From 63c100a90bc674f664724e359f8dace87aaa1889 Mon Sep 17 00:00:00 2001
From: Michael Baudis <675030+mbaudis@users.noreply.github.com>
Date: Fri, 16 Feb 2024 14:03:13 +0100
Subject: [PATCH] parameters & clean-up
---
src/components/Layout.js | 4 +
src/config/beaconSearchParameters.yaml | 24 --
src/config/celllines_searchExamples.yaml | 24 +-
src/config/celllines_searchParameters.yaml | 189 -------------
src/config/filtersearch_searchParameters.yaml | 51 ----
src/config/searchParameters.yaml | 263 ------------------
src/modules/data-pages/filtersearch_page.js | 23 --
src/modules/details-pages/subsetPage.js | 5 +-
src/pages/filterSearch.js | 12 -
9 files changed, 7 insertions(+), 588 deletions(-)
delete mode 100644 src/config/celllines_searchParameters.yaml
delete mode 100644 src/config/filtersearch_searchParameters.yaml
delete mode 100644 src/config/searchParameters.yaml
delete mode 100644 src/modules/data-pages/filtersearch_page.js
delete mode 100644 src/pages/filterSearch.js
diff --git a/src/components/Layout.js b/src/components/Layout.js
index 75678fd8..4d301ce9 100644
--- a/src/components/Layout.js
+++ b/src/components/Layout.js
@@ -125,13 +125,16 @@ function Side({ onClick }) {
isSub="isSub"
/>
*/}
+
{/*
diff --git a/src/config/beaconSearchParameters.yaml b/src/config/beaconSearchParameters.yaml
index db65eb70..59b183a6 100644
--- a/src/config/beaconSearchParameters.yaml
+++ b/src/config/beaconSearchParameters.yaml
@@ -40,76 +40,52 @@ parameters:
value: ""
- label: "1 (NC_000001.11)"
value: "refseq:NC_0000001.11"
- # value: "1"
- label: "2 (NC_000002.12)"
value: "refseq:NC_000002.12"
- # value: "2"
- label: "3 (NC_000003.12)"
value: "refseq:NC_000003.12"
- # value: "3"
- label: "4 (NC_000004.12)"
value: "refseq:NC_000004.12"
- # value: "4"
- label: "5 (NC_000005.10)"
value: "refseq:NC_000005.10"
- # value: "5"
- label: "6 (NC_000006.12)"
value: "refseq:NC_000006.12"
- # value: "6"
- label: "7 (NC_000007.14)"
value: "refseq:NC_000007.14"
- # value: "7"
- label: "8 (NC_000008.11)"
value: "refseq:NC_000008.11"
- # value: "8"
- label: "9 (NC_000009.12)"
value: "refseq:NC_000009.12"
- # value: "9"
- label: "10 (NC_000010.11)"
value: "refseq:NC_000010.11"
- # value: "10"
- label: "11 (NC_000011.10)"
value: "refseq:NC_000011.10"
- # value: "11"
- label: "12 (NC_000012.12)"
value: "refseq:NC_000012.12"
- # value: "12"
- label: "13 (NC_000013.11)"
value: "refseq:NC_000013.11"
- # value: "13"
- label: "14 (NC_000014.9)"
value: "refseq:NC_000014.9"
- # value: "14"
- label: "15 (NC_000015.10)"
value: "refseq:NC_000015.10"
- # value: "15"
- label: "16 (NC_000016.10)"
value: "refseq:NC_000016.10"
- # value: "16"
- label: "17 (NC_000017.11)"
value: "refseq:NC_000017.11"
- # value: "17"
- label: "18 (NC_000018.10)"
value: "refseq:NC_000018.10"
- # value: "18"
- label: "19 (NC_000019.10)"
value: "refseq:NC_000019.10"
