diff --git a/GenotypeAssays/resources/web/genotypeassays/window/PublishResultsWindow.js b/GenotypeAssays/resources/web/genotypeassays/window/PublishResultsWindow.js index bac163ba..1e5d754e 100644 --- a/GenotypeAssays/resources/web/genotypeassays/window/PublishResultsWindow.js +++ b/GenotypeAssays/resources/web/genotypeassays/window/PublishResultsWindow.js @@ -100,7 +100,7 @@ Ext4.define('GenotypeAssays.window.PublishResultsWindow', { }); }, this); - if (results.length == 1){ + if (results.length === 1){ field.setValue(results[0].id); } field.setDisabled(false); diff --git a/IDR/resources/referenceStudy/study/datasets/datasets_manifest.xml b/IDR/resources/referenceStudy/study/datasets/datasets_manifest.xml index a57ce797..ad696d8e 100644 --- a/IDR/resources/referenceStudy/study/datasets/datasets_manifest.xml +++ b/IDR/resources/referenceStudy/study/datasets/datasets_manifest.xml @@ -10,6 +10,9 @@ + + + diff --git a/IDR/resources/referenceStudy/study/datasets/datasets_metadata.xml b/IDR/resources/referenceStudy/study/datasets/datasets_metadata.xml index e5ae4f48..051a8eec 100644 --- a/IDR/resources/referenceStudy/study/datasets/datasets_metadata.xml +++ b/IDR/resources/referenceStudy/study/datasets/datasets_metadata.xml @@ -1035,4 +1035,61 @@ Kinship + + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + timestamp + urn:ehr.labkey.org/#EndDate + + + varchar + urn:ehr.labkey.org/#CaseId + + + timestamp + + + varchar + + + integer + urn:ehr.labkey.org/#Project + + + integer + + + varchar + + + entityid + urn:ehr.labkey.org/#ObjectId + true + + + varchar + urn:ehr.labkey.org/#VetReview + + + timestamp + urn:ehr.labkey.org/#VetReviewDate + + + varchar + + + Cases +
diff --git a/MccColony/resources/queries/study/departure/.qview.xml b/MccColony/resources/queries/study/departure/.qview.xml index b14b6365..baacd2b4 100644 --- a/MccColony/resources/queries/study/departure/.qview.xml +++ b/MccColony/resources/queries/study/departure/.qview.xml @@ -5,7 +5,7 @@ - + diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java index cd8bfa81..f3b0ca46 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java @@ -148,7 +148,8 @@ protected void addTracks(final String databaseId, String releaseId) FieldKey.fromString("url"), FieldKey.fromString("description"), FieldKey.fromString("isprimarytrack"), - FieldKey.fromString("vcfId/dataid/DataFileUrl") + FieldKey.fromString("vcfId/dataid/DataFileUrl"), + FieldKey.fromString("releaseId/luceneIndex/dataid/DataFileUrl") ); TableInfo tracksPerRelease = QueryService.get().getUserSchema(getContainerUser().getUser(), getContainerUser().getContainer(), mGAPSchema.NAME).getTable(mGAPSchema.TABLE_TRACKS_PER_RELEASE); @@ -270,7 +271,8 @@ private String getOrCreateJsonFile(Results rs, String fieldKey) throws SQLExcept if (isDefaultTrack) { - boolean hasLuceneIndex = StringUtils.trimToNull(rs.getString(FieldKey.fromString("luceneIndex/dataid/DataFileUrl"))) != null; + boolean hasLuceneIndex = StringUtils.trimToNull(rs.getString(FieldKey.fromString("releaseId/luceneIndex/dataid/DataFileUrl"))) != null; + getStatusLogger().info("Creating track JSON for primary track, has lucene index: " + hasLuceneIndex); row.put("trackJson", getTrackJson(hasLuceneIndex)); } else diff --git a/mGAP/src/org/labkey/mgap/mGAPController.java b/mGAP/src/org/labkey/mgap/mGAPController.java index a6afe145..e8f0ebbc 100644 --- a/mGAP/src/org/labkey/mgap/mGAPController.java +++ b/mGAP/src/org/labkey/mgap/mGAPController.java @@ -996,7 +996,7 @@ public URLHelper getRedirectURL(GenomeBrowserForm form) } else { - throw new IllegalArgumentException("Unable to find primary track for release: " + ctx.getString("mgapReleaseGUID")); + throw new IllegalArgumentException("Unable to find primary track for release: " + ctx.getString("mgapReleaseGUID") + ", with JBrowse ID: " + jbrowseDatabaseId); } } diff --git a/mGAP/src/org/labkey/mgap/mGapMaintenanceTask.java b/mGAP/src/org/labkey/mgap/mGapMaintenanceTask.java index 85a42523..5a858804 100644 --- a/mGAP/src/org/labkey/mgap/mGapMaintenanceTask.java +++ b/mGAP/src/org/labkey/mgap/mGapMaintenanceTask.java @@ -133,9 +133,10 @@ private void checkMGapFiles(Logger log, User u) if (!commandsToRun.isEmpty()) { - log.error("There are missing symlinks. Please run makeSymlinks.sh"); + File bashFile = new File(baseDir, "makeSymlinks.sh"); + log.error("There are missing symlinks. Please run " + bashFile.getPath()); - try (PrintWriter writer = PrintWriters.getPrintWriter(new File(baseDir, "makeSymlinks.sh"))) + try (PrintWriter writer = PrintWriters.getPrintWriter(bashFile)) { writer.println("#!