examples files, directory cleanup ...

src/components/searchForm/AggregatorSearchPanel.js

@@ -8,14 +8,15 @@ import PropTypes from "prop-types"
 // import cn from "classnames"
 
 AggregatorSearchPanel.propTypes = {
-  requestTypesConfig: PropTypes.object.isRequired,
+  requestTypeConfig: PropTypes.object.isRequired,
   parametersConfig: PropTypes.object.isRequired,
   collapsed: false
 }
 
 export default function AggregatorSearchPanel({
-  requestTypesConfig,
   parametersConfig,
+  requestTypeConfig,
+  requestTypeExamples,
   cytoBands,
   collapsed
 }) {
@@ -70,7 +71,8 @@ export default function AggregatorSearchPanel({
       >
         <BiosamplesSearchForm
           cytoBands={cytoBands}
-          requestTypesConfig={requestTypesConfig}
+          requestTypeConfig={requestTypeConfig}
+          requestTypeExamples={requestTypeExamples}
           parametersConfig={parametersConfig}
           isQuerying={isLoading}
           setSearchQuery={onValidFormQuery}

src/components/searchForm/BiosamplesSearchForm.js

@@ -35,7 +35,8 @@ BiosamplesSearchForm.propTypes = {
   cytoBands: PropTypes.object.isRequired,
   isQuerying: PropTypes.bool.isRequired,
   setSearchQuery: PropTypes.func.isRequired,
-  requestTypesConfig: PropTypes.object.isRequired,
+  requestTypeConfig: PropTypes.object.isRequired,
+  requestTypeExamples: PropTypes.object.isRequired,
   parametersConfig: PropTypes.object.isRequired
 }
 
@@ -73,15 +74,14 @@ export function Form({
   cytoBands,
   isQuerying,
   setSearchQuery,
-  requestTypesConfig,
+  requestTypeConfig,
+  requestTypeExamples,
   parametersConfig,
   urlQuery,
   setUrlQuery
 }) {
   // const autoExecuteSearch = urlQuery.executeSearch === "true"
 
-  const requestTypeId = Object.entries(requestTypesConfig)[0][0]
-  const requestTypeConfig = requestTypesConfig[requestTypeId]
   const [example, setExample] = useState(null)
   let parameters = useMemo(
     () =>
@@ -192,6 +192,7 @@ parameters = merge({}, parameters, {
               setUrlQuery
             )}
             requestTypeConfig={requestTypeConfig}
+        requestTypeExamples={requestTypeExamples}
           />
           <FormUtilitiesButtons
             onCytoBandClick={onCytoBandClick}
@@ -451,10 +452,10 @@ parameters = merge({}, parameters, {
   )
 }
 
-function ExamplesButtons({ requestTypeConfig, onExampleClicked }) {
+function ExamplesButtons({ requestTypeExamples, onExampleClicked }) {
   return (
     <div>
-      {Object.entries(requestTypeConfig?.examples || []).map(([id, value]) => (
+      {Object.entries(requestTypeExamples || []).map(([id, value]) => (
         <button
           key={id}
           className="button is-light"
@@ -604,23 +605,3 @@ function FilterLogicWarning({ isVisible }) {
   )
 }
 
-// function ShowMoreParameters() {
-
-//   const [isOpened, setIsOpened] = useState(false);
-
-//   function toggle() {
-//     setIsOpened(wasOpened => !wasOpened);
-//   }
-
-//   return (
-//     <>
-//       <h5><span onClick={toggle}>More Parameters (click to show/hide)</span></h5>
-//         {isOpened && (
-//           <div>
-//             <pre className="prettyprint">{ JSON.stringify(data, null, 2) }</pre>
-//           </div>
-//         )}
-//     </>
-//   )
-// }
-

src/components/searchForm/BiosamplesSearchPanel.js

@@ -8,14 +8,15 @@ import PropTypes from "prop-types"
 // import cn from "classnames"
 