- # value: "19"
- label: "20 (NC_000020.11)"
value: "refseq:NC_000020.11"
- # value: "20"
- label: "21 (NC_000021.9)"
value: "refseq:NC_000021.9"
- # value: "21"
- label: "22 (NC_000022.11)"
value: "refseq:NC_000022.11"
- # value: "22"
- label: "X (NC_000023.11)"
value: "refseq:NC_000023.11"
- # value: "23"
- label: "Y (NC_000024.10)"
value: "refseq:NC_000024.10"
- # value: "24"
variantType:
label: "Variant Type"
infoText: >-
diff --git a/src/config/celllines_searchExamples.yaml b/src/config/celllines_searchExamples.yaml
index 563399a2..b5d7fc58 100644
--- a/src/config/celllines_searchExamples.yaml
+++ b/src/config/celllines_searchExamples.yaml
@@ -35,8 +35,6 @@
isHidden: true
materialtype:
isHidden: true
- freeFilters:
- isHidden: true
filterLogic:
isHidden: true
accessid:
@@ -81,15 +79,9 @@
isHidden: true
materialtype:
isHidden: true
- freeFilters:
- isHidden: true
filterLogic:
isHidden: true
- accessid:
- isHidden: true
- geoCity:
- isHidden: true
- referenceid:
+ allTermsFilters:
defaultValue: ["cellosaurus:CVCL_0004"]
- label: "CDKN2A Deletion Example in CL"
note: "Example for focal CDKN2A deletion matches."
@@ -108,12 +100,8 @@
isHidden: true
variantMaxLength:
isHidden: true
- bioontology:
+ allTermsFilters:
defaultValue: ["NCIT:C3058"]
- accessid:
- isHidden: true
- geoCity:
- isHidden: true
- label: "MYC Duplication in CL"
note: "Example for focal MYC Duplications."
description: |
@@ -132,10 +120,6 @@
isHidden: true
variantMaxLength:
isHidden: true
- accessid:
- isHidden: true
- geoCity:
- isHidden: true
- label: "TP53 Del. in Cell Lines"
note: "Example for TP53 deletion"
description: >-
@@ -149,8 +133,4 @@
defaultValue: "7669608-10000000"
variantType:
defaultValue: "EFO:0030067"
- accessid:
- isHidden: true
- geoCity:
- isHidden: true
diff --git a/src/config/celllines_searchParameters.yaml b/src/config/celllines_searchParameters.yaml
deleted file mode 100644
index 0d5ad476..00000000
--- a/src/config/celllines_searchParameters.yaml
+++ /dev/null
@@ -1,189 +0,0 @@
----
-note: ""
-label: ""
-description: ""
-parameters:
- datasetIds:
- defaultValue: ["cellz"]
- assemblyId:
- isHidden: true
- referenceName:
- placeholder: "9"
- start:
- placeholder: "19000001-21975098"
- end:
- placeholder: "21967753-24000000"
- variantType:
- placeholder: "EFO:0030067"
- alternateBases:
- placeholder: ""
- isHidden: false
- referenceBases:
- placeholder: ""
- isHidden: false
- accessid:
- isHidden: true
- filterPrecision:
- isHidden: true
- materialtype:
- isHidden: true
- clinicalClasses:
- isHidden: true
-examples:
- - label: "HLF Cell Line"
- note: "Instances of HLF and daughter cell lines, searched by Cellosaurusid"
- description: >-
- The query retrieves all instances of HLF and derived cell lines using
- the "cellosaurus:CVCL_2947" identifier. HLF has a set of annotated
- variants including a Li-Fraumeni TP53 mutation.
