diff --git a/client/src/components/Panels/Common/ToolSearch.vue b/client/src/components/Panels/Common/ToolSearch.vue index 25a9d36958dc..7dd06964eb95 100644 --- a/client/src/components/Panels/Common/ToolSearch.vue +++ b/client/src/components/Panels/Common/ToolSearch.vue @@ -7,6 +7,8 @@ import axios from "axios"; import { getAppRoot } from "onload/loadConfig"; import { getGalaxyInstance } from "app"; import DelayedInput from "components/Common/DelayedInput"; +import MockAdapter from "axios-mock-adapter"; +import testToolsSearchResponse from "./../../ToolsView/testData/toolsSearch"; export default { name: "ToolSearch", @@ -48,12 +50,26 @@ export default { this.$emit("onResults", this.favoritesResults); } else { this.loading = true; + + let axiosMock; + axiosMock = new MockAdapter(axios); + axiosMock.onGet(`${getAppRoot()}api/tools`).reply(200, testToolsSearchResponse); + axios .get(`${getAppRoot()}api/tools`, { params: { q, view: this.currentPanelView }, }) .then((response) => { this.loading = false; + + if (axiosMock) { + let toolID = []; + (response.data).forEach(function(tool) { + toolID.push(tool.id); + }); + response.data = toolID; + } + this.$emit("onResults", response.data); }) .catch((err) => { diff --git a/client/src/components/Panels/utilities.js b/client/src/components/Panels/utilities.js index 8c02e3fb7b96..fe7beb530db7 100644 --- a/client/src/components/Panels/utilities.js +++ b/client/src/components/Panels/utilities.js @@ -6,17 +6,15 @@ export function filterToolSections(layout, results) { if (section.elems) { section.elems.forEach((el) => { if ( - (!el.text && results.includes(el.id)) || - (el.tool_shed_repository && results.includes(el.tool_shed_repository.name)) + (!el.text && toolNameExistsInResults(el.id, results)) || + (el.tool_shed_repository && toolNameExistsInResults(el.tool_shed_repository.name, results)) ) { toolRes.push(el); } }); } - // sort tools in section by rank in results - toolRes.sort((tool1, tool2) => { - return results.indexOf(tool1.id) - results.indexOf(tool2.id); - }); + + toolRes = sortToolsByResultsScore(toolRes, results); return { ...section, @@ -34,7 +32,7 @@ export function filterToolSections(layout, results) { if (sect1.elems.length == 0 || sect2.elems.length == 0) { return 0; } - return results.indexOf(sect1.elems[0].id) - results.indexOf(sect2.elems[0].id); + return results.indexOf(sect1.elems[0].id) - results.indexOf(sect2.elems[0].id); //TODO may need updates to Object }); } else { return layout; @@ -56,8 +54,8 @@ export function filterTools(layout, results) { if (section.elems) { section.elems.forEach((el) => { if ( - (!el.text && results.includes(el.id)) || - (el.tool_shed_repository && results.includes(el.tool_shed_repository.name)) + (!el.text && toolNameExistsInResults(el.id, results)) || + (el.tool_shed_repository && toolNameExistsInResults(el.tool_shed_repository.name, results)) ) { toolsResults.push(el); } @@ -66,9 +64,10 @@ export function filterTools(layout, results) { toolsResults.push(section); } }); - return toolsResults.sort((tool1, tool2) => { - return results.indexOf(tool1.id) - results.indexOf(tool2.id); - }); + + toolsResults = sortToolsByResultsScore(toolsResults, results); + + return toolsResults; } else { return layout; } @@ -84,3 +83,23 @@ function normalize_results(results) { }); return norm_results; } + +/** + * Where `results` is an Array of Objects + */ +function sortToolsByResultsScore(tools, results) { + tools.sort((tool1, tool2) => { + return results.indexOf(tool1.score) - results.indexOf(tool2.score); + }); + + return tools; +} + +/** + * Where `results` is an Array of Objects + */ +function toolNameExistsInResults(toolname, results) { + let matchedTools = results.filter((r) => r.id === toolname); + + return matchedTools && matchedTools.length > 0; +} diff --git a/client/src/components/ToolsView/testData/toolsSearch.json b/client/src/components/ToolsView/testData/toolsSearch.json new file mode 100644 index 000000000000..f06f2eb48e6c --- /dev/null +++ b/client/src/components/ToolsView/testData/toolsSearch.json @@ -0,0 +1,21648 @@ +[ + { + "name": "NCBI Datasets Genomes", + "id": "datasets_download_genome", + "description": "download genome sequence, annotation and metadata", + "tool_shed_repository": "ncbi_datasets", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_datasets/datasets_download_genome/13.4.0" + }, + { + "name": "NCBI Accession Download", + "id": "ncbi_acc_download", + "description": "Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API", + "tool_shed_repository": "ncbi_acc_download", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.7+galaxy0" + }, + { + "name": "UniProt", + "id": "uniprotxml_downloader", + "description": "download proteome as XML or fasta", + "tool_shed_repository": "uniprotxml_downloader", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.2.0" + }, + { + "name": "Unipept", + "id": "unipept", + "description": "retrieve taxonomy for peptides", + "tool_shed_repository": "unipept", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.5.0" + }, + { + "name": "IEDB", + "id": "iedb_api", + "description": "MHC Binding prediction", + "tool_shed_repository": "iedb_api", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/iedb_api/iedb_api/2.15.2" + }, + { + "name": "Download