 BiosamplesSearchPanel.propTypes = {
-  requestTypesConfig: PropTypes.object.isRequired,
+  requestTypeConfig: PropTypes.object.isRequired,
   parametersConfig: PropTypes.object.isRequired,
   collapsed: false
 }
 
 export default function BiosamplesSearchPanel({
-  requestTypesConfig,
+  requestTypeConfig,
   parametersConfig,
+  requestTypeExamples,
   cytoBands,
   collapsed
 }) {
@@ -40,9 +41,6 @@ export default function BiosamplesSearchPanel({
     setQuery(formValues)
   }
 
-  // button className="button ml-3"
-  //    className="icon has-text-info"
-
   return  (
     <>
       <Panel
@@ -70,7 +68,8 @@ export default function BiosamplesSearchPanel({
       >
         <BiosamplesSearchForm
           cytoBands={cytoBands}
-          requestTypesConfig={requestTypesConfig}
+          requestTypeConfig={requestTypeConfig}
+          requestTypeExamples={requestTypeExamples}
           parametersConfig={parametersConfig}
           isQuerying={isLoading}
           setSearchQuery={onValidFormQuery}

src/config/DIPG_searchExamples.yaml

@@ -0,0 +1,63 @@
+---
+- label: "SNV Example"
+  note: "Example for specific EIF4A1 mutation"
+  description: |
+    This example shows a core Beacon query, against a specific
+    mutation in the EIF4A1 gene, in the DIPG childhood brain tumor dataset.
+  parameters:
+    referenceName:
+      defaultValue: "refseq:NC_000017.11"
+    start:
+      defaultValue: 7577121
+    alternateBases:
+      defaultValue: "A"
+    referenceBases:
+      defaultValue: "G"
+- label: "SNV Range Example"
+  note: "Example for EIF4A1 transcript region matches (precise variants)"
+  description: >
+    As in the standard SNV query, this example shows a Beacon query against mutations in the EIF4A1 gene in the DIPG childhood brain tumor dataset. However, this range + wildcard query will return any variant with alternate bases (indicated through "N").
+    Since parameters will be interpreted using an "AND" paradigm, either <i>Alternate Bases</i> OR <i>Variant Type</i> should be specified. The exact variants which were being found can be retrieved through the variant handover [H—>O] link.
+  parameters:
+    referenceName:
+      defaultValue: "refseq:NC_000017.11"
+    start:
+      defaultValue: 7572826
+    end:
+      defaultValue: 7579005
+    variantType:
+      defaultValue: ""
+    alternateBases:
+      defaultValue: ""
+    referenceBases:
+      defaultValue: ""
+- label: "CDKN2A Deletion Example"
+  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) in Glioblastoma samples. 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"
+    bioontology:
+      defaultValue: ["NCIT:C3058"]
+- label: "MYC Duplication"
+  note: "Example for focal MYC Duplications."
+  description: |
+    The example parameters will select samples with a continuous, focal duplication of the complete MYC coding region. The serarch will be limited to  neoplastic samples (EFO:0009656).
+  parameters:
+    referenceName:
+      defaultValue: "refseq:NC_000008.11"
+    start:
+      defaultValue: "124000000-127736593"
+    end:
+      defaultValue: "127740957-130000000"
+    variantType:
+      defaultValue: "EFO:0030070"
+    materialtype:
+      defaultValue: "EFO:0009656"

src/config/DIPG_searchParameters.yaml

@@ -0,0 +1,18 @@
+---
+note: ""
+label: ""
+description: ""
+parameters:
+  datasetIds:
+    defaultValue: ["progenetix"]
+    isHidden: true
+  cohorts:
+    defaultValue: ["pgx:cohort-DIPG"]
+    isHidden: true
+  assemblyId:
+    defaultValue: "GRCh38"
+    isHidden: true
+  end:
+    isHidden: true
+  variantType:
+    isHidden: true

