From 8cf224142ce576e374d14b99edba22f6b6c05cfe Mon Sep 17 00:00:00 2001 From: Michael Baudis <675030+mbaudis@users.noreply.github.com> Date: Thu, 1 Feb 2024 09:40:34 +0100 Subject: [PATCH] more common/ --- docs/beaconplus.md | 2 +- docs/changelog.md | 2 +- docs/{ => common}/classifications-and-ontologies.md | 0 docs/common/plotting.md | 1 - docs/javascripts/tablesort.js | 6 ------ docs/news/2022-01-17-cnv-state-classes.md | 2 +- docs/pgxRpi.md | 2 +- mkdocs.yaml | 8 ++++---- 8 files changed, 8 insertions(+), 15 deletions(-) rename docs/{ => common}/classifications-and-ontologies.md (100%) delete mode 100644 docs/javascripts/tablesort.js diff --git a/docs/beaconplus.md b/docs/beaconplus.md index 70367b5f..927dfe7b 100644 --- a/docs/beaconplus.md +++ b/docs/beaconplus.md @@ -80,7 +80,7 @@ collections of MongoDB databases. These collections are addressed by scoped quer Filters represent a way to allow the resource provider to direct "self-scoped" query values to the corresponding attributes in their backend resource. In the Progenetix implementation, a lookup table followed by scope assignment is used to map prefixed filter values to the correct attributes and collections. Most of the filter options are based on ontology terms or identifiers in CURIE format (e.g. `NCIT:C4033`, `cellosaurus:CVCL_0030` or `PMID:16004614`). For use case examples please look below; documentation of available ontologies and how to find out about available -terms can be found on the [Classifications and Ontologies](classifications-and-ontologies.md) page. +terms can be found on the [Classifications and Ontologies](common/classifications-and-ontologies.md) page. In Beacon v2, the new `FilteringTerms` schema adds options to specify different types of filters (`OntologyFilter`, `AlphanumericFilter`, `CustomFilter`) which can diff --git a/docs/changelog.md b/docs/changelog.md index 8bf0e458..147101b6 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -38,7 +38,7 @@ terms used in a query. More information is available in the [Filtering Terms](be ## 2022-01-17: Introducing `variant_state` classes for CNVs -More information can be found in the [description of ontology use for CNVs](classifications-and-ontologies.md#genomic-variations-cnv-ontology). +More information can be found in the [description of ontology use for CNVs](common/classifications-and-ontologies.md#genomic-variations-cnv-ontology). ## 2022-01-10: BUG FIX Frequency Maps diff --git a/docs/classifications-and-ontologies.md b/docs/common/classifications-and-ontologies.md similarity index 100% rename from docs/classifications-and-ontologies.md rename to docs/common/classifications-and-ontologies.md diff --git a/docs/common/plotting.md b/docs/common/plotting.md index 56b33786..0c946920 100644 --- a/docs/common/plotting.md +++ b/docs/common/plotting.md @@ -10,7 +10,6 @@ The standard format for (plot-)images generated on Progenetix is Scalable Vector On most pages where plots are being displayed there is a download option for the images - (please alert us where those are missing). Browsers also have the option to export SVGs themselves e.g. as PDF. - ## The `byconaut` plotting library Functionality of the Progenetix and cancercellline.org plotting API is provided diff --git a/docs/javascripts/tablesort.js b/docs/javascripts/tablesort.js deleted file mode 100644 index 6a5afcf2..00000000 --- a/docs/javascripts/tablesort.js +++ /dev/null @@ -1,6 +0,0 @@ -document$.subscribe(function() { - var tables = document.querySelectorAll("article table:not([class])") - tables.forEach(function(table) { - new Tablesort(table) - }) -}) diff --git a/docs/news/2022-01-17-cnv-state-classes.md b/docs/news/2022-01-17-cnv-state-classes.md index b7474369..70a50744 100644 --- a/docs/news/2022-01-17-cnv-state-classes.md +++ b/docs/news/2022-01-17-cnv-state-classes.md @@ -5,4 +5,4 @@ description: More granular annotation of CNV types date: 2022-01-17 --- -More information can be found in the [description of ontology use for CNVs](classifications-and-ontologies.md#genomic-variations-cnv-ontology). +More information can be found in the [description of ontology use for CNVs](common/classifications-and-ontologies.md#genomic-variations-cnv-ontology). diff --git a/docs/pgxRpi.md b/docs/pgxRpi.md index bad306f7..a71d6ef0 100644 --- a/docs/pgxRpi.md +++ b/docs/pgxRpi.md @@ -4,7 +4,7 @@ ## Retrieve biosample information -You can select biosamples from specific groups of interests, chosen by a filter. The description about _filters_ is [here](https://docs.progenetix.org/classifications-and-ontologies/). +You can select biosamples from specific groups of interests, chosen by a filter. The description about _filters_ is [here](https://docs.progenetix.org/common/classifications-and-ontologies/). ``` biosamples <- pgxLoader(type="biosample", filters = "NCIT:C3512",codematches = TRUE) diff --git a/mkdocs.yaml b/mkdocs.yaml index edd3d638..b980d9f6 100644 --- a/mkdocs.yaml +++ b/mkdocs.yaml @@ -7,7 +7,7 @@ repo_url: https://github.com/progenetix/progenetix-web # vars for common files (shared between sites) ################################# -api_site_label: progenetix.org +api_site_label: '[Progenetix](https://progenetix.org)' api_web_root: https://progenetix.org ################################################################################ @@ -22,7 +22,7 @@ nav: - Analysis in R - pgxRpi: pgxRpi - Plotting & Visualizations: common/plotting - Use Case Examples: use-cases - - Classifications, Ontologies & Standards: classifications-and-ontologies + - Classifications, Ontologies & Standards: common/classifications-and-ontologies - Publication Collection: publication-collection - Data Review: progenetix-data-review - Technical Notes: technical-notes @@ -105,6 +105,6 @@ extra: link: https://github.com/progenetix extra_css: - css/theme_overrides.css -extra_javascript: - - https://cdnjs.cloudflare.com/ajax/libs/tablesort/5.2.1/tablesort.min.js +# extra_javascript: +# - https://cdnjs.cloudflare.com/ajax/libs/tablesort/5.2.1/tablesort.min.js \ No newline at end of file