From 47e21092488080d28288aeab5eebb2316e5aa891 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Wed, 10 Nov 2021 17:30:00 +0100 Subject: [PATCH 01/12] create dev branch --- package.json | 2 +- requirements.txt | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/package.json b/package.json index f2bddce..f801f2f 100644 --- a/package.json +++ b/package.json @@ -2,7 +2,7 @@ "name": "coral", "description": "Coral is a web-based cohort analysis tool to interactively create, refine, and analyze patient cohorts.", "homepage": "https://caleydo.org", - "version": "1.0.0", + "version": "1.0.1-SNAPSHOT", "author": { "name": "PatrickAdelberger", "email": "coral@caleydo.org", diff --git a/requirements.txt b/requirements.txt index 8c8b522..ae7a848 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,2 +1,2 @@ --e git+https://github.com/phovea/phovea_server.git@v7.2.0#egg=phovea_server --e git+https://github.com/datavisyn/tdp_core.git@v12.1.2#egg=tdp_core \ No newline at end of file +-e git+https://github.com/phovea/phovea_server.git@develop#egg=phovea_server +-e git+https://github.com/datavisyn/tdp_core.git@develop#egg=tdp_core \ No newline at end of file From bf2a1cc95ea6ff3cd91e115cd584765cdffdb565 Mon Sep 17 00:00:00 2001 From: Klaus Date: Wed, 10 Nov 2021 17:48:42 +0100 Subject: [PATCH 02/12] shorten tab title --- src/app.template.ejs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/app.template.ejs b/src/app.template.ejs index 9b45234..d968868 100644 --- a/src/app.template.ejs +++ b/src/app.template.ejs @@ -5,7 +5,7 @@ - Coral • Interactive Cohort Analysis + Coral From 53bfac0f4e47961607e5e5abf8504b14290394aa Mon Sep 17 00:00:00 2001 From: Klaus Date: Fri, 12 Nov 2021 09:13:50 +0100 Subject: [PATCH 03/12] Update paper reference --- README.md | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 32ce965..5de6b9c 100644 --- a/README.md +++ b/README.md @@ -13,11 +13,12 @@ Coral can be utilized to explore any type of cohort and sample set. Our focus, h ![screenshot](media/screenshot.full.png?raw=true "Screenshot") +The application welcomes you with an overview of Coral and its features. -Learn more about Coral by reading the [preprint](https://jku-vds-lab.at/publications/2021_preprint_coral/) and its supplemental material with two cancer genomics case studies. +Learn more about Coral by reading the [paper](https://jku-vds-lab.at/publications/2021_bioinformatics_coral/) and its supplemental material with two cancer genomics case studies. For a quick overview of Coral, see our preview video: -[](https://www.youtube.com/watch?v=eaYfPnrufyY) +[](https://www.youtube.com/watch?v=vSd3a9J63wQ) Feedback ------------ @@ -26,7 +27,7 @@ Your comments and feedback are welcome. Write an email to coral@caleydo.org and If you have discovered an issue or have a feature suggestion, feel free to [create an issue on GitHub](https://github.com/Caleydo/coral/issues). Future versions of Coral are planned in the milestones of the Github issue tracker. You can use the milestones to see what's currently planned for future releases. -Past releases and changelogs are available at https://github.com/Caleydo/coral/releases +Past releases and changelogs are available at https://github.com/Caleydo/coral/releases. Installation @@ -41,12 +42,17 @@ Please refer to [the product repository](https://github.com/Caleydo/coral_produc Citing Coral ------------ +Patrick Adelberger, Klaus Eckelt, Markus J. Bauer, Marc Streit, Christian Haslinger, Thomas Zichner +**Coral: a web-based visual analysis tool for creating and characterizing cohorts** +Bioinformatics, doi:10.1093/bioinformatics/btab695, 2021. + ``` -@article{2021_preprint_coral, +@article{2021_bioinformatics_coral, title = {Coral: a web-based visual analysis tool for creating and characterizing cohorts}, author = {Patrick Adelberger and Klaus Eckelt and Markus J. Bauer and Marc Streit and Christian Haslinger and Thomas Zichner}, - journal = {bioRxiv}, - doi = {10.1101/2021.05.26.445802}, + journal = {Bioinformatics}, + publisher = {Oxford University Press}, + doi = {10.1093/bioinformatics/btab695}, year = {2021} } ``` From 41fd0376602b794e09cdae02c43c5a7e4364e9ac Mon Sep 17 00:00:00 2001 From: Klaus Date: Fri, 12 Nov 2021 09:16:03 +0100 Subject: [PATCH 04/12] fix daily dev url --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5de6b9c..d2f2f4e 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,7 @@ Installation Coral is based on the [Target Discovery Platform](https://github.com/datavisyn/tdp_core) and uses the [Phovea Server](https://github.com/phovea/phovea_server) to run the backend and multiple other Phovea plugins. -The [Coral Product repository](https://github.com/Caleydo/coral_product) describes all parts needed to set up a a running instance of Coral and is used to deploy the [stable](https://coral.caleydoapp.org/) and [daily development]((https://coral-daily.caleydoapp.org/)) builds. +The [Coral Product repository](https://github.com/Caleydo/coral_product) describes all parts needed to set up a a running instance of Coral and is used to deploy the [stable](https://coral.caleydoapp.org/) and [daily development](https://coral-daily.caleydoapp.org/) builds. Please refer to [the product repository](https://github.com/Caleydo/coral_product) for setup instructions. From f5492169174832fe0f615ccc96f68d2ca7106361 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Thu, 18 Nov 2021 09:17:53 +0100 Subject: [PATCH 05/12] update package.json --- package.