src/config/TCGA_searchExamples.yaml

@@ -0,0 +1,33 @@
+---
+- label: "CDKN2A Deletion Example"
+  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) in Glioblastoma samples. 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"
+    bioontology:
+      defaultValue: ["NCIT:C3058"]
+- label: "MYC Duplication"
+  note: "Example for focal MYC Duplications."
+  description: |
+    The example parameters will select samples with a continuous, focal duplication of the complete MYC coding region. The serarch will be limited to  neoplastic samples (EFO:0009656).
+  parameters:
+    referenceName:
+      defaultValue: "refseq:NC_000008.11"
+    start:
+      defaultValue: "124000000-127736593"
+    end:
+      defaultValue: "127740957-130000000"
+    variantType:
+      defaultValue: "EFO:0030070"
+    materialtype:
+      defaultValue: "EFO:0009656"

src/config/TCGA_searchParameters.yaml

@@ -0,0 +1,33 @@
+---
+note: ""
+label: ""
+description: ""
+parameters:
+  datasetIds:
+    defaultValue: ["progenetix"]
+    isHidden: true
+  cohorts:
+    defaultValue: ["pgx:cohort-TCGA"]
+    # isHidden: true
+  assemblyId:
+    isHidden: true
+  referenceName:
+    placeholder: "9"
+  start:
+    placeholder: "19000001-21975098"
+  end:
+    placeholder: "21967753-24000000"
+  variantType:
+    placeholder: "EFO:0030067"
+  alternateBases:
+    placeholder: ""
+    isHidden: true
+  referenceBases:
+    placeholder: ""
+    isHidden: true
+  accessid:
+    isHidden: true
+  sex:
+    placeholder: ""
+  materialtype:
+    placeholder: "EFO:0009656" #"EFO:0009656"

src/config/arraymap_searchExamples.yaml

@@ -0,0 +1,69 @@
+---
+- label: "CDKN2A Deletion Example"
+  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"
+    bioontology:
+      defaultValue: ["NCIT:C3058"]
+- label: "MYC Duplication"
+  note: "Example for focal MYC Duplications."
+  description: |
+    The example parameters will select samples with a continuous, focal duplication
+    of the complete MYC coding region. The serarch will be limited to "pgx:icdom-80463"
+    (i.e. ICD-O 3 8046/3, Non-small cell carcinoma).
+  parameters:
+    referenceName:
+      defaultValue: "refseq:NC_000008.11"
+    start:
+      defaultValue: "124000000-127736593"
+    end:
+      defaultValue: "127740957-130000000"
+    variantType:
+      defaultValue: "EFO:0030070"
+    bioontology:
+      defaultValue: ["pgx:icdom-80463"]
+- label: "TP53 Del. in Cell Lines"
+  note: "Example for TP53 deletion"
+  description: >-
+    Query example for an "any overlap", focal deletion in TP53 where the
+    search will be limited to cell lines, searched with limit to the "EFO:0030035"
+    material code.
+  parameters:
+    referenceName:
+      defaultValue: "refseq:NC_000017.11"
+    start:
+      defaultValue: "5000000-7676592"
+    end:
+      defaultValue: "7669608-10000000"
+    variantType:
+      defaultValue: "EFO:0030067"
+    freeFilters:
+      defaultValue: "EFO:0030035"
+- 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" query.
+  parameters:
+    referenceName:
+      defaultValue: ""
+    start:
+      defaultValue: ""
+    end:
+      defaultValue: ""
+    variantType:
+      defaultValue: ""
+    referenceid:
+      defaultValue: ["cellosaurus:CVCL_0004"]

src/config/arraymap_searchParameters.yaml

@@ -0,0 +1,33 @@
+---
+note: ""
+label: ""
+description: ""
+parameters:
+  datasetIds:
+    defaultValue: ["progenetix"]
+    isHidden: true
+  cohorts:
+    defaultValue: ["pgx:cohort-arraymap"]
+    isHidden: true
+  assemblyId:
+    isHidden: true
+  referenceName:
+    placeholder: "9"
+  start:
+    placeholder: "19000001-21975098"
+  end:
+    placeholder: "21967753-24000000"
+  variantType:
+    placeholder: "EFO:0030067"
+  alternateBases:
+    placeholder: "N"
+    isHidden: true
+  referenceBases:
+    placeholder: ""
+    isHidden: true
+  accessid:
+    isHidden: true
+  sex:
+    placeholder: ""
+  materialtype:
+    placeholder: "" #"EFO:0009656"