From 3932f9292a048d7d13778dc69ee15af080106a0b Mon Sep 17 00:00:00 2001 From: wuzekai <3025054974@qq.com> Date: Fri, 21 Aug 2026 10:38:49 +0800 Subject: [PATCH] =?UTF-8?q?feat:=20=E7=95=8C=E9=9D=A2=E6=B1=89=E5=8C=96=20?= =?UTF-8?q?+=20OMAP=20=E5=93=81=E7=89=8C=E5=8C=96=20+=20AI=20=E8=AF=BB?= =?UTF-8?q?=E5=8F=96=E5=8E=86=E5=8F=B2=E6=95=B0=E6=8D=AE=E9=9B=86=E8=83=BD?= =?UTF-8?q?=E5=8A=9B?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - 汉化 /chatgxy、/upload 等路由界面 - 前端/后端提示词 OMAP 品牌化 - AI 问答新增读取当前历史数据集的能力(list_history_datasets / read_history_dataset) - 新增 AI 读取历史数据设计文档 --- .gitignore | 6 + client/src/api/schema/schema.ts | 5 + client/src/components/AboutGalaxy.vue | 32 +- .../components/ActivityBar/ActivityItem.vue | 2 +- .../AvailableDatatypes/AvailableDatatypes.vue | 2 +- client/src/components/BaseComponents/GTip.vue | 2 +- client/src/components/ChatGXY.vue | 27 +- client/src/components/ChatGXY/ActionCard.vue | 2 +- 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.../components/admin/DisplayApplications.vue | 2 +- client/src/components/admin/JobsList.vue | 12 +- .../admin/Notifications/BroadcastsList.vue | 2 +- client/src/components/admin/SanitizeAllow.vue | 10 +- client/src/composables/agentActions.ts | 2 +- client/src/nls/locale.js | 279 ++++++++++++++++++ client/src/nls/zh/locale.js | 277 +++++++++++++++++ client/src/stores/activitySetup.ts | 4 +- docs/ai_reads_history_design.md | 231 +++++++++++++++ lib/galaxy/agents/base.py | 3 +- lib/galaxy/agents/error_analysis.py | 24 +- lib/galaxy/agents/orchestrator.py | 16 +- .../agents/prompts/custom_tool_structured.md | 92 +++--- lib/galaxy/agents/prompts/error_analysis.md | 36 +-- lib/galaxy/agents/prompts/orchestrator.md | 38 +-- lib/galaxy/agents/prompts/router.md | 118 ++++---- .../agents/prompts/tool_recommendation.md | 58 ++-- lib/galaxy/agents/router.py | 150 +++++++++- lib/galaxy/agents/tools.py | 30 +- lib/galaxy/config/sample/galaxy.yml.sample | 1 + lib/galaxy/managers/agents.py | 23 +- lib/galaxy/schema/schema.py | 5 + lib/galaxy/webapps/galaxy/api/chat.py | 3 + tools/data_export/export_remote.xml | 20 +- tools/data_source/genbank.xml | 4 +- tools/data_source/microbial_import.xml | 18 +- tools/data_source/ncbi_datasets.xml | 2 +- tools/data_source/upload.xml | 16 +- .../parse_values_from_file.xml | 6 +- tools/expression_tools/pick_value.xml | 24 +- tools/extract/extract_genomic_dna.xml | 10 +- tools/extract/liftOver_wrapper.xml | 14 +- tools/filters/CreateInterval.xml | 10 +- tools/filters/axt_to_concat_fasta.xml | 6 +- tools/filters/axt_to_fasta.xml | 6 +- tools/filters/axt_to_lav.xml | 6 +- tools/filters/bed2gff.xml | 2 +- tools/filters/bed_to_bigbed.xml | 10 +- tools/filters/catWrapper.xml | 4 +- tools/filters/changeCase.xml | 8 +- tools/filters/commWrapper.xml | 6 +- tools/filters/compare.xml | 10 +- tools/filters/condense_characters.xml | 4 +- tools/filters/convert_characters.xml | 8 +- tools/filters/cutWrapper.xml | 6 +- tools/filters/fileGrep.xml | 8 +- 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.../filters/ucsc_gene_table_to_intervals.xml | 2 +- tools/filters/uniq.xml | 8 +- tools/filters/wc_gnu.xml | 6 +- tools/filters/wig_to_bigwig.xml | 12 +- tools/filters/wiggle_to_simple.xml | 2 +- .../interactive/interactivetool_askomics.xml | 2 +- .../interactive/interactivetool_bam_iobio.xml | 2 +- .../interactivetool_blobtoolkit.xml | 2 +- .../interactivetool_cellxgene_0.16.2.xml | 2 +- .../interactivetool_cellxgene_1.1.1.xml | 10 +- .../interactivetool_climate_notebook.xml | 8 +- .../interactive/interactivetool_ethercalc.xml | 2 +- .../interactivetool_geoexplorer.xml | 2 +- .../interactivetool_hicbrowser.xml | 2 +- tools/interactive/interactivetool_higlass.xml | 34 +-- tools/interactive/interactivetool_ilastik.xml | 10 +- tools/interactive/interactivetool_isee.xml | 2 +- .../interactivetool_jupyter_notebook.xml | 8 +- ...interactivetool_jupyter_notebook_1.0.0.xml | 58 ++-- ...interactivetool_jupyter_notebook_1.0.1.xml | 58 ++-- ...interactivetool_jupyter_notebook_1.0.3.xml | 58 ++-- .../interactive/interactivetool_metashark.xml | 2 +- .../interactivetool_mgnify_notebook.xml | 12 +- .../interactivetool_ml_jupyter_notebook.xml | 60 ++-- tools/interactive/interactivetool_neo4j.xml | 2 +- .../interactivetool_openrefine.xml | 2 +- .../interactivetool_pangeo_notebook.xml | 8 +- tools/interactive/interactivetool_panoply.xml | 2 +- .../interactive/interactivetool_paraview.xml | 2 +- tools/interactive/interactivetool_pavian.xml | 2 +- tools/interactive/interactivetool_phinch.xml | 2 +- tools/interactive/interactivetool_pyiron.xml | 8 +- ...nteractivetool_qiskit_jupyter_notebook.xml | 66 ++--- tools/interactive/interactivetool_radiant.xml | 2 +- tools/interactive/interactivetool_rstudio.xml | 2 +- .../interactivetool_rstudio_bioc_3.20.xml | 6 +- .../interactivetool_simtext_app.xml | 4 +- .../interactive/interactivetool_vcf_iobio.xml | 2 +- .../interactivetool_vrm_editor.xml | 4 +- tools/interactive/interactivetool_wallace.xml | 2 +- tools/interactive/interactivetool_wilson.xml | 2 +- tools/maf/genebed_maf_to_fasta.xml | 14 +- tools/maf/interval2maf.xml | 16 +- tools/maf/interval2maf_pairwise.xml | 4 +- tools/maf/interval_maf_to_merged_fasta.xml | 14 +- tools/maf/maf_by_block_number.xml | 8 +- tools/maf/maf_filter.xml | 48 +-- tools/maf/maf_limit_size.xml | 6 +- tools/maf/maf_limit_to_species.xml | 8 +- tools/maf/maf_reverse_complement.xml | 4 +- tools/maf/maf_split_by_species.xml | 4 +- tools/maf/maf_stats.xml | 10 +- tools/maf/maf_thread_for_species.xml | 4 +- tools/maf/maf_to_bed.xml | 6 +- tools/maf/maf_to_fasta.xml | 10 +- tools/maf/maf_to_interval.xml | 8 +- tools/maf/vcf_to_maf_customtrack.xml | 10 +- tools/meme/meme.xml | 120 ++++---- tools/metag_tools/blat_wrapper.xml | 14 +- tools/metag_tools/shrimp_color_wrapper.xml | 40 +-- tools/metag_tools/shrimp_wrapper.xml | 44 +-- .../next_gen_conversion/fastq_conversions.xml | 8 +- tools/next_gen_conversion/fastq_gen_conv.xml | 8 +- tools/next_gen_conversion/solid2fastq.xml | 18 +- tools/next_gen_conversion/solid_to_fastq.xml | 14 +- tools/ngs_simulation/ngs_simulation.xml | 22 +- tools/phenotype_association/beam.xml | 8 +- tools/phenotype_association/gpass.xml | 4 +- tools/phenotype_association/ldtools.xml | 6 +- tools/phenotype_association/linkToDavid.xml | 6 +- .../phenotype_association/linkToGProfile.xml | 8 +- tools/phenotype_association/lps.xml | 48 +-- tools/phenotype_association/master2gd_snp.xml | 10 +- tools/phenotype_association/master2pg.xml | 4 +- tools/phenotype_association/pass.xml | 8 +- tools/phenotype_association/sift.xml | 20 +- tools/plotting/bar_chart.xml | 18 +- tools/plotting/boxplot.xml | 26 +- tools/solid_tools/maq_cs_wrapper.xml | 20 +- tools/solid_tools/solid_qual_boxplot.xml | 2 +- tools/solid_tools/solid_qual_stats.xml | 2 +- tools/sr_assembly/velvetg.xml | 52 ++-- tools/sr_assembly/velveth.xml | 10 +- tools/sr_mapping/PerM.xml | 62 ++-- tools/sr_mapping/bfast_wrapper.xml | 60 ++-- tools/sr_mapping/fastq_statistics.xml | 2 +- tools/sr_mapping/mosaik.xml | 28 +- tools/sr_mapping/srma_wrapper.xml | 26 +- .../aggregate_binned_scores_in_intervals.xml | 8 +- tools/stats/filtering.xml | 6 +- tools/stats/filtering_1_1_0.xml | 6 +- tools/stats/grouping.xml | 14 +- tools/stats/gsummary.xml | 4 +- 452 files changed, 3185 insertions(+), 2225 deletions(-) create mode 100644 