markdown | 7 +++++++ 11 files changed, 77 insertions(+) create mode 100644 work/10.1186/S13321-022-00614-7.markdown create mode 100644 work/10.3389/FTOX.2022.981701.markdown create mode 100644 work/10.5281/ZENODO.7940162.markdown create mode 100644 work/10.5281/ZENODO.7965603.markdown create mode 100644 work/10.5281/ZENODO.7966134.markdown create mode 100644 work/10.5281/ZENODO.7989699.markdown create mode 100644 work/10.5281/ZENODO.7990086.markdown create mode 100644 work/10.5281/ZENODO.7990214.markdown create mode 100644 work/10.5281/ZENODO.7990251.markdown create mode 100644 work/10.5281/ZENODO.7990302.markdown create mode 100644 work/10.5281/ZENODO.8015080.markdown diff --git a/work/10.1186/S13321-022-00614-7.markdown b/work/10.1186/S13321-022-00614-7.markdown new file mode 100644 index 0000000..e1e68e5 --- /dev/null +++ b/work/10.1186/S13321-022-00614-7.markdown @@ -0,0 +1,7 @@ +--- +layout: work +title: "Work: European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials" +type: ScholarlyArticle +tag: doi:10.1186/S13321-022-00614-7 +doi: doi:10.1186/S13321-022-00614-7 +--- diff --git a/work/10.3389/FTOX.2022.981701.markdown b/work/10.3389/FTOX.2022.981701.markdown new file mode 100644 index 0000000..8e5b89b --- /dev/null +++ b/work/10.3389/FTOX.2022.981701.markdown @@ -0,0 +1,7 @@ +--- +layout: work +title: "Work: The alamar blue assay in the context of safety testing of nanomaterials" +type: ScholarlyArticle +tag: doi:10.3389/FTOX.2022.981701 +doi: doi:10.3389/FTOX.2022.981701 +--- diff --git a/work/10.5281/ZENODO.7940162.markdown b/work/10.5281/ZENODO.7940162.markdown new file mode 100644 index 0000000..941d04b --- /dev/null +++ b/work/10.5281/ZENODO.7940162.markdown @@ -0,0 +1,7 @@ +--- +layout: work +title: "Work: Physico-chemical characterization of sterilized ZnO nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7940162 +doi: 10.5281/ZENODO.7940162 +--- diff --git a/work/10.5281/ZENODO.7965603.markdown b/work/10.5281/ZENODO.7965603.markdown new file mode 100644 index 0000000..0ba44ea --- /dev/null +++ b/work/10.5281/ZENODO.7965603.markdown @@ -0,0 +1,7 @@ +--- +layout: work +title: "Work: Physico-chemical characterization of sterilized Ce0.1Zr0.9O2 nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7965603 +doi: doi:10.5281/ZENODO.7965603 +--- diff --git a/work/10.5281/ZENODO.7966134.markdown b/work/10.5281/ZENODO.7966134.markdown new file mode 100644 index 0000000..38ffe2f --- /dev/null +++ b/work/10.5281/ZENODO.7966134.markdown @@ -0,0 +1,7 @@ +--- +layout: work +title: "Work: Physico-chemical characterization of sterilized Ce0.75Zr0.25O2 nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7966134 +doi: doi:10.5281/ZENODO.7966134 +--- diff --git a/work/10.5281/ZENODO.7989699.markdown b/work/10.5281/ZENODO.7989699.markdown new file mode 100644 index 0000000..30f2ca0 --- /dev/null +++ b/work/10.5281/ZENODO.7989699.markdown @@ -0,0 +1,7 @@ +--- +layout: work +title: "Work: Physico-chemical characterization of CeO2/Co3O4 nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7989699 +doi: doi:10.5281/ZENODO.7989699 +--- diff --git a/work/10.5281/ZENODO.7990086.markdown b/work/10.5281/ZENODO.7990086.markdown new file mode 100644 index 0000000..3038ed9 --- /dev/null +++ b/work/10.5281/ZENODO.7990086.markdown @@ -0,0 +1,7 @@ +--- +layout: work +title: "Work: Physico-chemical characterization of Fe3O4 nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7990086 +doi: doi:10.5281/ZENODO.7990086 +--- diff --git a/work/10.5281/ZENODO.7990214.markdown b/work/10.5281/ZENODO.7990214.markdown new file mode 100644 index 0000000..3b90016 --- /dev/null +++ b/work/10.5281/ZENODO.7990214.markdown @@ -0,0 +1,7 @@ +--- +layout: work +title: "Work: Physico-chemical characterization of sterile ZnO nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7990214 +doi: doi:10.5281/ZENODO.7990214 +--- diff --git a/work/10.5281/ZENODO.7990251.markdown b/work/10.5281/ZENODO.7990251.markdown new file mode 100644 index 0000000..133d9df --- /dev/null +++ b/work/10.5281/ZENODO.7990251.markdown @@ -0,0 +1,7 @@ +--- +layout: work +title: "Work: Physico-chemical characterization of sterile citrated stabilized Au nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7990251 +doi: doi:10.5281/ZENODO.7990251 +--- diff --git a/work/10.5281/ZENODO.7990302.markdown b/work/10.5281/ZENODO.7990302.markdown new file mode 100644 index 0000000..d017e75 --- /dev/null +++ b/work/10.5281/ZENODO.7990302.markdown @@ -0,0 +1,7 @@ +--- +layout: work +title: "Work: Physico-chemical characterization of sterile Fe3O4 nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7990302 +doi: 10.5281/ZENODO.7990302 +--- diff --git a/work/10.5281/ZENODO.8015080.markdown b/work/10.5281/ZENODO.8015080.markdown new file mode 100644 index 0000000..701bc7d --- /dev/null +++ b/work/10.5281/ZENODO.8015080.markdown @@ -0,0 +1,7 @@ +--- +layout: work +title: "Work: Ontology IRIs for the JRC representative industrial nanomaterials" +type: Report +tag: doi:10.5281/ZENODO.8015080 +doi: doi:10.5281/ZENODO.8015080 +--- From d6c71be281ee12a4090248140fce77ba2bdc80e3 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 9 Jan 2024 20:30:06 +0100 Subject: [PATCH 14/18] Fixed the tag links in blog posts --- _config.yml | 2 +- _data/work/10.1186/S13321-022-00614-7.yml | 1 + _layouts/post.html | 10 +++++++++- 3 files changed, 11 insertions(+), 2 deletions(-) diff --git a/_config.yml b/_config.yml index 544cb3f..91e992d 100644 --- a/_config.yml +++ b/_config.yml @@ -27,4 +27,4 @@ page_gen: template: "substance" dir: "substance/ERM/" name_expr: "record['id'].sub('ERM', '')" - title_expr: "record['title']" \ No newline at end of file + title_expr: "record['title']" diff --git a/_data/work/10.1186/S13321-022-00614-7.yml b/_data/work/10.1186/S13321-022-00614-7.yml index ae0fe5b..32e7ab0 100644 --- a/_data/work/10.1186/S13321-022-00614-7.yml +++ b/_data/work/10.1186/S13321-022-00614-7.yml @@ -1,3 +1,4 @@ +id: 10.1186/S13321-022-00614-7 title: "Work: European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials" type: ScholarlyArticle tag: doi:10.1186/S13321-022-00614-7 diff --git a/_layouts/post.html b/_layouts/post.html index afe3b24..376e920 100644 --- a/_layouts/post.html +++ b/_layouts/post.html @@ -42,30 +42,38 @@

    {{ page.title | escape }} {% capture tag_name %}{{ tag }}{% endcapture %} {% assign type = "tag" %} {% assign icon = "tag" %} + {% assign href = type | append:'/' | append: tag_name | relative_url %} {% else %} {% capture tag_name %}{{ check[1] }}{% endcapture %} {% if check[0] == "inchikey" %} {% assign type = "molecule" %} {% assign icon = "flask-vial" %} + {% assign href = type | append:'/' | append: tag_name | relative_url %} {% elsif check[0] == "substance" %} {% assign type = "substance" %} {% assign icon = "flask-vial" %} + {% assign href = type | append:'/' | append: tag_name | relative_url %} {% elsif check[0] == "erm" %} {% assign type = "substance" %} {% assign icon = "flask-vial" %} + {% assign erm_num = tag_name | replace: 'ERM', '' %} + {% assign href = type | append: '/ERM/' | append: erm_num | relative_url %} + {% assign tag_name = "erm:" | append: tag_name %} {% elsif check[0] == "justdoi" %} {% assign type = "skip" %} {% elsif check[0] == "doi" %} {% assign type = "work" %} {% assign icon = "file" %} + {% assign href = type | append:'/' | append: tag_name | relative_url %} {% else %} {% assign type = "tag" %} {% assign icon = "tag" %} + {% assign href = type | append:'/' | append: tag_name | relative_url %} {% endif %} {% endif %} {% if type != "skip" %} - {{ tag_name }}  + {{ tag_name }}  {% endif %} {% endfor %} From acb6d659e0fa8587ec9e5aa6ddfcc1a5c194d55b Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 9 Jan 2024 20:33:52 +0100 Subject: [PATCH 15/18] Obselete test --- _data/work/10.1186/S13321-022-00614-7.