- parameters:
- variantType:
- defaultValue: ""
- isHidden: true
- referenceName:
- isHidden: true
- geneId:
- isHidden: true
- variantMinLength:
- isHidden: true
- variantMaxLength:
- isHidden: true
- clinicalClasses:
- isHidden: true
- start:
- isHidden: true
- end:
- isHidden: true
- alternateBases:
- isHidden: true
- referenceBases:
- isHidden: true
- bioontology:
- isHidden: true
- cohorts:
- isHidden: true
- sex:
- isHidden: true
- materialtype:
- isHidden: true
- freeFilters:
- isHidden: true
- filterLogic:
- isHidden: true
- accessid:
- isHidden: true
- geoCity:
- isHidden: true
- referenceid:
- defaultValue: ["cellosaurus:CVCL_2947"]
- - label: "K-562 Cell Line"
- note: "Instances of K-562 and daughter cell lines, searched by Cellosaurus id"
- description: >-
- The query retrieves all instances of K-562 and derived cell lines using
- the "cellosaurus:CVCL_0004" identifier. This is an example for a pure
- "non-variant" filter query.
- parameters:
- variantType:
- defaultValue: ""
- isHidden: true
- referenceName:
- isHidden: true
- geneId:
- isHidden: true
- variantMinLength:
- isHidden: true
- variantMaxLength:
- isHidden: true
- clinicalClasses:
- isHidden: true
- start:
- isHidden: true
- end:
- isHidden: true
- alternateBases:
- isHidden: true
- referenceBases:
- isHidden: true
- bioontology:
- isHidden: true
- cohorts:
- isHidden: true
- sex:
- isHidden: true
- materialtype:
- isHidden: true
- freeFilters:
- isHidden: true
- filterLogic:
- isHidden: true
- accessid:
- isHidden: true
- geoCity:
- isHidden: true
- referenceid:
- defaultValue: ["cellosaurus:CVCL_0004"]
- - label: "CDKN2A Deletion Example in CL"
- note: "Example for focal CDKN2A deletion matches."
- description: |
- This example shows the query for CNV deletion variants overlapping the CDKN2A gene's coding region with at least a single base, but limited to "highly focal" hits (here i.e. <= ~1Mbp in size). The query can be modified e.g. through changing the position parameters or diagnosis.
- parameters:
- referenceName:
- defaultValue: "refseq:NC_000009.12"
- start:
- defaultValue: "21500001-21975098"
- end:
- defaultValue: "21967753-22500000"
- variantType:
- defaultValue: "EFO:0030067"
- variantMinLength:
- isHidden: true
- variantMaxLength:
- isHidden: true
- bioontology:
- defaultValue: ["NCIT:C3058"]
- accessid:
- isHidden: true
- geoCity:
- isHidden: true
- - label: "MYC Duplication in CL"
- note: "Example for focal MYC Duplications."
- description: |
- The example parameters will select samples with a continuous, focal duplication
- of the complete MYC coding region.
- parameters:
- referenceName:
- defaultValue: "refseq:NC_000008.11"
- start:
- defaultValue: "124000000-127736593"
- end:
- defaultValue: "127740957-130000000"
- variantType:
- defaultValue: "EFO:0030070"
- variantMinLength:
- isHidden: true
- variantMaxLength:
- isHidden: true
- accessid:
- isHidden: true
- geoCity:
- isHidden: true
- - label: "TP53 Del. in Cell Lines"
- note: "Example for TP53 deletion"
- description: >-
- Query example for an "any overlap", focal deletion in TP53.
- parameters:
- referenceName:
- defaultValue: "refseq:NC_000017.11"
- start:
- defaultValue: "5000000-7676592"
- end:
- defaultValue: "7669608-10000000"
- variantType:
- defaultValue: "EFO:0030067"
- accessid:
- isHidden: true
- geoCity:
- isHidden: true
-
-
-
diff --git a/src/config/filtersearch_searchParameters.yaml b/src/config/filtersearch_searchParameters.yaml
deleted file mode 100644
index b8c237bd..00000000
--- a/src/config/filtersearch_searchParameters.yaml
+++ /dev/null
@@ -1,51 +0,0 @@
----
-note: ""
-label: ""
-description: >-
- This file limits the parameters displayed in a search form that i sbound to a
- provided filter (e.g. a page for a disease code which just should be used to
- query its samples, with limited options).
