Update the boxplot plugin.

open-prophetdb · Oct 10, 2024 · c500cb1 · c500cb1
1 parent 0965b8f
commit c500cb1
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Showing 10 changed files with 161 additions and 31 deletions.
diff --git a/cromwell-api-rs/.gitignore b/cromwell-api-rs/.gitignore
@@ -1,2 +1,5 @@
 .DS_Store
-/target
+/target
+cromwell-8*.jar
+cromwell-executions
+cromwell-workflow-logs
diff --git a/cromwell-api-rs/examples/README.md b/cromwell-api-rs/examples/README.md
@@ -0,0 +1,40 @@
+## How to test the workflow
+
+1. Start the cromwell server
+
+```bash
+java -jar cromwell-82.jar server
+```
+
+2. Install the dependencies
+
+```bash
+conda activate biomedgps
+conda install -c conda-forge xxx
+
+# Example for installing the R package
+R -e "devtools::install_git('file:///Users/jy006/Documents/Code/BioMiner/omix-insight-r')"
+```
+
+3. Run the workflow
+
+```bash
+cargo run --example hello_world
+```
+
+## How to deploy the workflow
+
+1. Rsync the workflow to the server
+
+```bash
+rsync -avP ./cromwell-api-rs/examples/boxplot/ [email protected]:/data/biomedgps/cromwell/workflows/boxplot-v0.1.0
+```
+
+2. Update the dependencies
+
+```bash
+# Login to the server
+
+# Update the dependencies
+/opt/miniconda3/envs/biomedgps/bin/R -e "devtools::install_git('file:///data/biomedgps/cromwell/workflows/boxplot-v0.1.0')"
+```
diff --git a/cromwell-api-rs/examples/boxplot/README.md b/cromwell-api-rs/examples/boxplot/README.md
@@ -6,7 +6,7 @@ Generate boxplot for selected genes / proteins across groups.
 
 - `exp_file`: Expression matrix file.
 - `sample_info_file`: Sample information file.
-- `which_entrez_ids`: Which entrez ids to select.
+- `which_ids`: Which ids to select.
 - `which_gene_symbols`: Which gene symbols to select.
 - `which_groups`: Which groups to select.
 - `output_file`: Output file.

diff --git a/cromwell-api-rs/examples/boxplot/boxplot.R b/cromwell-api-rs/examples/boxplot/boxplot.R
@@ -15,15 +15,15 @@ library(OmixInsightR)
 print("Running OmixInsightR for boxplot")
 
 print("Querying data from expression matrix and sample information")
-which_entrez_ids <- unlist(strsplit(args_json$which_entrez_ids, ","))
+which_ids <- unlist(strsplit(args_json$which_ids, ","))
 which_gene_symbols <- unlist(strsplit(args_json$which_gene_symbols, ","))
 which_groups <- unlist(strsplit(args_json$which_groups, ","))
 
-print(paste("Querying data from expression matrix and sample information:", args_json$exp_file, args_json$sample_info_file, which_entrez_ids, which_gene_symbols, which_groups))
+print(paste("Querying data from expression matrix and sample information:", args_json$exp_file, args_json$sample_info_file, which_ids, which_gene_symbols, which_groups))
 d <- query_data(
     exp_file = args_json$exp_file,
     sample_info_file = args_json$sample_info_file,
-    which_entrez_ids = which_entrez_ids,
+    which_ids = which_ids,
     which_gene_symbols = which_gene_symbols,
     which_groups = which_groups
 )