/bin/bash"); writer.println("set -e"); diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java index d01e83c7..278960bc 100644 --- a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java +++ b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java @@ -353,8 +353,9 @@ private File getTrackListFile(File outputDir) } @Override - public void complete(PipelineJob job, List inputs, List outputsCreated, SequenceAnalysisJobSupport support) throws PipelineJobException + public void complete(JobContext ctx, List inputs, List outputsCreated) throws PipelineJobException { + PipelineJob job = ctx.getJob(); if (outputsCreated.isEmpty()) { job.getLogger().error("no outputs found"); diff --git a/mcc/package-lock.json b/mcc/package-lock.json index 1293be11..3655ca75 100644 --- a/mcc/package-lock.json +++ b/mcc/package-lock.json @@ -10,28 +10,28 @@ "dependencies": { "@emotion/react": "^11.11.1", "@emotion/styled": "^11.11.0", - 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"version": "1.0.4", - "resolved": "https://registry.npmjs.org/side-channel/-/side-channel-1.0.4.tgz", - "integrity": "sha512-q5XPytqFEIKHkGdiMIrY10mvLRvnQh42/+GoBlFW3b2LXLE2xxJpZFdm94we0BaoV3RwJyGqg5wS7epxTv0Zvw==", + "version": "1.0.6", + "resolved": "https://registry.npmjs.org/side-channel/-/side-channel-1.0.6.tgz", + "integrity": "sha512-fDW/EZ6Q9RiO8eFG8Hj+7u/oW+XrPTIChwCOM2+th2A6OblDtYYIpve9m+KvI9Z4C9qSEXlaGR6bTEYHReuglA==", "dev": true, "dependencies": { - "call-bind": "^1.0.0", - "get-intrinsic": "^1.0.2", - "object-inspect": "^1.9.0" + "call-bind": "^1.0.7", + "es-errors": "^1.3.0", + "get-intrinsic": "^1.2.4", + "object-inspect": "^1.13.1" + }, + "engines": { + "node": ">= 0.4" }, "funding": { "url": "https://github.com/sponsors/ljharb" @@ -13352,19 +13435,19 @@ } }, "node_modules/style-loader": { - "version": "3.3.4", - "resolved": "https://registry.npmjs.org/style-loader/-/style-loader-3.3.4.tgz", - "integrity": "sha512-0WqXzrsMTyb8yjZJHDqwmnwRJvhALK9LfRtRc6B4UTWe8AijYLZYZ9thuJTZc2VfQWINADW/j+LiJnfy2RoC1w==", + "version": "4.0.0", + "resolved": "https://registry.npmjs.org/style-loader/-/style-loader-4.0.0.tgz", + "integrity": "sha512-1V4WqhhZZgjVAVJyt7TdDPZoPBPNHbekX4fWnCJL1yQukhCeZhJySUL+gL9y6sNdN95uEOS83Y55SqHcP7MzLA==", "dev": true, "engines": { - "node": ">= 12.13.0" + "node": ">= 18.12.0" }, "funding": { "type": "opencollective", "url": "https://opencollective.com/webpack" }, "peerDependencies": { - "webpack": "^5.0.0" + "webpack": "^5.27.0" } }, "node_modules/stylis": { @@ -13864,9 +13947,9 @@ } }, "node_modules/typescript": { - "version": "5.4.5", - "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.4.5.tgz", - "integrity": "sha512-vcI4UpRgg81oIRUFwR0WSIHKt11nJ7SAVlYNIu+QpqeyXP+gpQJy/Z4+F0aGxSE4MqwjyXvW/TzgkLAx2AGHwQ==", + "version": "5.5.4", + "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.5.4.tgz", + "integrity": "sha512-Mtq29sKDAEYP7aljRgtPOpTvOfbwRWlS6dPRzwjdE+C0R4brX/GUyhHSecbHMFLNBLcJIPt9nl9yG5TZ1weH+Q==", "dev": true, "bin": { "tsc": "bin/tsc", @@ -14032,9 +14115,13 @@ } }, "node_modules/uuid": { - "version": "9.0.0", - "resolved": "https://registry.npmjs.org/uuid/-/uuid-9.0.0.tgz", - "integrity": "sha512-MXcSTerfPa4uqyzStbRoTgt5XIe3x5+42+q1sDuy3R5MDk66URdLMOZe5aPX/SQd+kuYAh0FdP/pO28IkQyTeg==", + "version": "10.0.0", + "resolved": "https://registry.npmjs.org/uuid/-/uuid-10.0.0.tgz", + "integrity": "sha512-8XkAphELsDnEGrDxUOHB3RGvXz6TeuYSGEZBOjtTtPm2lwhGBjLgOzLHB63IUWfBpNucQjND6d3AOudO+H3RWQ==", + "funding": [ + "https://github.com/sponsors/broofa", + "https://github.com/sponsors/ctavan" + ], "bin": { "uuid": "dist/bin/uuid" } @@ -14115,9 +14202,9 @@ } }, "node_modules/webpack": { - "version": "5.91.0", - "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.91.0.tgz", - "integrity": "sha512-rzVwlLeBWHJbmgTC/8TvAcu5vpJNII+MelQpylD4jNERPwpBJOE2lEcko1zJX3QJeLjTTAnQxn/OJ8bjDzVQaw==", + "version": "5.93.0", + "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.93.0.tgz", + "integrity": "sha512-Y0m5oEY1LRuwly578VqluorkXbvXKh7U3rLoQCEO04M97ScRr44afGVkI0FQFsXzysk5OgFAxjZAb9rsGQVihA==", "dev": true, "dependencies": { "@types/eslint-scope": "^3.7.3", @@ -14126,10 +14213,10 @@ "@webassemblyjs/wasm-edit": "^1.12.1", "@webassemblyjs/wasm-parser": "^1.12.1", "acorn": "^8.7.1", - "acorn-import-assertions": "^1.9.0", + "acorn-import-attributes": "^1.9.5", "browserslist": "^4.21.10", "chrome-trace-event": "^1.0.2", - "enhanced-resolve": "^5.16.0", + "enhanced-resolve": "^5.17.0", "es-module-lexer": "^1.2.1", "eslint-scope": "5.1.1", "events": "^3.2.0", diff --git a/mcc/package.json b/mcc/package.json index ecb1a82c..7853ca02 100644 --- a/mcc/package.json +++ b/mcc/package.json @@ -13,28 +13,28 @@ "dependencies": { "@emotion/react": "^11.11.1", "@emotion/styled": "^11.11.0", - "@labkey/api": "^1.34.1", + "@labkey/api": "^1.35.0", "@mui/material": "^5.0.0", "@mui/styles": "^5.14.7", "@mui/x-data-grid": "^6.0.0", - "chart.js": "^4.4.3", + "chart.js": "^4.4.4", "react": "^17.0.2", "react-chartjs-2": "^5.2.0", "react-dom": "^17.0.2", - "react-tooltip": "^5.21.1", + "react-tooltip": "^5.28.0", "tsv": "^0.2.0", - "uuid": "^9.0.0" + "uuid": "^10.0.0" }, "devDependencies": { - "@labkey/build": "^7.3.0", - "@types/chart.js": "^2.9.37", + "@labkey/build": "^7.7.1", + "@types/chart.js": "^2.9.0", "@types/jest": "^29.0.0", "@types/jexl": "^2.3.1", "@types/jquery": "^3.0.0", "@types/node": "^18.17.1", "@types/react": "^17.0.68", "@types/react-dom": "^17.0.21", - "@types/tsv": "^0.2.1", + "@types/tsv": "^0.2.4", "@wojtekmaj/enzyme-adapter-react-17": "^0.8.0", "canvas": "^2.11.2", "enzyme": "^3.11.0", diff --git a/mcc/resources/etls/mcc.xml b/mcc/resources/etls/mcc.xml index 6698470d..f9379952 100644 --- a/mcc/resources/etls/mcc.xml +++ b/mcc/resources/etls/mcc.xml @@ -121,8 +121,12 @@ startdate enddate centerName + totalLiving + totalLivingU24 totalBreedingPairs - totalLivingOffspring + totalBreedingPairsU24 + totalOffspring + totalOffspringU24 survivalRates marmosetsShipped @@ -139,7 +143,7 @@ date source destination - mccTransfer + mccRequestId objectid diff --git a/mcc/resources/queries/mcc/requestScores/Completed Requests.qview.xml b/mcc/resources/queries/mcc/requestScores/Completed Requests.qview.xml new file mode 100644 index 00000000..7eaf0242 --- /dev/null +++ b/mcc/resources/queries/mcc/requestScores/Completed Requests.