-parameters:
- datasetIds:
- isHidden: true
- cohorts:
- isHidden: true
- assemblyId:
- isHidden: true
- referenceName:
- isHidden: true
- geneId:
- isHidden: true
- variantType:
- isHidden: true
- variantMinLength:
- isHidden: true
- variantMaxLength:
- isHidden: true
- start:
- isHidden: true
- end:
- isHidden: true
- referenceBases:
- isHidden: true
- alternateBases:
- isHidden: true
- sex:
- isHidden: true
- clinicalClasses:
- isHidden: true
- materialtype:
- isHidden: true
- accessid:
- isHidden: true
- filterLogic:
- isHidden: true
- geoCity:
- isHidden: true
- geodistanceKm:
- isHidden: true
- examples: []
- skip:
- isHidden: true
- limit:
- isHidden: true
diff --git a/src/config/searchParameters.yaml b/src/config/searchParameters.yaml
deleted file mode 100644
index b9459758..00000000
--- a/src/config/searchParameters.yaml
+++ /dev/null
@@ -1,263 +0,0 @@
----
-datasetIds:
- label: Dataset
- isMulti: true
- rules:
- required: true
- defaultValue: cellz
- options:
- - value: cellz
- label: Cancer Cell Lines Collection
- - value: progenetix
- label: Progenetix
-assemblyId:
- label: Genome Assembly
- infoText: |
- The genome reference assembly.
- defaultValue: GRCh38
- options:
- - value: GRCh38
- label: GRCh38 / hg38
-geneId:
- label: Gene Symbol
- infoText: The gene symbol (HUGO).
-referenceName:
- label: Chromosome
- infoText: The chromosome with the variant(s).
- placeholder: "refseq:NC_000009.12"
- options:
- - label: "NC_000001.11"
- value: "refseq:NC_000001.11"
- - label: "NC_000002.12"
- value: "refseq:NC_000002.12"
- - label: "NC_000003.12"
- value: "refseq:NC_000003.12"
- - label: "NC_000004.12"
- value: "refseq:NC_000004.12"
- - label: "NC_000005.10"
- value: "refseq:NC_000005.10"
- - label: "NC_000006.12"
- value: "refseq:NC_000006.12"
- - label: "NC_000007.14"
- value: "refseq:NC_000007.14"
- - label: "NC_000008.11"
- value: "refseq:NC_000008.11"
- - label: "NC_000009.12"
- value: "refseq:NC_000009.12"
- - label: "NC_000010.11"
- value: "refseq:NC_000010.11"
- - label: "NC_000011.10"
- value: "refseq:NC_000011.10"
- - label: "NC_000012.12"
- value: "refseq:NC_000012.12"
- - label: "NC_000013.11"
- value: "refseq:NC_000013.11"
- - label: "NC_000014.9"
- value: "refseq:NC_000014.9"
- - label: "NC_000015.10"
- value: "refseq:NC_000015.10"
- - label: "NC_000016.10"
- value: "refseq:NC_000016.10"
- - label: "NC_000017.11"
- value: "refseq:NC_000017.11"
- - label: "NC_000018.10"
- value: "refseq:NC_000018.10"
- - label: "NC_000019.10"
- value: "refseq:NC_000019.10"
- - label: "NC_000020.11"
- value: "refseq:NC_000020.11"
- - label: "NC_000021.9"
- value: "refseq:NC_000021.9"
- - label: "NC_000022.11"
- value: "refseq:NC_000022.11"
- - label: "NC_000023.11 (X)"
- value: "refseq:NC_000023.11"
- - label: "NC_000024.10 (Y)"
- value: "refseq:NC_000024.10"
-variantType:
- label: "Variant Type"
- infoText: >-
- The type of a structural variant for e.g. CNV searches.
- defaultValue: ""
- options:
- - value: ""
- label: ""
- - value: "EFO:0030067"
- label: "EFO:0030067 (copy number deletion)"
- - value: "EFO:0030070"
- label: "EFO:0030070 (copy number gain)"
- - value: "EFO:0030066"
- label: "EFO:0030066 (any relative CN variation)"
- - value: "SO:0001059"
- label: "SO:0001059 (any sequence alteration - SNV, INDEL...)"