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/package.json b/package.json index f801f2f..8d1e93a 100644 --- a/package.json +++ b/package.json @@ -97,9 +97,9 @@ "react-dom": "^16.13.0", "react-router-dom": "^5.2.0", "split-grid": "^1.0.9", - "tdp_publicdb": "github:caleydo/tdp_publicdb#keckelt/rem_dTiles_python_3.7", + "tdp_publicdb": "github:caleydo/tdp_publicdb#visyn_rem_dTiles_python", "tippy.js": "^6.2.6", - "tourdino": "github:caleydo/tourdino#keckelt/vega_boxplot", + "tourdino": "github:caleydo/tourdino#visyn_vega_boxplot", "vega": "~5.20.0", "vega-embed": "6.19.1", "vega-functions": "5.12.0", From bbb36eaefe7ca8216eddf7bb979cfaf862fafaa7 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Thu, 18 Nov 2021 09:17:57 +0100 Subject: [PATCH 06/12] update imports --- .yo-rc.json | 3 +-- dist/Cohort.d.ts | 2 +- dist/Cohort.js | 2 +- dist/Cohort.js.map | 2 +- dist/CohortInterfaces.d.ts | 2 +- dist/Overview/CohortOverview.d.ts | 2 +- dist/Overview/CohortOverview.js | 2 +- dist/Overview/CohortOverview.js.map | 2 +- dist/Provenance/CohortEV.d.ts | 6 +++--- dist/Provenance/CohortEV.js | 2 +- dist/Provenance/CohortEV.js.map | 2 +- dist/Provenance/General.d.ts | 4 ++-- dist/Provenance/General.js | 2 +- dist/Provenance/General.js.map | 2 +- dist/app.d.ts | 4 ++-- dist/app.js | 4 ++-- dist/app.js.map | 2 +- dist/app.template.ejs | 2 +- dist/cohortview.d.ts | 2 +- dist/menu/DatasetCard.js | 2 +- dist/menu/DatasetCard.js.map | 2 +- dist/pages/components/SourceCodeCard.js | 2 +- dist/pages/components/SourceCodeCard.js.map | 2 +- dist/phovea.d.ts | 2 +- dist/phovea.js | 4 ++-- dist/phovea.js.map | 2 +- dist/rest.js | 2 +- dist/rest.js.map | 2 +- jest.config.js | 2 +- phovea_registry.js | 6 +++--- src/Cohort.ts | 2 +- src/CohortInterfaces.ts | 2 +- src/Overview/CohortOverview.ts | 2 +- src/Provenance/CohortEV.ts | 2 +- src/Provenance/General.ts | 2 +- src/app.ts | 6 +++--- src/cohortview.ts | 2 +- src/menu/DatasetCard.tsx | 2 +- src/pages/components/SourceCodeCard.tsx | 2 +- src/phovea.ts | 4 ++-- src/rest.ts | 2 +- 41 files changed, 52 insertions(+), 53 deletions(-) diff --git a/.yo-rc.json b/.yo-rc.json index 7259dc3..50c937a 100644 --- a/.yo-rc.json +++ b/.yo-rc.json @@ -2,8 +2,7 @@ "generator-phovea": { "type": "app-slib", "modules": [ - "phovea_core", - "phovea_ui", + "tdp_core", "phovea_server" ], "vendors": { diff --git a/dist/Cohort.d.ts b/dist/Cohort.d.ts index 91d8596..d7bef54 100644 --- a/dist/Cohort.d.ts +++ b/dist/Cohort.d.ts @@ -1,4 +1,4 @@ -import { IDType, IDTypeLike } from 'phovea_core'; +import { IDType, IDTypeLike } from 'tdp_core'; import { IAllFilters, IRow, IServerColumn } from 'tdp_core'; import { ICohort, ICohortRep, IElement, IElementProvJSONCohort, IProvAttrAndValuesCohort } from './CohortInterfaces'; import { ICohortDepletionScoreFilterParams, ICohortEqualsFilterParams, ICohortGeneEqualsFilterParams, ICohortGeneNumFilterParams, ICohortNumFilterParams, ICohortPanelAnnotationFilterParams, ICohortRow, IEqualsList, INumRange } from './rest'; diff --git a/dist/Cohort.js b/dist/Cohort.js index c378772..793dd0b 100644 --- a/dist/Cohort.js +++ b/dist/Cohort.js @@ -1,5 +1,5 @@ import { format } from 'd3-format'; -import { IDTypeManager, UniqueIdManager } from 'phovea_core'; +import { IDTypeManager, UniqueIdManager } from 'tdp_core'; import { ElementProvType } from './CohortInterfaces'; import { createDBCohort, createDBCohortWithDepletionScoreFilter, createDBCohortWithEqualsFilter, createDBCohortWithGeneEqualsFilter, createDBCohortWithGeneNumFilter, createDBCohortWithNumFilter, createDBCohortWithPanelAnnotationFilter, createDBCohortWithTreatmentFilter, dataDBCohortDepletionScoreFilter, dataDBCohortGeneWithEqualsFilter, dataDBCohortGeneWithNumFilter, dataDBCohortPanelAnnotationFilter, dataDBCohortWithEqualsFilter, dataDBCohortWithNumFilter, getCohortData, getCohortSize, sizeDBCohortDepletionScoreFilter, sizeDBCohortGeneWithEqualsFilter, sizeDBCohortGeneWithNumFilter, sizeDBCohortPanelAnnotationFilter, sizeDBCohortWithEqualsFilter, sizeDBCohortWithNumFilter, updateCohortName, valueListDelimiter } from './rest'; import { mergeTwoAllFilters } from './Tasks'; diff --git a/dist/Cohort.js.map b/dist/Cohort.js.map index 50986d3..7aeeeb1 100644 --- a/dist/Cohort.js.map +++ b/dist/Cohort.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/CohortInterfaces.d.ts b/dist/CohortInterfaces.d.ts index 3de6b61..051bcbc 100644 --- a/dist/CohortInterfaces.d.ts +++ b/dist/CohortInterfaces.d.ts @@ -1,4 +1,4 @@ -import { IDType } from 'phovea_core'; +import { IDType } from 'tdp_core'; import { IServerColumn } from 'tdp_core'; import { Cohort } from './Cohort'; import { IAttribute, IAttributeJSON } from './data/Attribute'; diff --git a/dist/Overview/CohortOverview.d.ts b/dist/Overview/CohortOverview.d.ts index 591e423..da764d1 100644 --- a/dist/Overview/CohortOverview.d.ts +++ b/dist/Overview/CohortOverview.d.ts @@ -1,4 +1,4 @@ -import { IObjectRef, ProvenanceGraph } from 'phovea_core'; +import { IObjectRef, ProvenanceGraph } from 'tdp_core'; import { IDatabaseViewDesc } from 'tdp_core'; import { CohortApp } from '../app'; import { Cohort } from '../Cohort'; diff --git a/dist/Overview/CohortOverview.js b/dist/Overview/CohortOverview.js index 41ebf44..ab343d0 100644 --- a/dist/Overview/CohortOverview.js +++ b/dist/Overview/CohortOverview.js @@ -1,4 +1,4 @@ -import { ObjectRefUtils, UniqueIdManager } from 'phovea_core'; +import { ObjectRefUtils, UniqueIdManager } from 'tdp_core'; import tippy from 'tippy.js'; import { Cohort, createCohortFromDB } from '../Cohort'; import { ElementProvType, TaskType } from '../CohortInterfaces'; diff --git a/dist/Overview/CohortOverview.js.map b/dist/Overview/CohortOverview.js.map index 90d5f94..546f022 100644 --- a/dist/Overview/CohortOverview.js.map +++ b/dist/Overview/CohortOverview.