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/mcc/resources/queries/study/demographicsMostRecentDeparture.query.xml b/mcc/resources/queries/study/demographicsMostRecentDeparture.query.xml new file mode 100644 index 00000000..7136f001 --- /dev/null +++ b/mcc/resources/queries/study/demographicsMostRecentDeparture.query.xml @@ -0,0 +1,25 @@ + + + + + + + true + true + + + /query/executeQuery.view?schemaName=study& + query.queryName=departure& + query.Id~eq=${Id}& + query.sort=-Date& + + + + MCC Request Id(s) + + + MostRecentDeparture +
+ + + diff --git a/mcc/resources/queries/study/demographicsMostRecentDeparture.sql b/mcc/resources/queries/study/demographicsMostRecentDeparture.sql new file mode 100644 index 00000000..f504e2de --- /dev/null +++ b/mcc/resources/queries/study/demographicsMostRecentDeparture.sql @@ -0,0 +1,9 @@ +select + + T1.Id, + max(T1.date) as MostRecentDeparture, + group_concat(distinct t1.mccRequestId) as mccRequestId + +FROM study.departure T1 +WHERE T1.qcstate.publicdata = true +GROUP BY T1.Id diff --git a/mcc/resources/queries/study/departure.query.xml b/mcc/resources/queries/study/departure.query.xml index 81ee0cfb..93a87f0c 100644 --- a/mcc/resources/queries/study/departure.query.xml +++ b/mcc/resources/queries/study/departure.query.xml @@ -29,9 +29,8 @@ - - MCC U24 Transfer? - false + + MCC Request ID diff --git a/mcc/resources/queries/study/departure/.qview.xml b/mcc/resources/queries/study/departure/.qview.xml index 86b40496..dd18300d 100644 --- a/mcc/resources/queries/study/departure/.qview.xml +++ b/mcc/resources/queries/study/departure/.qview.xml @@ -4,7 +4,7 @@ - + diff --git a/mcc/resources/referenceStudy/study/datasets/datasets_manifest.xml b/mcc/resources/referenceStudy/study/datasets/datasets_manifest.xml index ccac6c93..76d65856 100644 --- a/mcc/resources/referenceStudy/study/datasets/datasets_manifest.xml +++ b/mcc/resources/referenceStudy/study/datasets/datasets_manifest.xml @@ -10,6 +10,9 @@ + + + diff --git a/mcc/resources/referenceStudy/study/datasets/datasets_metadata.xml b/mcc/resources/referenceStudy/study/datasets/datasets_metadata.xml index 805e4f0c..4535b215 100644 --- a/mcc/resources/referenceStudy/study/datasets/datasets_metadata.xml +++ b/mcc/resources/referenceStudy/study/datasets/datasets_metadata.xml @@ -77,7 +77,6 @@ varchar - http://cpas.labkey.com/Study#ParticipantId varchar @@ -712,9 +711,8 @@ varchar - - boolean - false + + integer entityid @@ -1037,7 +1035,6 @@ varchar - http://cpas.labkey.com/Study#ParticipantId double @@ -1081,4 +1078,61 @@ Genetic Datasets + + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + timestamp + urn:ehr.labkey.org/#EndDate + + + varchar + urn:ehr.labkey.org/#CaseId + + + timestamp + + + varchar + + + integer + urn:ehr.labkey.org/#Project + + + integer + + + varchar + + + entityid + urn:ehr.labkey.org/#ObjectId + true + + + varchar + urn:ehr.labkey.org/#VetReview + + + timestamp + urn:ehr.labkey.org/#VetReviewDate + + + varchar + + + Cases +
diff --git a/mcc/resources/schemas/dbscripts/postgresql/mcc-20.016-20.017.sql b/mcc/resources/schemas/dbscripts/postgresql/mcc-20.016-20.017.sql new file mode 100644 index 00000000..170e7768 --- /dev/null +++ b/mcc/resources/schemas/dbscripts/postgresql/mcc-20.016-20.017.sql @@ -0,0 +1,5 @@ +ALTER TABLE mcc.census DROP COLUMN totalLivingOffspring; + +ALTER TABLE mcc.census ADD totalOffspring int; +ALTER TABLE mcc.census ADD totalOffspringU24 int; +ALTER TABLE mcc.census ADD totalBreedingPairsU24 int; diff --git a/mcc/resources/schemas/dbscripts/postgresql/mcc-20.017-20.018.sql b/mcc/resources/schemas/dbscripts/postgresql/mcc-20.017-20.018.sql new file mode 100644 index 00000000..ec54e227 --- /dev/null +++ b/mcc/resources/schemas/dbscripts/postgresql/mcc-20.017-20.018.sql @@ -0,0 +1,2 @@ +ALTER TABLE mcc.census ADD totalLiving int; +ALTER TABLE mcc.census ADD totalLivingU24 int; diff --git a/mcc/resources/schemas/dbscripts/sqlserver/mcc-20.016-20.017.sql b/mcc/resources/schemas/dbscripts/sqlserver/mcc-20.016-20.017.sql new file mode 100644 index 00000000..5b5643f0 --- /dev/null +++ b/mcc/resources/schemas/dbscripts/sqlserver/mcc-20.016-20.017.sql @@ -0,0 +1,5 @@ +ALTER TABLE mcc.census DROP COLUMN totalLivingOffspring; + +ALTER TABLE mcc.census ADD totalOffspring int; +ALTER TABLE mcc.census ADD totalOffspringU24 int; +ALTER TABLE mcc.census ADD totalBreedingPairsU24 int; \ No newline at end of file diff --git a/mcc/resources/schemas/dbscripts/sqlserver/mcc-20.017-20.018.sql b/mcc/resources/schemas/dbscripts/sqlserver/mcc-20.017-20.018.sql new file mode 100644 index 00000000..ec54e227 --- /dev/null +++ b/mcc/resources/schemas/dbscripts/sqlserver/mcc-20.017-20.018.sql @@ -0,0 +1,2 @@ +ALTER TABLE mcc.census ADD totalLiving int; +ALTER TABLE mcc.census ADD totalLivingU24 int; diff --git a/mcc/resources/schemas/mcc.xml b/mcc/resources/schemas/mcc.xml index 412deaf9..86970ae2 100644 --- a/mcc/resources/schemas/mcc.xml +++ b/mcc/resources/schemas/mcc.xml @@ -700,6 +700,7 @@ /mcc/requestReview.view?requestId=${requestId}&mode=details Animal Request Reviews + DETAILED rowid @@ -776,7 +777,7 @@ - +