diff --git a/cromwell-api-rs/examples/boxplot/inputs.json b/cromwell-api-rs/examples/boxplot/inputs.json
@@ -1,7 +1,7 @@
 {
     "boxplot.boxplot_task.exp_file": "/Users/jy006/Documents/Code/BioMiner/omix-insight-r/examples/gene_expression.tsv",
     "boxplot.boxplot_task.sample_info_file": "/Users/jy006/Documents/Code/BioMiner/omix-insight-r/examples/sample_info.tsv",
-    "boxplot.boxplot_task.which_entrez_ids": [],
+    "boxplot.boxplot_task.which_ids": [],
     "boxplot.boxplot_task.which_gene_symbols": ["BDNF", "TP53"],
     "boxplot.boxplot_task.which_groups": ["Female_MECFS", "Female_Control"],
     "boxplot.boxplot_task.method": "t.test",

diff --git a/cromwell-api-rs/examples/boxplot/workflow.wdl b/cromwell-api-rs/examples/boxplot/workflow.wdl
@@ -9,7 +9,7 @@ task boxplot_task {
     input {
         String exp_file
         String sample_info_file
-        Array[String] which_entrez_ids
+        Array[String] which_ids
         Array[String] which_gene_symbols
         Array[String] which_groups
         String method
@@ -23,7 +23,7 @@ task boxplot_task {
         echo "Generating a args file, named args.json"
         echo "exp_file: ~{exp_file}"
         echo "sample_info_file: ~{sample_info_file}"
-        echo "which_entrez_ids: ~{sep=", " which_entrez_ids}"
+        echo "which_ids: ~{sep=", " which_ids}"
         echo "which_gene_symbols: ~{sep=", " which_gene_symbols}"
         echo "which_groups: ~{sep=", " which_groups}"
         echo "method: ~{method}"
@@ -36,7 +36,7 @@ task boxplot_task {
         {
             "exp_file": "~{exp_file}",
             "sample_info_file": "~{sample_info_file}",
-            "which_entrez_ids": "~{sep=',' which_entrez_ids}",
+            "which_ids": "~{sep=',' which_ids}",
             "which_gene_symbols": "~{sep=',' which_gene_symbols}",
             "which_groups": "~{sep=',' which_groups}",
             "method": "~{method}",