and Extract Reads in BAM", + "id": "sam_dump", + "description": "format from NCBI SRA", + "tool_shed_repository": "sra_tools", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0" + }, + { + "name": "Protein Database Downloader", + "id": "dbbuilder", + "description": "", + "tool_shed_repository": "dbbuilder", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.2" + }, + { + "name": "Download and Generate Pileup Format", + "id": "sra_pileup", + "description": "from NCBI SRA", + "tool_shed_repository": "sra_tools", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.10.3" + }, + { + "name": "Get species occurrences data", + "id": "spocc_occ", + "description": "from GBIF, ALA, iNAT and others", + "tool_shed_repository": "spocc_occ", + "panel_section_name": "Animal Detection on Acoustic Recordings", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/ecology/spocc_occ/spocc_occ/0.9.0" + }, + { + "name": "NCBI ESearch", + "id": "ncbi_eutils_esearch", + "description": "search NCBI Databases by text query", + "tool_shed_repository": "ncbi_eutils_esearch", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_esearch/ncbi_eutils_esearch/1.2" + }, + { + "name": "NCBI EGQuery", + "id": "ncbi_eutils_egquery", + "description": "Provides the number of records retrieved in all Entrez databases by a single text query.", + "tool_shed_repository": "ncbi_eutils_egquery", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_egquery/ncbi_eutils_egquery/1.2" + }, + { + "name": "NCBI ECitMatch", + "id": "ncbi_eutils_ecitmatch", + "description": "search NCBI for citations in PubMed", + "tool_shed_repository": "ncbi_eutils_ecitmatch", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_ecitmatch/ncbi_eutils_ecitmatch/1.2" + }, + { + "name": "NCBI EPost", + "id": "ncbi_eutils_epost", + "description": "post UIDs to NCBI History Server", + "tool_shed_repository": "ncbi_eutils_epost", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_epost/ncbi_eutils_epost/1.2" + }, + { + "name": "NCBI ELink", + "id": "ncbi_eutils_elink", + "description": "link UIDs from one database to another", + "tool_shed_repository": "ncbi_eutils_elink", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_elink/ncbi_eutils_elink/1.2" + }, + { + "name": "NCBI EInfo", + "id": "ncbi_eutils_einfo", + "description": "fetch NCBI database metadata", + "tool_shed_repository": "ncbi_eutils_einfo", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_einfo/ncbi_eutils_einfo/1.2" + }, + { + "name": "NCBI ESummary", + "id": "ncbi_eutils_esummary", + "description": "fetch summary of history/ids", + "tool_shed_repository": "ncbi_eutils_esummary", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_esummary/ncbi_eutils_esummary/1.2" + }, + { + "name": "NCBI EFetch", + "id": "ncbi_eutils_efetch", + "description": "fetch records from NCBI", + "tool_shed_repository": "ncbi_eutils_efetch", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_efetch/ncbi_eutils_efetch/1.2" + }, + { + "name": "UniProt", + "id": "uniprot", + "description": "ID mapping and retrieval", + "tool_shed_repository": "uniprot_rest_interface", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2" + }, + { + "name": "Get sequences by Ensembl ID", + "id": "get_sequences", + "description": "using REST API", + "tool_shed_repository": "ensembl_get_sequences", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_sequences/get_sequences/0.1.2" + }, + { + "name": "Get gene tree by Ensembl ID", + "id": "get_genetree", + "description": "using REST API", + "tool_shed_repository": "ensembl_get_genetree", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_genetree/get_genetree/0.1.2" + }, + { + "name": "Get features by Ensembl ID", + "id": "get_feature_info", + "description": "using REST API", + "tool_shed_repository": "ensembl_get_feature_info", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_feature_info/get_feature_info/0.1.2" + }, + { + "name": "Search ENA data", + "id": "enasearch_search_data", + "description": "given a query", + "tool_shed_repository": "enasearch_search_data", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/enasearch_search_data/enasearch_search_data/0.1.1.0" + }, + { + "name": "Retrieve ENA data", + "id": "enasearch_retrieve_data", + "description": "(other than taxon and project)", + "tool_shed_repository": "enasearch_retrieve_data", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_data/enasearch_retrieve_data/0.1.1.0" + }, + { + "name": "Retrieve ENA taxon data", + "id": "enasearch_retrieve_taxons", + "description": "", + "tool_shed_repository": "enasearch_retrieve_taxons", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_taxons/enasearch_retrieve_taxons/0.1.1.0" + }, + { + "name": "Retrieve an analysis report", + "id": "enasearch_retrieve_analysis_report", + "description": "", + "tool_shed_repository": "enasearch_retrieve_analysis_report", + "panel_section_name": "Get Data", + "help": "", + "guid": "toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_analysis_report/enasearch_retrieve_analysis_report/0.1.1.0" + }, + { + "name": "Retrieve a run report", + "id": "enasearch_retrieve_run_report", + "description": "", + "tool_shed_repository": "enasearch_retrieve_run_report", + 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