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Provenance/CohortEV.d.ts b/dist/Provenance/CohortEV.d.ts index 41e9a68..be139cd 100644 --- a/dist/Provenance/CohortEV.d.ts +++ b/dist/Provenance/CohortEV.d.ts @@ -1,11 +1,11 @@ -import { ICmdResult, IObjectRef } from 'phovea_core'; +import { ICmdResult, IObjectRef } from 'tdp_core'; import { CohortApp } from '../app'; import { IElementProvJSON } from '../CohortInterfaces'; import { CohortOverview } from '../Overview/CohortOverview'; /*********************************************** ----- Cohort Evolution View (CohortEV) -------- ************************************************/ -export declare function addOverviewCohortAction(provider: IObjectRef, providerApp: IObjectRef, newDataset: IElementProvJSON[], oldDataset: IElementProvJSON[]): import("phovea_core").IAction; +export declare function addOverviewCohortAction(provider: IObjectRef, providerApp: IObjectRef, newDataset: IElementProvJSON[], oldDataset: IElementProvJSON[]): import("tdp_core").IAction; export declare function addOverviewCohortImpl(inputs: IObjectRef[], parameter: any): Promise; -export declare function removeOverviewCohortAction(provider: IObjectRef, providerApp: IObjectRef, newDataset: IElementProvJSON[], oldDataset: IElementProvJSON[]): import("phovea_core").IAction; +export declare function removeOverviewCohortAction(provider: IObjectRef, providerApp: IObjectRef, newDataset: IElementProvJSON[], oldDataset: IElementProvJSON[]): import("tdp_core").IAction; export declare function removeOverviewCohortImpl(inputs: IObjectRef[], parameter: any): Promise; diff --git a/dist/Provenance/CohortEV.js b/dist/Provenance/CohortEV.js index 03f658b..ad7e00e 100644 --- a/dist/Provenance/CohortEV.js +++ b/dist/Provenance/CohortEV.js @@ -1,4 +1,4 @@ -import { ActionMetaData, ActionUtils, ObjectRefUtils } from 'phovea_core'; +import { ActionMetaData, ActionUtils, ObjectRefUtils } from 'tdp_core'; import { log } from '../util'; /*********************************************** ----- Cohort Evolution View (CohortEV) -------- diff --git a/dist/Provenance/CohortEV.js.map b/dist/Provenance/CohortEV.js.map index 8d326e1..d8ea781 100644 --- a/dist/Provenance/CohortEV.js.map +++ b/dist/Provenance/CohortEV.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/Provenance/General.d.ts b/dist/Provenance/General.d.ts index 0154bce..973b03b 100644 --- a/dist/Provenance/General.d.ts +++ b/dist/Provenance/General.d.ts @@ -1,11 +1,11 @@ -import { ICmdResult, IObjectRef } from 'phovea_core'; +import { ICmdResult, IObjectRef } from 'tdp_core'; import { CohortApp } from '../app'; import { IElementProvJSON, IElementProvJSONCohort } from '../CohortInterfaces'; import { IEntitySourceConfig } from '../utilIdTypes'; /****************************** ---------- GENERAL ---------- *******************************/ -export declare function setDatasetAction(provider: IObjectRef, newDataset: IDatasetDesc, oldDataset: IDatasetDesc): import("phovea_core").IAction; +export declare function setDatasetAction(provider: IObjectRef, newDataset: IDatasetDesc, oldDataset: IDatasetDesc): import("tdp_core").IAction; export declare function setDatasetImpl(inputs: IObjectRef[], parameter: any): Promise; export interface IPanelDesc { id: string; diff --git a/dist/Provenance/General.js b/dist/Provenance/General.js index 8301602..cc339b6 100644 --- a/dist/Provenance/General.js +++ b/dist/Provenance/General.js @@ -1,4 +1,4 @@ -import { ActionMetaData, ActionUtils, ObjectRefUtils } from 'phovea_core'; +import { ActionMetaData, ActionUtils, ObjectRefUtils } from 'tdp_core'; import { log } from '../util'; /****************************** ---------- GENERAL ---------- diff --git a/dist/Provenance/General.js.map b/dist/Provenance/General.js.map index 15585c3..adb8636 100644 --- a/dist/Provenance/General.js.map +++ b/dist/Provenance/General.js.map @@ -1 +1 @@ -{"version":3,"file":"General.js","sourceRoot":"","sources":["../../src/Provenance/General.