diff --git a/studio/src/StatEngine/components/ArgumentForm/index.tsx b/studio/src/StatEngine/components/ArgumentForm/index.tsx
@@ -18,13 +18,80 @@ type DataItem = {
 const datasets = [
   {
     datasetName: "GSE251790_Female_CSF",
+    datasetDescription: "[Protein] Deep phenotyping of Post-infectious Myalgic Encephalomyelitis/Chronic Fatigue Syndrome",
     fieldValue: {
-      exp_file: "/data/biomedgps/cromwell/data/gene_expression.tsv",
-      sample_info_file: "/data/biomedgps/cromwell/data/sample_info.tsv",
+      exp_file: "/data/biomedgps/cromwell/data/GSE251790_Female_CSF/expression_data.tsv",
+      sample_info_file: "/data/biomedgps/cromwell/data/GSE251790_Female_CSF/sample_info.tsv",
     },
     fieldValueEnum: {
       which_groups: ["Female_MECFS", "Female_Control"]
     }
+  },
+  {
+    datasetName: "GSE245661_Female_Muscle",
+    datasetDescription: "[RNA-seq] Deep phenotyping of Post-infectious Myalgic Encephalomyelitis/Chronic Fatigue Syndrome",
+    fieldValue: {
+      exp_file: "/data/biomedgps/cromwell/data/GSE245661_Female_Muscle/expression_data.tsv",
+      sample_info_file: "/data/biomedgps/cromwell/data/GSE245661_Female_Muscle/sample_info.tsv",
+    },
+    fieldValueEnum: {
+      which_groups: ["HV", "MECFS"]
+    }
+  },
+  {
+    datasetName: "GSE254030_Female_Plasma",
+    datasetDescription: "[Protein] Deep phenotyping of Post-infectious Myalgic Encephalomyelitis/Chronic Fatigue Syndrome",
+    fieldValue: {
+      exp_file: "/data/biomedgps/cromwell/data/GSE254030_Female_Plasma/expression_data.tsv",
+      sample_info_file: "/data/biomedgps/cromwell/data/GSE254030_Female_Plasma/sample_info.tsv",
+    },
+    fieldValueEnum: {
+      which_groups: ["Female_MECFS", "Female_Control"]
+    }
+  },
+  {
+    datasetName: "GSE254030_Full_Plasma",
+    datasetDescription: "[Protein] Deep phenotyping of Post-infectious Myalgic Encephalomyelitis/Chronic Fatigue Syndrome",
+    fieldValue: {
+      exp_file: "/data/biomedgps/cromwell/data/GSE254030_Full_Plasma/expression_data.tsv",
+      sample_info_file: "/data/biomedgps/cromwell/data/GSE254030_Full_Plasma/sample_info.tsv",
+    },
+    fieldValueEnum: {
+      which_groups: ["MECFS", "Control"]
+    }
+  },
+  {
+    datasetName: "GSE254030_Male_Plasma",
+    datasetDescription: "[Protein] Deep phenotyping of Post-infectious Myalgic Encephalomyelitis/Chronic Fatigue Syndrome",
+    fieldValue: {
+      exp_file: "/data/biomedgps/cromwell/data/GSE254030_Male_Plasma/expression_data.tsv",
+      sample_info_file: "/data/biomedgps/cromwell/data/GSE254030_Male_Plasma/sample_info.tsv",
+    },
+    fieldValueEnum: {
+      which_groups: ["Male_MECFS", "Male_Control"]
+    }
+  },
+  {
+    datasetName: "MaureenHanson_Female_Plasma",
+    datasetDescription: "[Protein] In-Depth Analysis of the Plasma Proteome in ME/CFS Exposes Disrupted Ephrin-Eph and Immune System Signaling",
+    fieldValue: {
+      exp_file: "/data/biomedgps/cromwell/data/MaureenHanson_Female_Plasma/expression_data.tsv",
+      sample_info_file: "/data/biomedgps/cromwell/data/MaureenHanson_Female_Plasma/sample_info.tsv",
+    },
+    fieldValueEnum: {
+      which_groups: ["MECFS", "Control"]
+    }
+  },
+  {
+    datasetName: "Zenodo7781290_Bacterial_Viral",
+    datasetDescription: "A multi-platform approach to identify a blood-based host protein signature for distinguishing between bacterial and viral infections in febrile children (PERFORM): a multi-cohort machine learning study",
+    fieldValue: {
+      exp_file: "/data/biomedgps/cromwell/data/Zenodo7781290_Bacterial_Viral/expression_data.tsv",
+      sample_info_file: "/data/biomedgps/cromwell/data/Zenodo7781290_Bacterial_Viral/sample_info.tsv",
+    },
+    fieldValueEnum: {
+      which_groups: ["DefiniteBacterial", "DefiniteViral", "HealthyControl"]
+    }
   }
 ]
 
@@ -133,8 +200,10 @@ const ArgumentForm: React.FC<ArgumentProps> = (props) => {
                   })
                 }}>
                   {datasets.map((dataset) => (
-                    <Select.Option key={dataset.datasetName} value={dataset.datasetName}>
-                      {dataset.datasetName}
+                    <Select.Option key={dataset.datasetName} value={dataset.datasetName} style={{ width: '100%' }}>
+                      <span>{dataset.datasetName}</span>
+                      <br />
+                      <span style={{ fontSize: '12px', color: 'gray', wordBreak: 'break-all', whiteSpace: 'normal' }}>{dataset.datasetDescription}</span>
                     </Select.Option>
                   ))}
                 </Select>

diff --git a/studio/src/StatEngine/components/ResultPanel/index.tsx b/studio/src/StatEngine/components/ResultPanel/index.tsx
@@ -24,6 +24,7 @@ import type { ChartResult } from '../WorkflowList/data';
 import type { PlotlyChart } from 'biominer-components/dist/PlotlyViewer/data';
 import { fetchFileByFileName } from '../../../services/swagger/KnowledgeGraph';
 import type { Workflow, TaskHistory, FileMeta } from '../WorkflowList/data';
+import { formatDuration } from './util';
 