@@ -807,14 +808,27 @@ Center Name false + + # Living (Total) + + + # Living (U24) + - # Breeding Pairs + # In Active Breeding (Total) + + + # In Active Breeding (U24) - - # Living Offspring + + # Offspring (Total) + + + # Offspring (U24) Survival Rates + true # Animals Shipped diff --git a/mcc/resources/views/mccRequestSummary.html b/mcc/resources/views/mccRequestSummary.html index 1cb37799..3ef51431 100644 --- a/mcc/resources/views/mccRequestSummary.html +++ b/mcc/resources/views/mccRequestSummary.html @@ -31,10 +31,11 @@ LDK.Utils.getBasicQWP({ containerPath: ctx.MCCRequestContainer, - title: 'All Requests', + title: 'Completed Requests', frame: 'left-nav', schemaName: 'mcc', queryName: 'requestScores', + viewName: 'Completed Requests', showRecordSelectors: true, showDetailsColumn: true, maxRows: 10 diff --git a/mcc/resources/views/requestLogin.view.xml b/mcc/resources/views/requestLogin.view.xml index 8927f2fe..1bb1e023 100644 --- a/mcc/resources/views/requestLogin.view.xml +++ b/mcc/resources/views/requestLogin.view.xml @@ -1,5 +1,5 @@ - + diff --git a/mcc/resources/web/mcc/panel/MccImportPanel.js b/mcc/resources/web/mcc/panel/MccImportPanel.js index 705e8574..e00d01a6 100644 --- a/mcc/resources/web/mcc/panel/MccImportPanel.js +++ b/mcc/resources/web/mcc/panel/MccImportPanel.js @@ -903,6 +903,7 @@ Ext4.define('MCC.panel.MccImportPanel', { QCStateLabel: 'Completed', QCState: null, date: dateVal, + colony: f.sourceRecord.colony, destination: otherVal }); } else { diff --git a/mcc/resources/web/mcc/window/MarkShippedWindow.js b/mcc/resources/web/mcc/window/MarkShippedWindow.js index 3e3896e4..ad39ba21 100644 --- a/mcc/resources/web/mcc/window/MarkShippedWindow.js +++ b/mcc/resources/web/mcc/window/MarkShippedWindow.js @@ -83,11 +83,6 @@ Ext4.define('MCC.window.MarkShippedWindow', { } } } - },{ - xtype: 'checkbox', - itemId: 'isMccTransfer', - fieldLabel: 'Is MCC Transfer', - checked: true }, this.getAnimalIdFields()], buttons: [{ text: 'Submit', @@ -123,6 +118,11 @@ Ext4.define('MCC.window.MarkShippedWindow', { fields = fields.concat([{ xtype: 'displayfield', value: animalId, + },{ + xtype: 'ldk-integerfield', + minValue: 1, + itemId: 'requestId-' + animalId, + allowBlank: true },{ xtype: 'checkbox', itemId: 'usePreviousId-' + animalId, @@ -173,7 +173,6 @@ Ext4.define('MCC.window.MarkShippedWindow', { var effectiveDate = win.down('#effectiveDate').getValue(); var centerName = win.down('#centerName').getValue(); var targetFolder = win.down('#targetFolder').getValue(); - var isMccTransfer = win.down('#isMccTransfer').getValue(); if (!effectiveDate || !centerName || !targetFolder) { Ext4.Msg.alert('Error', 'Must provide date, center name, and target folder'); @@ -215,10 +214,14 @@ Ext4.define('MCC.window.MarkShippedWindow', { var commands = []; Ext4.Array.forEach(results.rows, function(row){ var effectiveId = win.down('#usePreviousId-' + row.Id).getValue() ? row.Id : win.down('#newId-' + row.Id).getValue(); + var requestId = win.down('#requestId-' + row.Id).getValue(); // This should be checked above, although perhaps case sensitivity could get involved: LDK.Assert.assertNotEmpty('Missing effective ID after query', effectiveId); - var shouldAddDeparture = !row['Id/MostRecentDeparture/MostRecentDeparture'] || row['Id/MostRecentDeparture/MostRecentDeparture'] !== Ext4.Date.format(row.effectiveDate, 'Y-m-d') || row.Id !== effectiveId; + var shouldAddDeparture = !row['Id/MostRecentDeparture/MostRecentDeparture'] || + row['Id/MostRecentDeparture/MostRecentDeparture'] !== Ext4.Date.format(row.effectiveDate, 'Y-m-d') || + row['Id/MostRecentDeparture/mccRequestId'] !== requestId || + row.Id !== effectiveId; if (shouldAddDeparture) { commands.push({ command: 'insert', @@ -229,7 +232,7 @@ Ext4.define('MCC.window.MarkShippedWindow', { date: effectiveDate, source: row.colony, destination: centerName, - mccTransfer: isMccTransfer, + mccRequestId: requestId, description: row.colony ? 'Original center: ' + row.colony : null, qcstate: null, objectId: null, diff --git a/mcc/src/client/RequestReview/components/ReadOnlyRequest.tsx b/mcc/src/client/RequestReview/components/ReadOnlyRequest.tsx index b6b02709..b492f30c 100644 --- a/mcc/src/client/RequestReview/components/ReadOnlyRequest.tsx +++ b/mcc/src/client/RequestReview/components/ReadOnlyRequest.tsx @@ -272,6 +272,35 @@ export default function ReadOnlyRequest(props: {requestData: AnimalRequestModel} {requestData.request.comments} + {requestData.shipments.length ? ( + <> + + Shipments: + + + +
+ + Source Colony + Date + MCC Id + + + + {requestData.shipments.map((shipment, idx) => { + return( + + {shipment.source} + {shipment.date ? new Intl.DateTimeFormat("en-US").format(new Date(shipment.date)) : ''} + {shipment.Id} + + ) + })} + +