-start:
- label: Start or Position
- infoText: |
- The 1-based genomic position of the variant, or the start of a range query,
- specified through a single value.
- However, in case of fuzzy requests for e.g. copy number variants, the start
- position will usually be provided as a range for the possible occurrence of
- the CNV start (e.g. "21500001-21975098").
-end:
- label: End (Range or Structural Var.)
- infoText: |
- The 1-based genomic end position of a range query, specified through a
- single value, or in case of fuzzy requests for e.g. copy number variants
- the end provided as a range for the possible occurrence of
- the CNV end (e.g. "21967753-22500000").
-variantMinLength:
- label: Minimum Variant Length
- type: number
- infoText: The minimal length, in bases, of a genomic variant. This parameter can be applied to e.g. CNV queries.
-variantMaxLength:
- label: Maximal Variant Length
- type: number
- infoText: The maximal length, in bases, of a genomic variant. This parameter can be applied to e.g. CNV queries.
-referenceBases:
- label: Reference Base(s)
-alternateBases:
- label: Alternate Base(s)
-cohorts:
- label: Cohorts
- infoText: >
- An aggregation of samples by origin (e.g. study, external resource), shared features or use in a publication.
- rules:
- required: false
- defaultValue: ""
- isHidden: True
- # options:
- # - value: ""
- # label: "(no selection)"
- # - value: pgx:cohort-arraymap
- # label: arrayMap Samples
-bioontology:
- label: Cancer Classification(s)
- infoLink: "https://info.progenetix.org/doc/filters-documentation.html"
- infoText: |
- Special filter type for disease classification codes. If using multiple
- codes please be aware that probably use of an "OR" filter logic will be appropriate.
- isMulti: true
- options:
- - value: ""
- label: "(no selection)"
-referenceid:
- label: ID(s)/ Name(s)
- infoText: |
- Special filter type for external reference codes such as PMIDs or cellosaurus
- id values.
- If using multiple codes please be aware that probably use of an "OR" filter
- logic will be appropriate.
- isMulti: true
- options:
- - value: ""
- label: "(no selection)"
-clinicalClasses:
- label: Clinical Classes
- infoText: |
- Clinical and diagnostic support classifications, such as tumor grading or staging.
- isMulti: true
- options:
- - value: ""
- label: "(no selection)"
-# materialtype:
-# label: Biosample Type
-# infoText: |
-# Special filter type, to e.g. limit responses to neoplastic or reference
-# samples, respectively, when not using specific cancer classification codes.
-# defaultValue: ""
-# isHidden: True
-# options:
-# - value: ""
-# label: "(no selection)"
-# - value: EFO:0009656
-# label: neoplastic sample
-# - value: EFO:0030035
-# label: cancer cell line sample
-# - value: EFO:0009654
-# label: reference sample
-sex:
- label: Genotypic Sex
- infoText: |
- Genotypic sex of the individual.
- defaultValue: ""
- options:
- - value: ""
- label: "(no selection)"
- - value: PATO:0020002
- label: Female genotypic Sex
- - value: PATO:0020001
- label: Male genotypic Sex
-freeFilters:
- label: Filters
- infoLink: "https://info.progenetix.org/doc/filters-documentation.html"
- infoText: |
- Add free comma-concatenated **filters** to the search. These will usually
- correspond to CURIE values supported by the resource (e.g.
- "cellosaurus:CVCL_0004"; "NCIT:C3222"; "PMID:18559507"). Please see the
- Documentation for details.
-accessid:
- label: Accession Prefilter
-filterLogic:
- label: Filter Logic
- infoText: |
- Boolean logic for filter values; the default **AND** assumes different
- logical scopes for used filters (e.g. collision occurr if multiple cancer
- diagnoses are used with AND). Please be aware that "Filters" here include
- the "Cancer Classification", "Biosample Type" and "Filters" fields.