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,cAAc,EAAE,WAAW,EAA0B,cAAc,EAAC,MAAM,aAAa,CAAC;AAGhG,OAAO,EAAC,GAAG,EAAC,MAAM,SAAS,CAAC;AAI5B;;gCAEgC;AAEhC,+BAA+B;AAC/B,+BAA+B;AAC/B,+BAA+B;AAC/B,MAAM,UAAU,gBAAgB,CAAC,QAA+B,EAAE,UAAwB,EAAE,UAAwB;IAClH,GAAG,CAAC,KAAK,CAAC,0BAA0B,CAAC,CAAC;IACtC,OAAO,WAAW,CAAC,MAAM,CAAC,cAAc,CAAC,UAAU,CAAC,gBAAgB,EAAE,cAAc,CAAC,QAAQ,CAAC,IAAI,EAAE,cAAc,CAAC,SAAS,CAAC,MAAM,CAAC,EAAE,eAAe,EAAE,cAAc,EAAE,CAAC,QAAQ,CAAC,EAAE;QACjL,UAAU;QACV,UAAU;KACX,CAAC,CAAC;AACL,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,cAAc,CAAC,MAA+B,EAAE,SAAc;IAClF,GAAG,CAAC,KAAK,CAAC,iBAAiB,EAAE,SAAS,CAAC,UAAU,EAAE,SAAS,CAAC,UAAU,CAAC,CAAC;IACzE,MAAM,GAAG,GAAc,MAAM,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IACzC,MAAM,GAAG,CAAC,UAAU,CAAC,SAAS,CAAC,UAAU,CAAC,CAAC;IAC3C,OAAO;QACL,OAAO,EAAE,gBAAgB,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,SAAS,CAAC,UAAU,EAAE,SAAS,CAAC,UAAU,CAAC;KACjF,CAAC;AACJ,CAAC"} \ No newline at end of file +{"version":3,"file":"General.js","sourceRoot":"","sources":["../../src/Provenance/General.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,cAAc,EAAE,WAAW,EAA0B,cAAc,EAAC,MAAM,UAAU,CAAC;AAG7F,OAAO,EAAC,GAAG,EAAC,MAAM,SAAS,CAAC;AAI5B;;gCAEgC;AAEhC,+BAA+B;AAC/B,+BAA+B;AAC/B,+BAA+B;AAC/B,MAAM,UAAU,gBAAgB,CAAC,QAA+B,EAAE,UAAwB,EAAE,UAAwB;IAClH,GAAG,CAAC,KAAK,CAAC,0BAA0B,CAAC,CAAC;IACtC,OAAO,WAAW,CAAC,MAAM,CAAC,cAAc,CAAC,UAAU,CAAC,gBAAgB,EAAE,cAAc,CAAC,QAAQ,CAAC,IAAI,EAAE,cAAc,CAAC,SAAS,CAAC,MAAM,CAAC,EAAE,eAAe,EAAE,cAAc,EAAE,CAAC,QAAQ,CAAC,EAAE;QACjL,UAAU;QACV,UAAU;KACX,CAAC,CAAC;AACL,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,cAAc,CAAC,MAA+B,EAAE,SAAc;IAClF,GAAG,CAAC,KAAK,CAAC,iBAAiB,EAAE,SAAS,CAAC,UAAU,EAAE,SAAS,CAAC,UAAU,CAAC,CAAC;IACzE,MAAM,GAAG,GAAc,MAAM,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IACzC,MAAM,GAAG,CAAC,UAAU,CAAC,SAAS,CAAC,UAAU,CAAC,CAAC;IAC3C,OAAO;QACL,OAAO,EAAE,gBAAgB,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,SAAS,CAAC,UAAU,EAAE,SAAS,CAAC,UAAU,CAAC;KACjF,CAAC;AACJ,CAAC"} \ No newline at end of file diff --git a/dist/app.d.ts b/dist/app.d.ts index 42f64e5..8012e2e 100644 --- a/dist/app.d.ts +++ b/dist/app.d.ts @@ -1,5 +1,5 @@ -import { CLUEGraphManager } from 'phovea_clue'; -import { IObjectRef, ProvenanceGraph } from 'phovea_core'; +import { CLUEGraphManager } from 'tdp_core'; +import { IObjectRef, ProvenanceGraph } from 'tdp_core'; import { ATDPApplication } from 'tdp_core'; import { Cohort } from './Cohort'; import { IElementProvJSON, IElementProvJSONCohort } from './CohortInterfaces'; diff --git a/dist/app.js b/dist/app.js index 7f6ceb7..f04f9d6 100644 --- a/dist/app.js +++ b/dist/app.js @@ -1,6 +1,6 @@ import { select } from 'd3-selection'; -import { AppContext, ObjectRefUtils } from 'phovea_core'; -import { AppMetaDataUtils } from 'phovea_ui'; +import { AppContext, ObjectRefUtils } from 'tdp_core'; +import { AppMetaDataUtils } from 'tdp_core'; import SplitGrid from 'split-grid'; import { ATDPApplication, NotificationHandler, RestBaseUtils } from 'tdp_core'; import { cellline, tissue } from 'tdp_publicdb'; diff --git a/dist/app.js.map b/dist/app.js.map index 7ae664a..0577414 100644 --- a/dist/app.js.map +++ b/dist/app.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/app.template.ejs b/dist/app.template.ejs index 9b45234..d968868 100644 --- a/dist/app.template.ejs +++ b/dist/app.template.ejs @@ -5,7 +5,7 @@ - Coral • Interactive Cohort Analysis + Coral diff --git a/dist/cohortview.d.ts b/dist/cohortview.d.ts index 8c1e966..97da4c1 100644 --- a/dist/cohortview.d.ts +++ b/dist/cohortview.d.ts @@ -1,4 +1,4 @@ -import { IObjectRef, ProvenanceGraph } from 'phovea_core'; +import { IObjectRef, ProvenanceGraph } from 'tdp_core'; import { IDatabaseViewDesc } from 'tdp_core'; import { CohortApp } from './app'; import { Cohort } from './Cohort'; diff --git a/dist/menu/DatasetCard.js b/dist/menu/DatasetCard.js index 74db991..f0c2a8a 100644 --- a/dist/menu/DatasetCard.js +++ b/dist/menu/DatasetCard.js @@ -1,7 +1,7 @@ import React from 'react'; import { ENamedSetType, RestBaseUtils, RestStorageUtils, StoreUtils } from 'tdp_core'; import { NamedSetList, useAsync, OrdinoContext } from 'ordino'; -import { UserSession, UniqueIdManager, I18nextManager, IDTypeManager } from 'phovea_core'; +import { UserSession, UniqueIdManager, I18nextManager, IDTypeManager } from 'tdp_core'; import { DatasetSearchBox } from './DatasetSearchBox'; import { Species, SpeciesUtils } from 'tdp_gene'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }) { diff --git a/dist/menu/DatasetCard.js.map b/dist/menu/DatasetCard.js.map index 2acaf8e..9ab2687 100644 --- a/dist/menu/DatasetCard.js.map +++ b/dist/menu/DatasetCard.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/pages/components/SourceCodeCard.js b/dist/pages/components/SourceCodeCard.js index b407ab1..65d8dfb 100644 --- a/dist/pages/components/SourceCodeCard.js +++ b/dist/pages/components/SourceCodeCard.js @@ -1,5 +1,5 @@ import { useAsync } from 'ordino'; -import { AppMetaDataUtils } from 'phovea_ui'; +import { AppMetaDataUtils } from 'tdp_core'; import React from 'react'; export function SourceCodeCard() { const loadMetaData = React.useMemo(() => () => AppMetaDataUtils.getMetaData(), []); diff --git a/dist/pages/components/SourceCodeCard.js.map b/dist/pages/components/SourceCodeCard.js.map index f714875..0e5587d 100644 --- a/dist/pages/components/SourceCodeCard.js.map +++ b/dist/pages/components/SourceCodeCard.js.map @@ -1 +1 @@ -{"version":3,"file":"SourceCodeCard.js","sourceRoot":"","sources":["../../../src/pages/components/SourceCodeCard.