+ + + ) : null } Status: diff --git a/mcc/src/client/U24Dashboard/Dashboard.tsx b/mcc/src/client/U24Dashboard/Dashboard.tsx index d0204d84..7acbdd8e 100644 --- a/mcc/src/client/U24Dashboard/Dashboard.tsx +++ b/mcc/src/client/U24Dashboard/Dashboard.tsx @@ -4,7 +4,7 @@ import React, { useEffect, useState } from 'react'; import { ActionURL, Filter, getServerContext, Query } from '@labkey/api'; import PieChart from '../components/dashboard/PieChart'; -import BarChart from '../components/dashboard/BarChart'; +import BarChart, { ColorType } from '../components/dashboard/BarChart'; import { ActiveElement, Chart, ChartEvent } from 'chart.js/dist/types/index'; export function Dashboard() { @@ -86,7 +86,7 @@ export function Dashboard() { containerPath: containerPath, schemaName: 'mcc', queryName: 'census', - columns: 'yearNo,startdate,enddate,centerName,totalBreedingPairs,totalLivingOffspring,survivalRates,marmosetsShipped', + columns: 'yearNo,startdate,enddate,centerName,totalLiving,totalLivingU24,totalBreedingPairs,totalBreedingPairsU24,totalOffspring,totalOffspringU24,marmosetsShipped', success: function(results) { if (isApiSubscribed) { setCensusRows(results.rows); @@ -99,7 +99,7 @@ export function Dashboard() { })) setBirthData(results.rows.flatMap(row => { - return Array(row.totalLivingOffspring).fill({ + return Array(row.totalOffspring).fill({ yearNo: row.yearNo, centerName: row.centerName }) @@ -164,7 +164,7 @@ export function Dashboard() {
-
Center (All Animals)
+
U24 Animals By Center
@@ -184,7 +184,7 @@ export function Dashboard() {
Age (Living Animals)
- +
@@ -194,7 +194,7 @@ export function Dashboard() {
U24 Births By Year
- +
@@ -202,7 +202,7 @@ export function Dashboard() {
U24 Breeding Pairs
- +
diff --git a/mcc/src/client/components/RequestUtils.tsx b/mcc/src/client/components/RequestUtils.tsx index f36bcd37..b25c4a8e 100644 --- a/mcc/src/client/components/RequestUtils.tsx +++ b/mcc/src/client/components/RequestUtils.tsx @@ -1,11 +1,12 @@ import React from 'react'; -import { Filter, Query } from '@labkey/api'; +import { Filter, getServerContext, Query } from '@labkey/api'; import { v4 as uuidv4 } from 'uuid'; export class AnimalRequestModel { request: AnimalRequestProps = new AnimalRequestProps(); coinvestigators: CoInvestigatorModel[] = []; cohorts: AnimalCohort[] = []; + shipments: ShipmentModel[] = []; dataLoaded: boolean = false; } @@ -51,6 +52,13 @@ export class AnimalRequestProps { comments: string; } +export class ShipmentModel { + Id: string; + date: string; + source: string; + objectid: string; +} + export class CoInvestigatorModel { rowid: number; requestId: string; @@ -70,6 +78,18 @@ export class AnimalCohort { uuid: string = uuidv4().toUpperCase(); } +function canReadMccStudy() { + const ctx = getServerContext().getModuleContext('mcc') || {}; + + return !!ctx.hasAnimalDataReadPermission && !!ctx.hasMccStudyReadPermission +} + +function getMccDataContainerPath() { + const ctx = getServerContext().getModuleContext('mcc') || {}; + + return ctx.hasAnimalDataReadPermission ? ctx.MCCContainer : null +} + export async function queryRequestInformation(requestId, handleFailure) { const requestData = new AnimalRequestModel() @@ -194,10 +214,43 @@ export async function queryRequestInformation(requestId, handleFailure) { }) })] + if (canReadMccStudy()) { + promises.push(new Promise((resolve, reject) => { + Query.selectRows({ + containerPath: getMccDataContainerPath(), + schemaName: "study", + queryName: "departure", + columns: [ + "Id", + "date", + "source", + "objectid" + ], + filterArray: [ + Filter.create('mccRequestId/objectId', requestId) + ], + success: function (resp) { + // NOTE: abort so that we preserve the default value of one empty row + if (!resp.rows.length) { + requestData.shipments = [] + } else { + requestData.shipments = resp.rows + } + + resolve(requestData.shipments) + }, + failure: handleFailure + }) + })) + } + return await Promise.all(promises).then(values => { requestData.request = values[0] requestData.coinvestigators = values[1] requestData.cohorts = values[2] + if (promises.length > 3) { + requestData.shipments = values[3] + } requestData.dataLoaded = true return(requestData) diff --git a/mcc/src/client/components/dashboard/BarChart.tsx b/mcc/src/client/components/dashboard/BarChart.tsx index 693dfd7c..92f5f99b 100644 --- a/mcc/src/client/components/dashboard/BarChart.tsx +++ b/mcc/src/client/components/dashboard/BarChart.tsx @@ -5,22 +5,35 @@ import { ActiveElement, ChartEvent } from 'chart.js/dist/types/index'; Chart.register(Legend, BarController, BarElement, CategoryScale, LinearScale, Tooltip); const colors = [ - 'rgb(42, 49, 116)', - 'rgb(75, 77, 135)', - 'rgb(110, 107, 155)', - 'rgb(147, 145, 181)', - 'rgb(194, 192, 210)' + "#E41A1C", + "#377EB8", + "#4DAF4A", + "#984EA3", + "#FF7F00", + "#FFFF33", + "#A65628", + "#F781BF", + "#999999" ]; -export default function BarChart(props: {demographics: [], fieldName: string, groupField?: string, indexAxis?: 'x' | 'y', onClick?: (event: ChartEvent, elements: ActiveElement[], chart: Chart) => void }) { +export enum ColorType { + PRIMARY = "primary", + GROUP = "group" +} + +export default function BarChart(props: {demographics: [], fieldName: string, groupField?: string, colorBy?: ColorType, showLegend?: boolean, indexAxis?: 'x' | 'y', missingDataTerm?: string, onClick?: (event: ChartEvent, elements: ActiveElement[], chart: Chart) => void }) { const canvas = useRef(null); const { demographics, fieldName, groupField, onClick} = props + const { colorBy = ColorType.PRIMARY } = props + const { showLegend = false } = props + const { missingDataTerm = 'None' } = props + const indexAxis: 'x' | 'y' = props.indexAxis || 'y' const collectedData = demographics.reduce((acc, curr: {}, idx) => { const value = curr[fieldName] === null ? 