- defaultValue: "AND"
- options:
- - value: AND
- label: AND
- - value: OR
- label: OR
-includeDescendantTerms:
- label: Include Child Terms
- infoText: >-
- As standard, any selected filter will also include matches on its child
- terms; i.e. NCIT:C3052 - Digestive System Neoplasm will include results
- from gastric, esophagus, colon ... cancer. However, this parameter allows
- to limit searches to the exact code match.
- defaultValue: "True"
- options:
- - value: "true"
- label: always match child terms
- - value: "false"
- label: only match exact code(s)
-# filterPrecision:
-# label: Filter Precision
-# infoText: |
-# Logic for the matching of filter terms. The use of "start" will e.g.
-# allow to match all "icdom-8500_" values (i.e. ductal breast carcinomas
-# and precursors - "...85000, ...85001, ...85002, ...85003")
-# defaultValue: "exact"
-# options:
-# - value: exact
-# label: Exact term match
-# - value: start
-# label: Start-anchored term match
-geoCity:
- label: City
- infoText: |
- Selector for a city for which the samples have been annotated, usually corresponding to origin of the data.
-geodistanceKm:
- infoText: |
- Proximity of the data matches to the selected city, to allow for fuzzy
- annotations or large geographic area searches (e.g. "European samples" through
- "Zurich + 2000km").
- label: Range (km)
- type: number
- defaultValue: 100
-skip:
- label: Skip Pages
- infoText: >
- The number of result pages to skip when retrieving data.
- rules:
- required: false
- defaultValue: 0
-limit:
- label: Response Limit / Page Size
- infoText: >
- The maximum number of biosamples to retrieve per page and also the size of response pages.
- rules:
- required: false
- defaultValue: 1000
\ No newline at end of file
diff --git a/src/modules/data-pages/filtersearch_page.js b/src/modules/data-pages/filtersearch_page.js
deleted file mode 100644
index 83efffca..00000000
--- a/src/modules/data-pages/filtersearch_page.js
+++ /dev/null
@@ -1,23 +0,0 @@
-import React from "react"
-import { Layout } from "../../components/Layout"
-import parametersConfig from "../../config/searchParameters.yaml"
-import requestTypeConfig from "../../config/filtersearch_searchParameters.yaml"
-import BiosamplesSearchPanel from "../../components/searchForm/BiosamplesSearchPanel"
-// import Link from "next/link"
-
-export default function filtersearch_page({cytoBands}) {
-
- return (
-
-
-
- )
-}
diff --git a/src/modules/details-pages/subsetPage.js b/src/modules/details-pages/subsetPage.js
index 8b9eacdf..291d7ebf 100644
--- a/src/modules/details-pages/subsetPage.js
+++ b/src/modules/details-pages/subsetPage.js
@@ -64,16 +64,13 @@ function SubsetResponse({ response, datasetIds }) {
if (!response.response.results[0]) {
return NoResultsHelp(exampleId, "subsetdetails")
}
-
return
}
function Subset({ subset, datasetIds }) {
-
const filters = subset.id
- const sampleFilterScope = "freeFilters"
+ const sampleFilterScope = "allTermsFilters"
const searchPage = "search"
-
return (
diff --git a/src/pages/filterSearch.js b/src/pages/filterSearch.js
deleted file mode 100644
index 22ba6e9b..00000000
--- a/src/pages/filterSearch.js
+++ /dev/null
@@ -1,12 +0,0 @@
-import Page from "../modules/data-pages/filtersearch_page"
-import { getCytoBands } from "../utils/genome"
-export default Page
-
-// This function gets called at build time on server-side.
-export const getStaticProps = async () => ({
- props: {
- cytoBands: await getCytoBands()
- }
-})
-
-// This page is an alias for search.js since /biosamples has been shared berfore...
\ No newline at end of file