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAC,QAAQ,EAAC,MAAM,QAAQ,CAAC;AAChC,OAAO,EAAC,gBAAgB,EAAC,MAAM,WAAW,CAAC;AAC3C,OAAO,KAAK,MAAM,OAAO,CAAC;AAE1B,MAAM,UAAU,cAAc;IAC5B,MAAM,YAAY,GAAG,KAAK,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,CAAC,gBAAgB,CAAC,WAAW,EAAE,EAAE,EAAE,CAAC,CAAC;IACnF,MAAM,EAAC,MAAM,EAAE,KAAK,EAAC,GAAG,QAAQ,CAAC,YAAY,CAAC,CAAC;IAE/C,OAAO,CACL;QACE,6BAAK,SAAS,EAAC,oBAAoB;YACjC,6BAAK,SAAS,EAAC,WAAW;gBACxB,2BAAG,SAAS,EAAC,WAAW;;oBACkB,2BAAG,IAAI,EAAC,kCAAkC,EAAC,MAAM,EAAC,QAAQ,EAAC,GAAG,EAAC,UAAU,aAAW;wBAC1H;gBACJ,2BAAG,SAAS,EAAC,WAAW,4NAKpB;gBACJ,2BAAG,SAAS,EAAC,WAAW;oBAAC,2CAAgB;;oBAAE,CAAC,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,8BAA8B,CAAK,CACnH,CACF,CACL,CACJ,CAAC;AACJ,CAAC"} \ No newline at end of file +{"version":3,"file":"SourceCodeCard.js","sourceRoot":"","sources":["../../../src/pages/components/SourceCodeCard.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAC,QAAQ,EAAC,MAAM,QAAQ,CAAC;AAChC,OAAO,EAAC,gBAAgB,EAAC,MAAM,UAAU,CAAC;AAC1C,OAAO,KAAK,MAAM,OAAO,CAAC;AAE1B,MAAM,UAAU,cAAc;IAC5B,MAAM,YAAY,GAAG,KAAK,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,CAAC,gBAAgB,CAAC,WAAW,EAAE,EAAE,EAAE,CAAC,CAAC;IACnF,MAAM,EAAC,MAAM,EAAE,KAAK,EAAC,GAAG,QAAQ,CAAC,YAAY,CAAC,CAAC;IAE/C,OAAO,CACL;QACE,6BAAK,SAAS,EAAC,oBAAoB;YACjC,6BAAK,SAAS,EAAC,WAAW;gBACxB,2BAAG,SAAS,EAAC,WAAW;;oBACkB,2BAAG,IAAI,EAAC,kCAAkC,EAAC,MAAM,EAAC,QAAQ,EAAC,GAAG,EAAC,UAAU,aAAW;wBAC1H;gBACJ,2BAAG,SAAS,EAAC,WAAW,4NAKpB;gBACJ,2BAAG,SAAS,EAAC,WAAW;oBAAC,2CAAgB;;oBAAE,CAAC,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,8BAA8B,CAAK,CACnH,CACF,CACL,CACJ,CAAC;AACJ,CAAC"} \ No newline at end of file diff --git a/dist/phovea.d.ts b/dist/phovea.d.ts index 8f747c9..bd2c133 100644 --- a/dist/phovea.d.ts +++ b/dist/phovea.d.ts @@ -1,2 +1,2 @@ -import { IRegistry } from 'phovea_core'; +import { IRegistry } from 'tdp_core'; export default function (registry: IRegistry): void; diff --git a/dist/phovea.js b/dist/phovea.js index 68974fc..b74f722 100644 --- a/dist/phovea.js +++ b/dist/phovea.js @@ -3,9 +3,9 @@ * Copyright (c) The Caleydo Team. All rights reserved. * Licensed under the new BSD license, available at http://caleydo.org/license **************************************************************************** */ -import { PluginRegistry } from 'phovea_core'; +import { PluginRegistry } from 'tdp_core'; import { EP_ORDINO_HEADER_MENU, EP_ORDINO_FOOTER_MENU, EP_ORDINO_START_MENU_TAB, EP_ORDINO_LOGO, EStartMenuSection, EP_ORDINO_START_MENU_TAB_SHORTCUT } from 'ordino'; -import { EXTENSION_POINT_CUSTOMIZED_LOGIN_FORM } from 'phovea_security_flask'; +import { EXTENSION_POINT_CUSTOMIZED_LOGIN_FORM } from 'tdp_core'; export default function (registry) { // Coral's custom login form registry.push(EXTENSION_POINT_CUSTOMIZED_LOGIN_FORM, 'tdpBioinfoLoginForm', () => import('./LoginDialog'), {}); diff --git a/dist/phovea.js.map b/dist/phovea.js.map index c97c031..1356d89 100644 --- a/dist/phovea.js.map +++ b/dist/phovea.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/rest.js b/dist/rest.js index 0e3605f..7fa2840 100644 --- a/dist/rest.js +++ b/dist/rest.js @@ -1,4 +1,4 @@ -import { Ajax, AppContext } from 'phovea_core'; +import { Ajax, AppContext } from 'tdp_core'; import { deepCopy, log } from './util'; export const valueListDelimiter = '⸱'; /** diff --git a/dist/rest.js.map b/dist/rest.js.map index d3ea3d4..54a0f17 100644 --- a/dist/rest.js.map +++ b/dist/rest.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/jest.config.js b/jest.config.js index 42948de..69f1c97 100644 --- a/jest.config.js +++ b/jest.config.js @@ -12,7 +12,7 @@ if(pluginsToTransform.length > 0) { } /** - * TODO check if we can process inline webpack loaders (e.g. as found in https://github.com/phovea/phovea_ui/blob/master/src/_bootstrap.ts) + * TODO check if we can process inline webpack loaders (e.g. as found in https://github.com/datavisyn/tdp_core/blob/develop/src/webpack/_bootstrap.ts) * see also https://jestjs.io/docs/en/webpack#mocking-css-modules */ module.exports = { diff --git a/phovea_registry.js b/phovea_registry.js index 2a0a553..187ed92 100644 --- a/phovea_registry.js +++ b/phovea_registry.js @@ -4,14 +4,14 @@ * Licensed under the new BSD license, available at http://caleydo.org/license **************************************************************************** */ -import {PluginRegistry} from 'phovea_core'; +import {PluginRegistry} from 'tdp_core'; import reg from './dist/phovea'; /** * build a registry by registering all phovea modules */ //other modules -import 'phovea_core/phovea_registry.js'; -import 'phovea_ui/phovea_registry.js'; +import 'tdp_core/phovea_registry.js'; +import 'tdp_core/phovea_registry.js'; //self PluginRegistry.getInstance().register('coral', reg); diff --git a/src/Cohort.ts b/src/Cohort.ts index 25a7000..662abc8 100644 --- a/src/Cohort.ts +++ b/src/Cohort.ts @@ -1,5 +1,5 @@ import {format} from 'd3-format'; -import {IDType, IDTypeLike, IDTypeManager, UniqueIdManager} from 'phovea_core'; +import {IDType, IDTypeLike, IDTypeManager, UniqueIdManager} from 'tdp_core'; import {IAllFilters, IRow, IServerColumn} from 'tdp_core'; import {ElementProvType, ICohort, ICohortRep, IElement, IElementProvJSONCohort, IProvAttrAndValuesCohort} from './CohortInterfaces'; import {createDBCohort, createDBCohortWithDepletionScoreFilter, createDBCohortWithEqualsFilter, createDBCohortWithGeneEqualsFilter, createDBCohortWithGeneNumFilter, createDBCohortWithNumFilter, createDBCohortWithPanelAnnotationFilter, createDBCohortWithTreatmentFilter, dataDBCohortDepletionScoreFilter, dataDBCohortGeneWithEqualsFilter, dataDBCohortGeneWithNumFilter, dataDBCohortPanelAnnotationFilter, dataDBCohortWithEqualsFilter, dataDBCohortWithNumFilter, getCohortData, getCohortSize, ICohortDBDataParams, ICohortDBParams, ICohortDBSizeParams, ICohortDBWithDepletionScoreFilterParams, ICohortDBWithEqualsFilterParams, ICohortDBWithGeneEqualsFilterParams, ICohortDBWithGeneNumFilterParams, ICohortDBWithNumFilterParams, ICohortDBWithPanelAnnotationFilterParams, ICohortDBWithTreatmentFilterParams, ICohortDepletionScoreFilterParams, ICohortEqualsFilterParams, ICohortGeneEqualsFilterParams, ICohortGeneNumFilterParams, ICohortNumFilterParams, ICohortPanelAnnotationFilterParams, ICohortRow, IEqualsList, INumRange, sizeDBCohortDepletionScoreFilter, sizeDBCohortGeneWithEqualsFilter, sizeDBCohortGeneWithNumFilter, sizeDBCohortPanelAnnotationFilter, sizeDBCohortWithEqualsFilter, sizeDBCohortWithNumFilter, updateCohortName, valueListDelimiter} from './rest'; diff --git a/src/CohortInterfaces.ts b/src/CohortInterfaces.ts index 8353fb6..dec4c83 100644 --- a/src/CohortInterfaces.ts +++ b/src/CohortInterfaces.ts @@ -1,4 +1,4 @@ -import {IDType} from 'phovea_core'; +import {IDType} from 'tdp_core'; import {IServerColumn} from 'tdp_core'; import {Cohort} from './Cohort'; import {IAttribute, IAttributeJSON} from './data/Attribute'; diff --git a/src/Overview/CohortOverview.ts b/src/Overview/CohortOverview.ts index 9aaa23c..032b3b0 100644 --- a/src/Overview/CohortOverview.ts +++ b/src/Overview/CohortOverview.ts @@ -1,4 +1,4 @@ -import {IObjectRef, ObjectRefUtils, ProvenanceGraph, UniqueIdManager} from 'phovea_core'; +import {IObjectRef, ObjectRefUtils, ProvenanceGraph, UniqueIdManager} from 'tdp_core'; import {IDatabaseViewDesc} from 'tdp_core'; import tippy from 'tippy.js'; import {CohortApp} from '../app'; diff --git a/src/Provenance/CohortEV.ts b/src/Provenance/CohortEV.ts index 7e733ef..49cdb84 100644 --- a/src/Provenance/CohortEV.ts +++ b/src/Provenance/CohortEV.ts @@ -1,4 +1,4 @@ -import {ActionMetaData, ActionUtils, ICmdResult, IObjectRef, ObjectRefUtils} from 'phovea_core'; +import {ActionMetaData, ActionUtils, ICmdResult, IObjectRef, ObjectRefUtils} from 'tdp_core'; import {CohortApp} from '../app'; import {IElementProvJSON} from '../CohortInterfaces'; import {CohortOverview} from '../Overview/CohortOverview'; diff --git a/src/Provenance/General.ts b/src/Provenance/General.ts index c195c10..a2af63a 100644 --- a/src/Provenance/General.ts +++ b/src/Provenance/General.ts @@ -1,4 +1,4 @@ -import {ActionMetaData, ActionUtils, ICmdResult, IObjectRef, ObjectRefUtils} from 'phovea_core'; +import {ActionMetaData, ActionUtils, ICmdResult, IObjectRef, ObjectRefUtils} from 'tdp_core'; import {CohortApp} from '../app'; import {IElementProvJSON, IElementProvJSONCohort} from '../CohortInterfaces'; import {log} from '../util'; diff --git a/src/app.ts b/src/app.ts index 629c309..5b947a9 100644 --- a/src/app.ts +++ b/src/app.ts @@ -1,7 +1,7 @@ import {select, Selection} from 'd3-selection'; -import {CLUEGraphManager} from 'phovea_clue'; -import {AppContext, IObjectRef, ObjectRefUtils, ProvenanceGraph} from 'phovea_core'; -import {AppMetaDataUtils} from 'phovea_ui'; +import {CLUEGraphManager} from 'tdp_core'; +import {AppContext, IObjectRef, ObjectRefUtils, ProvenanceGraph} from 'tdp_core'; +import {AppMetaDataUtils} from 'tdp_core'; import SplitGrid from 'split-grid'; import {ATDPApplication, IDatabaseViewDesc, IServerColumn, NotificationHandler, RestBaseUtils} from 'tdp_core'; import {cellline, tissue} from 'tdp_publicdb'; diff --git a/src/cohortview.ts b/src/cohortview.ts index cc4afd0..9922b25 100644 --- a/src/cohortview.ts +++ b/src/cohortview.ts @@ -1,4 +1,4 @@ -import {IObjectRef, ProvenanceGraph} from 'phovea_core'; +import {IObjectRef, ProvenanceGraph} from 'tdp_core'; import {IDatabaseViewDesc, RestBaseUtils} from 'tdp_core'; import {CohortApp, CohortSelectionListener} from './app'; import {Cohort} from './Cohort'; diff --git a/src/menu/DatasetCard.tsx b/src/menu/DatasetCard.tsx index 4bd35f3..5584568 100644 --- a/src/menu/DatasetCard.tsx +++ b/src/menu/DatasetCard.tsx @@ -1,7 +1,7 @@ import React from 'react'; import {INamedSet, ENamedSetType, RestBaseUtils, RestStorageUtils, StoreUtils, IdTextPair} from 'tdp_core'; import {NamedSetList, useAsync, OrdinoContext} from 'ordino'; -import {UserSession, UniqueIdManager, I18nextManager, IDTypeManager} from 'phovea_core'; +import {UserSession, UniqueIdManager, I18nextManager, IDTypeManager} from 'tdp_core'; import {DatasetSearchBox} from './DatasetSearchBox'; import {Species, SpeciesUtils, IACommonListOptions} from 'tdp_gene'; import {IPublicDbStartMenuDatasetSectionDesc} from '../base/extensions'; diff --git a/src/pages/components/SourceCodeCard.tsx b/src/pages/components/SourceCodeCard.tsx index dcf15c2..8ae90a1 100644 --- a/src/pages/components/SourceCodeCard.tsx +++ b/src/pages/components/SourceCodeCard.tsx @@ -1,5 +1,5 @@ import {useAsync} from 'ordino'; -import {AppMetaDataUtils} from 'phovea_ui'; +import {AppMetaDataUtils} from 'tdp_core'; import React from 'react'; export function SourceCodeCard() { diff --git