'Unknown' : curr[fieldName]; - const group = groupField == null ? 'counts' : curr[groupField] || 'None' + const group = groupField == null ? 'counts' : curr[groupField] || missingDataTerm if (!acc[group]) { acc[group] = {} @@ -35,13 +48,15 @@ export default function BarChart(props: {demographics: [], fieldName: string, gr return acc; }, {}); - const labels = [...new Set(Object.keys(collectedData).flatMap(groupName => Object.keys(collectedData[groupName])))]; - const dataArr: any[] = Object.keys(collectedData).map(groupName => { + const labels = [...new Set(Object.keys(collectedData).flatMap(groupName => Object.keys(collectedData[groupName])))].sort(Intl.Collator().compare) + const groupNames = Object.keys(collectedData).sort(Intl.Collator().compare) + + const dataArr: any[] = groupNames.map(groupName => { const dat = labels.map(label => collectedData[groupName] ? collectedData[groupName][label] || 0 : 0) return { label: groupName, data: dat, - backgroundColor: colors.slice(0, labels.length) + backgroundColor: colorBy == ColorType.PRIMARY ? colors.slice(0, labels.length) : colors[groupNames.indexOf(groupName)] } }); @@ -64,7 +79,8 @@ export default function BarChart(props: {demographics: [], fieldName: string, gr }, plugins: { legend: { - display: false + display: showLegend, + position: 'right' } } } diff --git a/mcc/src/client/components/dashboard/PieChart.tsx b/mcc/src/client/components/dashboard/PieChart.tsx index 55b422aa..b9a28ec8 100644 --- a/mcc/src/client/components/dashboard/PieChart.tsx +++ b/mcc/src/client/components/dashboard/PieChart.tsx @@ -10,11 +10,15 @@ import { Chart.register(ArcElement, Legend, PieController, Tooltip); const colors = [ - 'rgb(42, 49, 116)', - 'rgb(75, 77, 135)', - 'rgb(110, 107, 155)', - 'rgb(147, 145, 181)', - 'rgb(194, 192, 210)' + "#E41A1C", + "#377EB8", + "#4DAF4A", + "#984EA3", + "#FF7F00", + "#FFFF33", + "#A65628", + "#F781BF", + "#999999" ]; export default function PieChart(props) { @@ -34,7 +38,7 @@ export default function PieChart(props) { return acc; }, {}); - const labels = Object.keys(collectedData).sort(); + const labels = Object.keys(collectedData).sort(Intl.Collator().compare); const data = labels.map(label => collectedData[label]); useEffect(() => { diff --git a/mcc/src/org/labkey/mcc/MccModule.java b/mcc/src/org/labkey/mcc/MccModule.java index f421e3ab..673b3d95 100644 --- a/mcc/src/org/labkey/mcc/MccModule.java +++ b/mcc/src/org/labkey/mcc/MccModule.java @@ -29,7 +29,10 @@ import org.labkey.api.module.ModuleContext; import org.labkey.api.query.DefaultSchema; import org.labkey.api.query.QuerySchema; +import org.labkey.api.security.permissions.ReadPermission; import org.labkey.api.security.roles.RoleManager; +import org.labkey.api.study.Study; +import org.labkey.api.study.StudyService; import org.labkey.api.util.SystemMaintenance; import org.labkey.api.view.WebPartFactory; import org.labkey.api.view.template.ClientDependency; @@ -71,7 +74,7 @@ public String getName() @Override public @Nullable Double getSchemaVersion() { - return 20.016; + return 20.018; } @Override @@ -109,6 +112,17 @@ public JSONObject getPageContextJson(ContainerUser context) ret.put("hasRabPermission", requestContainer != null && requestContainer.hasPermission(context.getUser(), MccRabReviewPermission.class)); ret.put("hasFinalDecisionPermission", requestContainer != null && requestContainer.hasPermission(context.getUser(), MccFinalReviewPermission.class)); + Container dataContainer = MccManager.get().getMCCContainer(context.getContainer()); + ret.put("hasAnimalDataReadPermission", dataContainer != null && dataContainer.hasPermission(context.getUser(), ReadPermission.class)); + if (dataContainer != null) + { + Study s = StudyService.get().getStudy(dataContainer); + if (s != null) + { + ret.put("hasMccStudyReadPermission", s.hasPermission(context.getUser(), ReadPermission.class)); + } + } + return ret; } diff --git a/mcc/src/org/labkey/mcc/MccUserSchema.java b/mcc/src/org/labkey/mcc/MccUserSchema.java index a60589d6..00481485 100644 --- a/mcc/src/org/labkey/mcc/MccUserSchema.java +++ b/mcc/src/org/labkey/mcc/MccUserSchema.java @@ -116,9 +116,7 @@ else if (MccSchema.TABLE_REQUEST_SCORE.equalsIgnoreCase(name)) ret.addPermissionMapping(UpdatePermission.class, MccViewRequestsPermission.class); ret.addPermissionMapping(DeletePermission.class, MccRequestAdminPermission.class); - ret = ret.init(); - - return addScoreColumns(ret); + return ret.init(); } else if (MccSchema.TABLE_CENSUS.equalsIgnoreCase(name)) { @@ -218,9 +216,12 @@ private TableInfo getCensusQuery() " d.startdate,\n" + " d.enddate,\n" + " d.centerName,\n" + + " d.totalLiving,\n" + + " d.totalLivingU24,\n" + " d.totalBreedingPairs,\n" + - " d.totalLivingOffspring,\n" + - " d.survivalRates,\n" + + " d.totalBreedingPairsU24,\n" + + " d.totalOffspring,\n" + + " d.totalOffspringU24,\n" + " d.marmosetsShipped,\n" + " d.container\n" + "\n" + @@ -237,11 +238,11 @@ private TableInfo getDepartureQuery() " d.date,\n" + " d.source,\n" + " d.destination,\n" + - " d.mccTransfer,\n" + + " d.mccRequestId,\n" + " d.objectid,\n" + " d.container\n" + "\n" + - "FROM \"\".study.departure d WHERE d.qcstate.publicdata = true AND