 // AG Grid theme
 import 'ag-grid-enterprise';
@@ -207,23 +208,7 @@ const ResultPanel: React.FC<ResultPanelProps> = (props) => {
       duration = finishedTime - startedTime;
     }
 
-    const durationInSeconds = duration / 1000;
-
-    if (durationInSeconds <= 0) {
-      return '0s';
-    }
-
-    if (durationInSeconds < 60) {
-      return `${Math.round(durationInSeconds)}s`;
-    } else if (durationInSeconds < 3600) {
-      const minutes = Math.floor(durationInSeconds / 60);
-      const seconds = Math.round(durationInSeconds % 60);
-      return seconds > 0 ? `${minutes}min ${seconds}s` : `${minutes}min`;
-    } else {
-      const hours = Math.floor(durationInSeconds / 3600);
-      const minutes = Math.floor((durationInSeconds % 3600) / 60);
-      return minutes > 0 ? `${hours}h ${minutes}min` : `${hours}h`;
-    }
+    return formatDuration(duration);
   };
 
   useEffect(() => {

diff --git a/studio/src/StatEngine/components/ResultPanel/util.ts b/studio/src/StatEngine/components/ResultPanel/util.ts
@@ -0,0 +1,19 @@
+export const formatDuration = (duration: number) => {
+    const durationInSeconds = duration / 1000;
+
+    if (durationInSeconds <= 0) {
+        return '0s';
+    }
+
+    if (durationInSeconds < 60) {
+        return `${Math.round(durationInSeconds)}s`;
+    } else if (durationInSeconds < 3600) {
+        const minutes = Math.floor(durationInSeconds / 60);
+        const seconds = Math.round(durationInSeconds % 60);
+        return seconds > 0 ? `${minutes}min ${seconds}s` : `${minutes}min`;
+    } else {
+        const hours = Math.floor(durationInSeconds / 3600);
+        const minutes = Math.floor((durationInSeconds % 3600) / 60);
+        return minutes > 0 ? `${hours}h ${minutes}min` : `${hours}h`;
+    }
+};
diff --git a/studio/src/pages/OmicsData/TaskHistory.tsx b/studio/src/pages/OmicsData/TaskHistory.tsx
@@ -3,6 +3,7 @@ import { Table, Row, Tag, Space, message, Popover, Button, Input } from 'antd';
 import type { ColumnsType } from 'antd/es/table';
 import { TaskHistory, TaskHistoryTableData } from '../../StatEngine/components/WorkflowList/data';
 import { fetchTasks, deleteTask } from '@/services/swagger/KnowledgeGraph';
+import { formatDuration } from '../../StatEngine/components/ResultPanel/util';
 
 type TaskHistoryTableProps = {
     page?: number;
@@ -35,7 +36,7 @@ const TaskHistoryTable: React.FC<TaskHistoryTableProps> = forwardRef((props, ref
             align: 'center',
             dataIndex: 'task_name',
             fixed: 'left',
-            width: 150,
+            width: 200,
         },
         {
             title: 'Description',
@@ -90,6 +91,19 @@ const TaskHistoryTable: React.FC<TaskHistoryTableProps> = forwardRef((props, ref
             },
             width: 200,
         },
+        {
+            title: 'Duration',
+            key: 'duration',
+            align: 'center',
+            width: 100,
+            render: (text, record) => {
+                const finishedTime = record.finished_time ? new Date(record.finished_time).getTime() : new Date().getTime();
+                const submittedTime = new Date(record.submitted_time).getTime();
+                const duration = finishedTime - submittedTime;
+
+                return formatDuration(duration);
+            },
+        },
         {
             title: 'Status',
             dataIndex: 'status',