docs/ai_reads_history_design.md diff --git a/.gitignore b/.gitignore index f65dcce..b8e1b3f 100644 --- a/.gitignore +++ b/.gitignore @@ -194,3 +194,9 @@ involucro .DS_Store *.rej *~ + +# build artifacts +client/dist_new/ + +# temporary scripts +client/src/translate_rare.py diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts index d4f3536..0c03531 100644 --- a/client/src/api/schema/schema.ts +++ b/client/src/api/schema/schema.ts @@ -8284,6 +8284,11 @@ export interface components { * @description The ID of an existing chat exchange to continue. */ exchange_id?: string | null; + /** + * History ID + * @description The (encoded) ID of the current history, used by the AI to read datasets for analysis. + */ + history_id?: string | null; /** * Query * @description The query to be sent to the chatbot. diff --git a/client/src/components/AboutGalaxy.vue b/client/src/components/AboutGalaxy.vue index 3e2a7b5..4d6c633 100644 --- a/client/src/components/AboutGalaxy.vue +++ b/client/src/components/AboutGalaxy.vue @@ -30,12 +30,12 @@ const versionUserDocumentationUrl = computed(() => {
{{ localize(tooltip) }} - No tooltip available for this item + 此项目没有可用的提示
diff --git a/client/src/components/Panels/Upload/methods/RuleBasedImportUpload.vue b/client/src/components/Panels/Upload/methods/RuleBasedImportUpload.vue index 1884b25..7492f42 100644 --- a/client/src/components/Panels/Upload/methods/RuleBasedImportUpload.vue +++ b/client/src/components/Panels/Upload/methods/RuleBasedImportUpload.vue @@ -12,6 +12,6 @@ onMounted(() => { diff --git a/client/src/components/Panels/Upload/shared/UploadTableBulkDbKeyHeader.vue b/client/src/components/Panels/Upload/shared/UploadTableBulkDbKeyHeader.vue index f1fe1c3..1cd9928 100644 --- a/client/src/components/Panels/Upload/shared/UploadTableBulkDbKeyHeader.vue +++ b/client/src/components/Panels/Upload/shared/UploadTableBulkDbKeyHeader.vue @@ -18,14 +18,14 @@ interface Props { const props = withDefaults(defineProps(), { disabled: false, - tooltip: "Set database key for all items", + tooltip: "为所有项目设置数据库键", }); const emit = defineEmits<{ (e: "input", value: string): void; }>(); -const optionsWithDefault = computed(() => [{ id: "", text: "Set all..." }, ...(props.dbKeys || [])]); +const optionsWithDefault = computed(() => [{ id: "", text: "全部设置…" }, ...(props.dbKeys || [])]); function onItemSelection(item: DbKey) { emit("input", item.id); @@ -34,7 +34,7 @@ function onItemSelection(item: DbKey) { diff --git a/client/src/components/SelectionDialog/SelectionDialog.vue b/client/src/components/SelectionDialog/SelectionDialog.vue index 0efd8fa..0b9234d 100644 --- a/client/src/components/SelectionDialog/SelectionDialog.vue +++ b/client/src/components/SelectionDialog/SelectionDialog.vue @@ -271,12 +271,12 @@ defineExpose({ No search results found for: {{ filter }}. -
No entries.
+
没有条目。
- Please wait... + 请稍候...
diff --git a/client/src/components/Tool/CustomToolEditor.vue b/client/src/components/Tool/CustomToolEditor.vue index 41c3d7c..fb836f1 100644 --- a/client/src/components/Tool/CustomToolEditor.vue +++ b/client/src/components/Tool/CustomToolEditor.vue @@ -199,7 +199,7 @@ async function generateViaLLM() { {{ errorMsg.err_msg }}
- Tool Editor + 工具编辑器 { - You have already provided credentials for this tool. You can update or delete + 您已为此工具提供了凭据。 You can update or delete your credentials using the {{ provideCredentialsButtonTitle }} button. diff --git a/client/src/components/Tool/ToolFooter.vue b/client/src/components/Tool/ToolFooter.vue index 3860d5d..e562439 100644 --- a/client/src/components/Tool/ToolFooter.vue +++ b/client/src/components/Tool/ToolFooter.vue @@ -32,7 +32,7 @@
- External links + 外部链接
-