d.mccTransfer = true\n"; + "FROM \"\".study.departure d WHERE d.qcstate.publicdata = true AND d.mccRequestId IS NOT NULL\n"; return makeAggregatedQuery(TABLE_AGGREGATED_DEPARTURES, template); } @@ -317,41 +318,4 @@ private TableInfo makeAggregatedQuery(String queryName, String sqlTemplate) return ti; } - - private CustomPermissionsTable addScoreColumns(CustomPermissionsTable ti) - { - if (ti.getColumn("rabReviewStatus") == null) - { - SQLFragment sql = new SQLFragment("(SELECT CONCAT(COALESCE(CAST(sum(CASE WHEN r.review IS NULL THEN 0 ELSE 1 END) as varchar), '0'), ' of ', cast(count(*) as varchar), ' completed') as expr FROM mcc.requestReviews r WHERE r.requestId = " + ExprColumn.STR_TABLE_ALIAS + ".requestId)"); - ExprColumn newCol = new ExprColumn(ti, "rabReviewStatus", sql, JdbcType.VARCHAR, ti.getColumn("requestId")); - newCol.setSortFieldKeys(Collections.singletonList(FieldKey.fromString("pendingRabReviews"))); - - newCol.setLabel("RAB Review Status"); - newCol.setDisplayColumnFactory(colInfo -> { - return new DataColumn(colInfo) - { - @Override - public boolean isFilterable() - { - return false; - } - - @Override - public boolean isSortable() - { - return false; - } - }; - }); - - ti.addColumn(newCol); - - SQLFragment sql2 = new SQLFragment("(SELECT COALESCE(sum(CASE WHEN r.review IS NULL THEN 1 ELSE 0 END), -1) as expr FROM mcc.requestReviews r WHERE r.requestId = " + ExprColumn.STR_TABLE_ALIAS + ".requestId)"); - ExprColumn newCol2 = new ExprColumn(ti, "pendingRabReviews", sql2, JdbcType.INTEGER, ti.getColumn("requestId")); - newCol2.setLabel("Pending RAB Reviews"); - ti.addColumn(newCol2); - } - - return ti; - } } diff --git a/mcc/src/org/labkey/mcc/query/MccEhrCustomizer.java b/mcc/src/org/labkey/mcc/query/MccEhrCustomizer.java index dfb202f9..e917e4ac 100644 --- a/mcc/src/org/labkey/mcc/query/MccEhrCustomizer.java +++ b/mcc/src/org/labkey/mcc/query/MccEhrCustomizer.java @@ -5,6 +5,7 @@ import org.labkey.api.data.AbstractTableInfo; import org.labkey.api.data.BaseColumnInfo; import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.Container; import org.labkey.api.data.JdbcType; import org.labkey.api.data.MutableColumnInfo; import org.labkey.api.data.SQLFragment; @@ -15,7 +16,9 @@ import org.labkey.api.query.FieldKey; import org.labkey.api.query.LookupForeignKey; import org.labkey.api.query.QueryForeignKey; +import org.labkey.api.query.QueryService; import org.labkey.api.query.UserSchema; +import org.labkey.mcc.MccManager; import org.labkey.mcc.MccSchema; public class MccEhrCustomizer extends AbstractTableCustomizer @@ -48,6 +51,10 @@ else if (matches(table, "study", "kinship")) { customizeKinship((AbstractTableInfo)table); } + else if (matches(table, "study", "departure")) + { + customizeDeparture((AbstractTableInfo)table); + } } } @@ -62,6 +69,29 @@ private void customizeKinship(AbstractTableInfo ti) addMccAlias(ti, "Id2", "id2MccAlias", "Id 2 MCC Alias"); } + private void customizeDeparture(AbstractTableInfo ti) + { + MutableColumnInfo ci = ti.getMutableColumn("mccRequestId"); + if (ci == null) + { + return; + } + + Container requestContainer = MccManager.get().getMCCRequestContainer(ti.getUserSchema().getContainer()); + if (requestContainer == null) + { + return; + } + + final UserSchema us = getUserSchema(ti, MccSchema.NAME, requestContainer); + + ci.setFk(QueryForeignKey.from(us, null) + .table(us.getTable(MccSchema.TABLE_ANIMAL_REQUESTS)) + .container(us.getContainer()) + .key("rowid") + .display("rowid")); + } + private void customizeWeight(AbstractTableInfo ti) { String name = "weightGrams"; diff --git a/mcc/src/org/labkey/mcc/query/MccRequestCustomizer.java b/mcc/src/org/labkey/mcc/query/MccRequestCustomizer.java new file mode 100644 index 00000000..cf0f8607 --- /dev/null +++ b/mcc/src/org/labkey/mcc/query/MccRequestCustomizer.java @@ -0,0 +1,100 @@ +package org.labkey.mcc.query; + +import org.labkey.api.data.Container; +import org.labkey.api.data.DataColumn; +import org.labkey.api.data.JdbcType; +import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.TableInfo; +import org.labkey.api.exp.api.StorageProvisioner; +import org.labkey.api.ldk.table.AbstractTableCustomizer; +import org.labkey.api.ldk.table.CustomPermissionsTable; +import org.labkey.api.query.ExprColumn; +import org.labkey.api.query.FieldKey; +import org.labkey.api.study.Dataset; +import org.labkey.api.study.Study; +import org.labkey.api.study.StudyService; +import org.labkey.mcc.MccManager; +import org.labkey.mcc.MccSchema; + +import java.util.Collections; + +public class MccRequestCustomizer extends AbstractTableCustomizer +{ + @Override + public void customize(TableInfo tableInfo) + { + if (tableInfo instanceof CustomPermissionsTable ati) + { + customizeRequestScore(ati); + } + } + + private void customizeRequestScore(CustomPermissionsTable ti) + { + if (ti.getColumn("rabReviewStatus") == null) + { + SQLFragment sql = new SQLFragment("(SELECT CONCAT(COALESCE(CAST(sum(CASE WHEN r.review IS NULL THEN 0 ELSE 1 END) as varchar), '0'), ' of ', cast(count(*) as varchar), ' completed') as expr FROM mcc.requestReviews r WHERE r.requestId = " + ExprColumn.STR_TABLE_ALIAS + ".requestId)"); + ExprColumn newCol = new ExprColumn(ti, "rabReviewStatus", sql, JdbcType.VARCHAR, ti.getColumn("requestId")); + newCol.setSortFieldKeys(Collections.singletonList(FieldKey.fromString("pendingRabReviews"))); + + newCol.setLabel("RAB