Merge pull request #2022 from trendscenter/secopt-hotfix

add sec options to get past pthread issues on docker

Author: rssk

packages/coinstac-api-server/seed/data/coinstac-dcsbm.json

@@ -0,0 +1,109 @@
+{
+    "meta": {
+        "name": "Decentralized Source Based Morphometry",
+        "id": "coinstac-dsbm",
+        "version": "v1.0.0",
+        "compspecVersion": 2,
+        "repository": "https://github.com/trendscenter/decentralized-source-based-morphometry",
+        "description": "A Demo for Decentralized Source Based Morphometry"
+    },
+    "computation": {
+        "display": {
+            "type": "iframe"
+        },
+        "input": {
+            "data": {
+                "label": "Data",
+                "type": "files",
+                "items": [
+                    "NiFTI"
+                ],
+                "extensions": [
+                    [
+                        "nii"
+                    ]
+                ],
+                "source": "member",
+                "order": 1
+            },
+            "mask": {
+                "group": "options",
+                "default": "/computation/local_data/mask.nii",
+                "label": "Mask Filename",
+                "type": "string",
+                "source": "owner",
+                "tooltip": "Nifti file name to be use as the mask",
+                "order": 2
+            },
+            "scica_template": {
+                "group": "options",
+                "default": "/computation/local_data/Neuromark_sMRI_1.0_modelorder-30_2x2x2.nii",
+                "label": "Spatially Constrained ICA Template Name",
+                "type": "string",
+                "source": "owner",
+                "tooltip": "Nifti file name to be use as the template for spatially constrained ICA",
+                "order": 3
+            },
+            "subsample_nifti_images": {
+                "group": "options",
+                "default": "false",
+                "label": "Perform input nifti subsampling",
+                "type": "boolean",
+                "source": "owner",
+                "tooltip": "true to subsample nifti images else false",
+                "order": 4
+            },
+            "voxel_size": {
+                "group": "options",
+                "default": "2",
+                "label": "Voxel size (subsampling)",
+                "type": "number",
+                "source": "owner",
+                "tooltip": "Voxel size to subsample nifti images",
+                "order": 4
+            },
+            "covariates": {
+                "group": "Regression variables",
+                "label": "Covariates",
+                "type": "csv",
+                "items": ["boolean", "number", "string"],
+                "source": "member",
+                "tooltip": "csv file with nifti file name, covariates information of each subject in a separate line",
+                 "order": 5
+            },
+            "reference_columns": {
+                "group": "Regression variables",
+                "label": "Regression reference column(s) and value(s)",
+                "default": {},
+                "type": "object",
+                "source": "owner",
+                "tooltip": "Used in regression for dummy encoding categorical covariate columns. Required only if specific value(s) should be used for dummy encoding a column(s); Example : { \"reference_column_name\": \"reference_value\" }",
+                "order": 6
+            },
+            "group_col_name": {
+                "group": "Regression variables",
+                "label": "Patient/Control column name",
+                "default": "",
+                "type": "string",
+                "source": "owner",
+                "tooltip": "Column name in the covariates file that contains patients and controls information.",
+                "order": 6
+            }
+        },
+        "output": {},
+        "type": "docker",
+        "dockerImage": "coinstacteam/coinstac-dsbm",
+        "command": [
+            "python",
+            "/computation/local.py"
+        ],
+        "remote": {
+            "type": "docker",
+            "dockerImage": "coinstacteam/coinstac-dsbm",
+            "command": [
+                "python",
+                "/computation/remote.py"
+            ]
+        }
+    }
+}

packages/coinstac-api-server/seed/populate.js

@@ -9,6 +9,7 @@ const dlmeFS = require('./data/coinstac-dlme-fs.json');
 const dlmeVBM = require('./data/coinstac-dlme-vbm.json');
 const dpica = require('./data/coinstac-dpica.json');
 const dsneMS = require('./data/coinstac-dsne-ms.json');
+const dcsbm = require('./data/coinstac-dcsbm.json');
 const drneVbm = require('./data/coinstac-schema-regression-vbm.json');
 // const ssrVbm = require('./data/coinstac-schema-regression-ss-vbm');
 const msrVbm = require('./data/coinstac-schema-regression-ms-vbm.json');
@@ -43,7 +44,7 @@ const CONSORTIA_IDS = generateUniqueIDs(2);
 
 const PIPELINE_IDS = generateUniqueIDs(4);
 
-const COMPUTATION_IDS = generateUniqueIDs(28);
+const COMPUTATION_IDS = generateUniqueIDs(29);
 
 const USER_IDS = generateUniqueIDs(6);
 
@@ -81,6 +82,8 @@ async function populateComputations() {
     { ...dlmeVBM, submittedBy: 'author', _id: COMPUTATION_IDS[25] },
     { ...transfer, submittedBy: 'author', _id: COMPUTATION_IDS[26] },
     { ...stress, submittedBy: 'author', _id: COMPUTATION_IDS[27] },
+    { ...dcsbm, submittedBy: 'author', _id: COMPUTATION_IDS[28] },
+
   ];
   const currentComps = await db.collection('computations').find().toArray();
   const operations = comps2Insert.reduce((ops, comp) => {

packages/coinstac-container-manager/src/services/docker.js

@@ -118,6 +118,7 @@ module.exports = {
         Image: dockerImage,
         HostConfig: {
           Binds: [...mounts],
+          SecurityOpt: ['seccomp=unconfined'],
         },
       }, containerOptions),
     };
@@ -176,6 +177,7 @@ module.exports = {
             [tcpOpt]: [{ HostPort: `${port}`, HostIp: process.env.CI ? '' : '127.0.0.1' }],
             ...(process.LOGLEVEL === 'debug' && { '4444/tcp': [{ HostPort: `44${portmunge}`, HostIp: '127.0.0.1' }] }),
           },
+          SecurityOpt: ['seccomp=unconfined'],
         },
         Tty: true,
       };