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/_data/work/10.1186/S13321-022-00614-7.yml b/_data/work/10.1186/S13321-022-00614-7.yml index 32e7ab0..ae0fe5b 100644 --- a/_data/work/10.1186/S13321-022-00614-7.yml +++ b/_data/work/10.1186/S13321-022-00614-7.yml @@ -1,4 +1,3 @@ -id: 10.1186/S13321-022-00614-7 title: "Work: European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials" type: ScholarlyArticle tag: doi:10.1186/S13321-022-00614-7 From 4641027132a603b365a01034677fc8e6d045f1fc Mon Sep 17 00:00:00 2001 From: jmillanacosta Date: Wed, 10 Jan 2024 13:54:27 +0100 Subject: [PATCH 16/18] custom step to capitalize data pages --- .github/workflows/jekyll.yml | 82 +++++++++++++++++++ .../workflows/placeholder_create_erm_datasets | 0 .../placeholder_create_erm_literature | 0 3 files changed, 82 insertions(+) create mode 100644 .github/workflows/jekyll.yml delete mode 100644 .github/workflows/placeholder_create_erm_datasets delete mode 100644 .github/workflows/placeholder_create_erm_literature diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml new file mode 100644 index 0000000..c32a1d9 --- /dev/null +++ b/.github/workflows/jekyll.yml @@ -0,0 +1,82 @@ +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +# Sample workflow for building and deploying a Jekyll site to GitHub Pages +name: Deploy Jekyll site to Pages + +on: + # Runs on pushes targeting the default branch + push: + branches: ["main"] + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages +permissions: + contents: read + pages: write + id-token: write + +# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued. +# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete. +concurrency: + group: "pages" + cancel-in-progress: false + +jobs: + # Build job + build: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Setup Ruby + uses: ruby/setup-ruby@8575951200e472d5f2d95c625da0c7bec8217c42 # v1.161.0 + with: + ruby-version: '3.1' # Not needed with a .ruby-version file + bundler-cache: true # runs 'bundle install' and caches installed gems automatically + cache-version: 0 # Increment this number if you need to re-download cached gems + - name: Setup Pages + id: pages + uses: actions/configure-pages@v4 + - name: Build with Jekyll + # Outputs to the './_site' directory by default + run: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}" + env: + JEKYLL_ENV: production + - name: fix capitalization + run: | + # Navigate to the directory containing the erm + cd /substance/erm + + # Loop through all files containing 'erm*' + for file in erm*; do + # Check if the file exists + if [ -e "$file" ]; then + # Create the new file name with 'ERM*' + new_name=$(echo "$file" | sed 's/erm*/ERM*/') + + # Rename the file + mv "$file" "$new_name" + + echo "Renamed: $file to $new_name" + fi + done + - name: Upload artifact + # Automatically uploads an artifact from the './_site' directory by default + uses: actions/upload-pages-artifact@v3 + + # Deployment job + deploy: + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + runs-on: ubuntu-latest + needs: build + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 \ No newline at end of file diff --git a/.github/workflows/placeholder_create_erm_datasets b/.github/workflows/placeholder_create_erm_datasets deleted file mode 100644 index e69de29..0000000 diff --git a/.github/workflows/placeholder_create_erm_literature b/.github/workflows/placeholder_create_erm_literature deleted file mode 100644 index e69de29..0000000 