Review Status"); + newCol.setDisplayColumnFactory(colInfo -> { + return new DataColumn(colInfo) + { + @Override + public boolean isFilterable() + { + return false; + } + + @Override + public boolean isSortable() + { + return false; + } + }; + }); + + ti.addColumn(newCol); + + SQLFragment sql2 = new SQLFragment("(SELECT COALESCE(sum(CASE WHEN r.review IS NULL THEN 1 ELSE 0 END), -1) as expr FROM mcc.requestReviews r WHERE r.requestId = " + ExprColumn.STR_TABLE_ALIAS + ".requestId)"); + ExprColumn newCol2 = new ExprColumn(ti, "pendingRabReviews", sql2, JdbcType.INTEGER, ti.getColumn("requestId")); + newCol2.setLabel("Pending RAB Reviews"); + ti.addColumn(newCol2); + } + + if (ti.getColumn("transferIds") == null) + { + Container dataContainer = MccManager.get().getMCCContainer(ti.getContainer()); + if (dataContainer != null) + { + Study s = StudyService.get().getStudy(dataContainer); + if (s == null) + { + return; + } + + Dataset d = s.getDatasetByName("departure"); + if (d == null) + { + _log.error("Unable to find study.departure"); + return; + } + + TableInfo dti = StorageProvisioner.createTableInfo(d.getDomain()); + + SQLFragment sql = new SQLFragment("(SELECT "). + append(ti.getSqlDialect().getGroupConcat(new SQLFragment("d." + dti.getColumn("participantid").getSelectName()), true, true, new SQLFragment("', '"))). + append(" as expr FROM "). + append(" mcc." + MccSchema.TABLE_ANIMAL_REQUESTS + " ar JOIN studydataset.").append(dti.getName()). + append(" d ON (d.mccRequestId = ar.rowId)"). + append(" WHERE ar.objectid = " + ExprColumn.STR_TABLE_ALIAS + ".requestId)"); + + ExprColumn newCol = new ExprColumn(ti, "transferIds", sql, JdbcType.VARCHAR, ti.getColumn("requestId")); + newCol.setLabel("Animal ID(s)"); + newCol.setWidth("100"); + ti.addColumn(newCol); + } + } + } +} diff --git a/primeseq/src/org/labkey/primeseq/analysis/MethylationRateComparisonHandler.java b/primeseq/src/org/labkey/primeseq/analysis/MethylationRateComparisonHandler.java index ef7dd9ae..633a0827 100644 --- a/primeseq/src/org/labkey/primeseq/analysis/MethylationRateComparisonHandler.java +++ b/primeseq/src/org/labkey/primeseq/analysis/MethylationRateComparisonHandler.java @@ -143,13 +143,13 @@ public SequenceOutputProcessor getProcessor() public class Processor implements SequenceOutputProcessor { @Override - public void complete(PipelineJob job, List inputs, List outputsCreated, SequenceAnalysisJobSupport support) throws PipelineJobException + public void complete(JobContext ctx, List inputs, List outputsCreated) throws PipelineJobException { for (SequenceOutputFile so : outputsCreated) { if (so.getFile().getName().endsWith(".bed") && METHYLATION_RATE_COMPARISON.equals(so.getCategory())) { - job.getLogger().debug("preparing JBrowse files: " + so.getFile().getName()); + ctx.getJob().getLogger().debug("preparing JBrowse files: " + so.getFile().getName()); JSONObject json = new JSONObject(); json.put("type", "JBrowse/View/Track/Wiggle/XYPlot"); @@ -157,7 +157,7 @@ public void complete(PipelineJob job, List inputs, List inputFiles, List outputsCreated, SequenceAnalysisJobSupport support) throws PipelineJobException + public void complete(JobContext ctx, List inputFiles, List outputsCreated) throws PipelineJobException { for (SequenceOutputFile so : outputsCreated) { if (CATEGORY.equals(so.getCategory())) { - CellHashingService.get().processMetrics(so, job, true); + CellHashingService.get().processMetrics(so, ctx.getJob(), true); } } - if (StringUtils.trimToNull(job.getParameters().get(TARGET_ASSAY)) == null) + if (StringUtils.trimToNull(ctx.getJob().getParameters().get(TARGET_ASSAY)) == null) { - job.getLogger().info("No assay selected, will not import"); + ctx.getJob().getLogger().info("No assay selected, will not import"); } else { - Integer assayId = ConvertHelper.convert(job.getParameters().get(TARGET_ASSAY), Integer.class); + Integer assayId = ConvertHelper.convert(ctx.getJob().getParameters().get(TARGET_ASSAY), Integer.class); if (assayId == null) { - throw new PipelineJobException("Invalid assay Id, cannot import: " + job.getParameters().get(TARGET_ASSAY)); + throw new PipelineJobException("Invalid assay Id, cannot import: " + ctx.getJob().getParameters().get(TARGET_ASSAY)); } boolean deleteExistingData = false; - if (job.getParameters().get(DELETE_EXISTING_ASSAY_DATA) != null) + if (ctx.getJob().getParameters().get(DELETE_EXISTING_ASSAY_DATA) != null) { - deleteExistingData = ConvertHelper.convert(job.getParameters().get(DELETE_EXISTING_ASSAY_DATA), Boolean.class); + deleteExistingData = ConvertHelper.convert(ctx.getJob().getParameters().get(DELETE_EXISTING_ASSAY_DATA), Boolean.class); } for (SequenceOutputFile so : inputFiles) { - AnalysisModel model = support.getCachedAnalysis(so.getAnalysis_id()); - new CellRangerVDJUtils(job.getLogger()).importAssayData(job, model, so.getFile(), job.getLogFile().getParentFile(), assayId, null, deleteExistingData); + AnalysisModel model = ctx.getSequenceSupport().getCachedAnalysis(so.getAnalysis_id()); + new CellRangerVDJUtils(ctx.getJob().getLogger()).importAssayData(ctx.getJob(), model, so.getFile(), ctx.getJob().getLogFile().getParentFile(), assayId, null, deleteExistingData); } } }