a/src/phovea.ts b/src/phovea.ts index f06d8af..8e9513f 100644 --- a/src/phovea.ts +++ b/src/phovea.ts @@ -3,9 +3,9 @@ * Copyright (c) The Caleydo Team. All rights reserved. * Licensed under the new BSD license, available at http://caleydo.org/license **************************************************************************** */ -import {IRegistry, PluginRegistry} from 'phovea_core'; +import {IRegistry, PluginRegistry} from 'tdp_core'; import {EP_ORDINO_HEADER_MENU, EP_ORDINO_FOOTER_MENU, EP_ORDINO_START_MENU_TAB, EP_ORDINO_LOGO, EStartMenuSection, EP_ORDINO_START_MENU_TAB_SHORTCUT, IOrdinoFooterMenuDesc, IOrdinoLogoDesc, IOrdinoHeaderMenuDesc,IStartMenuTabShortcutDesc} from 'ordino'; -import {EXTENSION_POINT_CUSTOMIZED_LOGIN_FORM} from 'phovea_security_flask'; +import {EXTENSION_POINT_CUSTOMIZED_LOGIN_FORM} from 'tdp_core'; export default function (registry: IRegistry) { // Coral's custom login form diff --git a/src/rest.ts b/src/rest.ts index 31878a3..e2b1554 100644 --- a/src/rest.ts +++ b/src/rest.ts @@ -1,4 +1,4 @@ -import {Ajax, AppContext} from 'phovea_core'; +import {Ajax, AppContext} from 'tdp_core'; import {IParams, IRow} from 'tdp_core'; import {deepCopy, log} from './util'; From 4ad7fd3e8e0fdcc664661f868723a8629f067b93 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Thu, 18 Nov 2021 09:23:15 +0100 Subject: [PATCH 07/12] delete cache --- .circleci/config.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 2c7505b..647157e 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -30,7 +30,7 @@ jobs: command: | (!(test -f docker_packages.txt) || (cat docker_packages.txt | xargs sudo apt-get install -y)) - restore_cache: - key: deps2-{{ .Branch }}-{{ checksum "requirements.txt" }}-{{ checksum "requirements_dev.txt" }} + key: deps1-{{ .Branch }}-{{ checksum "requirements.txt" }}-{{ checksum "requirements_dev.txt" }} - run: name: Install pip requirements command: | @@ -39,7 +39,7 @@ jobs: pip install -r requirements_dev.txt pip install -r requirements.txt - save_cache: - key: deps2-{{ .Branch }}-{{ checksum "requirements.txt" }}-{{ checksum "requirements_dev.txt" }} + key: deps1-{{ .Branch }}-{{ checksum "requirements.txt" }}-{{ checksum "requirements_dev.txt" }} paths: - ~/venv - run: @@ -99,7 +99,7 @@ jobs: node -v npm -v - restore_cache: - key: deps1-{{ .Branch }}-{{ checksum "package.json" }} + key: deps2-{{ .Branch }}-{{ checksum "package.json" }} - run: name: Install npm dependencies command: npm install @@ -108,7 +108,7 @@ jobs: command: | (grep -l '._resolved.: .\(git[^:]*\|bitbucket\):' ./node_modules/*/package.json || true) | xargs -r dirname | xargs -r rm -rf - save_cache: - key: deps1-{{ .Branch }}-{{ checksum "package.json" }} + key: deps2-{{ .Branch }}-{{ checksum "package.json" }} paths: ./node_modules - run: name: Install npm dependencies from git repositories (always get latest commit) From 765de85711c0d91081f2bf481a0abb1ada5dc8c3 Mon Sep 17 00:00:00 2001 From: Klaus Date: Thu, 18 Nov 2021 13:27:35 +0100 Subject: [PATCH 08/12] rem duplicate line --- phovea_registry.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/phovea_registry.js b/phovea_registry.js index 187ed92..ab2588e 100644 --- a/phovea_registry.js +++ b/phovea_registry.js @@ -12,6 +12,6 @@ import reg from './dist/phovea'; */ //other modules import 'tdp_core/phovea_registry.js'; -import 'tdp_core/phovea_registry.js'; + //self PluginRegistry.getInstance().register('coral', reg); From 49e71231c03b8754c5be1ac9f80d9a529dc89e19 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Thu, 18 Nov 2021 14:35:54 +0100 Subject: [PATCH 09/12] update useAsync import --- dist/menu/DatasetCard.js | 4 ++-- dist/menu/DatasetCard.js.map | 2 +- dist/pages/components/SourceCodeCard.js | 2 +- dist/pages/components/SourceCodeCard.js.map | 2 +- src/menu/DatasetCard.tsx | 4 ++-- src/pages/components/SourceCodeCard.tsx | 2 +- 6 files changed, 8 insertions(+), 8 deletions(-) diff --git a/dist/menu/DatasetCard.js b/dist/menu/DatasetCard.js index f0c2a8a..7502945 100644 --- a/dist/menu/DatasetCard.js +++ b/dist/menu/DatasetCard.js @@ -1,7 +1,7 @@ import React from 'react'; import { ENamedSetType, RestBaseUtils, RestStorageUtils, StoreUtils } from 'tdp_core'; -import { NamedSetList, useAsync, OrdinoContext } from 'ordino'; -import { UserSession, UniqueIdManager, I18nextManager, IDTypeManager } from 'tdp_core'; +import { NamedSetList, OrdinoContext } from 'ordino'; +import { UserSession, UniqueIdManager, I18nextManager, IDTypeManager, useAsync } from 'tdp_core'; import { DatasetSearchBox } from './DatasetSearchBox'; import { Species, SpeciesUtils } from 'tdp_gene'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }) { diff --git a/dist/menu/DatasetCard.js.map b/dist/menu/DatasetCard.js.map index 9ab2687..de0f8a5 100644 --- a/dist/menu/DatasetCard.js.map +++ b/dist/menu/DatasetCard.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/pages/components/SourceCodeCard.js b/dist/pages/components/SourceCodeCard.js index 65d8dfb..22a1382 100644 --- a/dist/pages/components/SourceCodeCard.js +++ b/dist/pages/components/SourceCodeCard.js @@ -1,4 +1,4 @@ -import { useAsync } from 'ordino'; +import { useAsync } from 'tdp_core'; import { AppMetaDataUtils } from 'tdp_core'; import React from 'react'; export function SourceCodeCard() { diff --git a/dist/pages/components/SourceCodeCard.js.map b/dist/pages/components/SourceCodeCard.js.map index 0e5587d..388813b 100644 --- a/dist/pages/components/SourceCodeCard.js.map +++ b/dist/pages/components/SourceCodeCard.js.map @@ -1 +1 @@ -{"version":3,"file":"SourceCodeCard.js","sourceRoot":"","sources":["../../../src/pages/components/SourceCodeCard.