From 60e8b34a73f97196c6d8e0f6a0d18eda8462b32a Mon Sep 17 00:00:00 2001 From: jmillanacosta Date: Wed, 10 Jan 2024 14:28:34 +0100 Subject: [PATCH 17/18] Fixes capitalization issue for substance/erm/ERM* pages --- .github/workflows/jekyll.yml | 28 ++++++++++++++++++++-------- 1 file changed, 20 insertions(+), 8 deletions(-) diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml index c32a1d9..7490173 100644 --- a/.github/workflows/jekyll.yml +++ b/.github/workflows/jekyll.yml @@ -3,13 +3,15 @@ # separate terms of service, privacy policy, and support # documentation. +# Note: added step to capitalize the ERMs +# Note: if deploy fails, remove deployment branches and tags restrictions for the environment github-pages from /erm-database/settings/environments + # Sample workflow for building and deploying a Jekyll site to GitHub Pages -name: Deploy Jekyll site to Pages +name: Custom Deploy Jekyll site to Pages on: - # Runs on pushes targeting the default branch push: - branches: ["main"] + branches: ["data-setup"] # Allows you to run this workflow manually from the Actions tab workflow_dispatch: @@ -47,17 +49,21 @@ jobs: run: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}" env: JEKYLL_ENV: production - - name: fix capitalization + - name: fix capitalization for ERM* pages + env: + JEKYLL_ENV: production run: | # Navigate to the directory containing the erm - cd /substance/erm + cd _site/substance/erm + echo before: + ls # Loop through all files containing 'erm*' for file in erm*; do # Check if the file exists if [ -e "$file" ]; then - # Create the new file name with 'ERM*' - new_name=$(echo "$file" | sed 's/erm*/ERM*/') + # Create the new file name with 'ERM' + new_name=$(echo "$file" | sed 's/erm/ERM/') # Rename the file mv "$file" "$new_name" @@ -65,6 +71,8 @@ jobs: echo "Renamed: $file to $new_name" fi done + echo after: + ls - name: Upload artifact # Automatically uploads an artifact from the './_site' directory by default uses: actions/upload-pages-artifact@v3 @@ -79,4 +87,8 @@ jobs: steps: - name: Deploy to GitHub Pages id: deployment - uses: actions/deploy-pages@v4 \ No newline at end of file + uses: actions/deploy-pages@v4 + permissions: + contents: read + pages: write + id-token: write From 7f28fdd7aefd0c4f0ac11cca2232f28b8c41e75a Mon Sep 17 00:00:00 2001 From: jmillanacosta Date: Wed, 10 Jan 2024 14:32:13 +0100 Subject: [PATCH 18/18] Fix hrefs to ERMs --- _config.yml | 4 ++-- identifier.markdown | 2 +- ontology.markdown | 2 +- tags.markdown | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/_config.yml b/_config.yml index 91e992d..a92ed4c 100644 --- a/_config.yml +++ b/_config.yml @@ -25,6 +25,6 @@ tags: page_gen: - data: "erm" template: "substance" - dir: "substance/ERM/" - name_expr: "record['id'].sub('ERM', '')" + dir: "substance/erm/" + name_expr: "record['id']" title_expr: "record['title']" diff --git a/identifier.markdown b/identifier.markdown index 546d289..beb8e48 100644 --- a/identifier.markdown +++ b/identifier.markdown @@ -9,7 +9,7 @@ permalink: /identifiers/ {% for erm_hash in site.data.erm %} {% assign erm = erm_hash[1] %}
  • - + {{ erm.id | replace: 'ERM', 'erm:ERM' }}
    • diff --git a/ontology.markdown b/ontology.markdown index a621dab..f563423 100644 --- a/ontology.markdown +++ b/ontology.markdown @@ -17,7 +17,7 @@ permalink: /enmo/ {% assign erm = erm_hash[1] %} {% if enmo.curie == erm.a %}
  • - {{ erm.id | replace: 'ERM', 'erm:ERM'}} + {{ erm.id | replace: 'ERM', 'erm:ERM'}}
    • {% endif %} diff --git a/tags.markdown b/tags.markdown index 3356caa..75b29b5 100644 --- a/tags.markdown +++ b/tags.markdown @@ -11,7 +11,7 @@ permalink: /tags/ {% assign tag_name = tag[0] %} {% if tag_name contains "erm:" %} - {{ tag | first }} + {{ tag | first }} {% endif %} {% endfor %}