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAC,QAAQ,EAAC,MAAM,QAAQ,CAAC;AAChC,OAAO,EAAC,gBAAgB,EAAC,MAAM,UAAU,CAAC;AAC1C,OAAO,KAAK,MAAM,OAAO,CAAC;AAE1B,MAAM,UAAU,cAAc;IAC5B,MAAM,YAAY,GAAG,KAAK,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,CAAC,gBAAgB,CAAC,WAAW,EAAE,EAAE,EAAE,CAAC,CAAC;IACnF,MAAM,EAAC,MAAM,EAAE,KAAK,EAAC,GAAG,QAAQ,CAAC,YAAY,CAAC,CAAC;IAE/C,OAAO,CACL;QACE,6BAAK,SAAS,EAAC,oBAAoB;YACjC,6BAAK,SAAS,EAAC,WAAW;gBACxB,2BAAG,SAAS,EAAC,WAAW;;oBACkB,2BAAG,IAAI,EAAC,kCAAkC,EAAC,MAAM,EAAC,QAAQ,EAAC,GAAG,EAAC,UAAU,aAAW;wBAC1H;gBACJ,2BAAG,SAAS,EAAC,WAAW,4NAKpB;gBACJ,2BAAG,SAAS,EAAC,WAAW;oBAAC,2CAAgB;;oBAAE,CAAC,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,8BAA8B,CAAK,CACnH,CACF,CACL,CACJ,CAAC;AACJ,CAAC"} \ No newline at end of file +{"version":3,"file":"SourceCodeCard.js","sourceRoot":"","sources":["../../../src/pages/components/SourceCodeCard.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAC,QAAQ,EAAC,MAAM,UAAU,CAAC;AAClC,OAAO,EAAC,gBAAgB,EAAC,MAAM,UAAU,CAAC;AAC1C,OAAO,KAAK,MAAM,OAAO,CAAC;AAE1B,MAAM,UAAU,cAAc;IAC5B,MAAM,YAAY,GAAG,KAAK,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,CAAC,gBAAgB,CAAC,WAAW,EAAE,EAAE,EAAE,CAAC,CAAC;IACnF,MAAM,EAAC,MAAM,EAAE,KAAK,EAAC,GAAG,QAAQ,CAAC,YAAY,CAAC,CAAC;IAE/C,OAAO,CACL;QACE,6BAAK,SAAS,EAAC,oBAAoB;YACjC,6BAAK,SAAS,EAAC,WAAW;gBACxB,2BAAG,SAAS,EAAC,WAAW;;oBACkB,2BAAG,IAAI,EAAC,kCAAkC,EAAC,MAAM,EAAC,QAAQ,EAAC,GAAG,EAAC,UAAU,aAAW;wBAC1H;gBACJ,2BAAG,SAAS,EAAC,WAAW,4NAKpB;gBACJ,2BAAG,SAAS,EAAC,WAAW;oBAAC,2CAAgB;;oBAAE,CAAC,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,8BAA8B,CAAK,CACnH,CACF,CACL,CACJ,CAAC;AACJ,CAAC"} \ No newline at end of file diff --git a/src/menu/DatasetCard.tsx b/src/menu/DatasetCard.tsx index 5584568..06d93b4 100644 --- a/src/menu/DatasetCard.tsx +++ b/src/menu/DatasetCard.tsx @@ -1,7 +1,7 @@ import React from 'react'; import {INamedSet, ENamedSetType, RestBaseUtils, RestStorageUtils, StoreUtils, IdTextPair} from 'tdp_core'; -import {NamedSetList, useAsync, OrdinoContext} from 'ordino'; -import {UserSession, UniqueIdManager, I18nextManager, IDTypeManager} from 'tdp_core'; +import {NamedSetList, OrdinoContext} from 'ordino'; +import {UserSession, UniqueIdManager, I18nextManager, IDTypeManager, useAsync} from 'tdp_core'; import {DatasetSearchBox} from './DatasetSearchBox'; import {Species, SpeciesUtils, IACommonListOptions} from 'tdp_gene'; import {IPublicDbStartMenuDatasetSectionDesc} from '../base/extensions'; diff --git a/src/pages/components/SourceCodeCard.tsx b/src/pages/components/SourceCodeCard.tsx index 8ae90a1..428c515 100644 --- a/src/pages/components/SourceCodeCard.tsx +++ b/src/pages/components/SourceCodeCard.tsx @@ -1,4 +1,4 @@ -import {useAsync} from 'ordino'; +import {useAsync} from 'tdp_core'; import {AppMetaDataUtils} from 'tdp_core'; import React from 'react'; From b0c54c971d7f1070064e41b31b7b78884e4124cc Mon Sep 17 00:00:00 2001 From: Klaus Date: Thu, 18 Nov 2021 16:51:15 +0100 Subject: [PATCH 10/12] reset branches to develop after merge https://github.com/Caleydo/tourdino/pull/85 https://github.com/Caleydo/tdp_publicdb/pull/166 --- package.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/package.json b/package.json index 8d1e93a..0a648ef 100644 --- a/package.json +++ b/package.json @@ -97,9 +97,9 @@ "react-dom": "^16.13.0", "react-router-dom": "^5.2.0", "split-grid": "^1.0.9", - "tdp_publicdb": "github:caleydo/tdp_publicdb#visyn_rem_dTiles_python", + "tdp_publicdb": "github:caleydo/tdp_publicdb#keckelt/rem_dTiles", "tippy.js": "^6.2.6", - "tourdino": "github:caleydo/tourdino#visyn_vega_boxplot", + "tourdino": "github:caleydo/tourdino#keckelt/vega_boxplot", "vega": "~5.20.0", "vega-embed": "6.19.1", "vega-functions": "5.12.0", From 44e1513a45821c016559926588e3f80044f965c6 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Mon, 29 Nov 2021 08:33:15 +0100 Subject: [PATCH 11/12] update version --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index bbfc77a..675fb06 100644 --- a/package.json +++ b/package.json @@ -2,7 +2,7 @@ "name": "coral", "description": "Coral is a web-based cohort analysis tool to interactively create, refine, and analyze patient cohorts.", "homepage": "https://caleydo.org", - "version": "1.0.1-SNAPSHOT", + "version": "1.0.1", "author": { "name": "PatrickAdelberger", "email": "coral@caleydo.org", From b1ad1815a55edf72f10153eb693d0d825e3c1fe2 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Mon, 29 Nov 2021 08:36:53 +0100 Subject: [PATCH 12/12] remove ordino dependency again --- package.json | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/package.json b/package.json index 675fb06..fc524af 100644 --- a/package.json +++ b/package.json @@ -104,8 +104,7 @@ "vega-embed": "6.19.1", "vega-functions": "5.12.0", "vega-lite": "5.1.1", - "vega-parser": "6.1.3", - "ordino": "github:caleydo/ordino#v10.0.0" + "vega-parser": "6.1.3" }, "devDependencies": {