Merge conflicts

.gitignore

@@ -1,4 +1,5 @@
 *.iml
+Callback*
 .*_history
 .project
 .idea

README.md

@@ -4,18 +4,17 @@
 # orion-data
   **Description**: Repo for the KPMP upload tool back-end
 
+## Documentation
+Visit [kpmp.github.io/dlu](http://kpmp.io.github.io/dlu)
+
 ## RegenerateZipFiles
 To regenerate zip files:
  1. Connect to mongo
  2. Set `regenerateZip` to true for any packages you want to regenerate zip files for
  3. Connect to server you need to regenerate zips for
- 4. Navigate to heavens-docker/orion
- 5. Bash into the spring container
- `docker exec -it spring bash`
- 6. Rebuild the orion-data jar
- `./gradlew build -x test`
+ 4. Navigate to orion-data/scripts/processLargeFileUpload
  7. Run the zip generator
- `java -cp build/libs/orion-data.jar -Dloader.main=org.kpmp.RegenerateZipFiles org.springframework.boot.loader.PropertiesLauncher`
+ `java -cp ../../build/libs/orion-data.jar -Dloader.main=org.kpmp.RegenerateZipFiles org.springframework.boot.loader.PropertiesLauncher`
 
 ## Getting and storing the credentials for Google Drive
  1. Get the credentials.json file from kpmp-secure/orion-data and put it in the `src/main/resources` directory.

build.gradle

@@ -15,7 +15,7 @@ apply plugin: 'io.spring.dependency-management'
 
 jar {
     baseName='orion-data'
-    version= '2.7'
+    version= '2.8'
 }
 
 repositories {

data/packageTypeIcons.json

@@ -0,0 +1,6 @@
+{"_id":{"$oid":"5c99063ed5928f3d4502a9b3"},"iconType":"Metabolomics","packageTypes":["Spatial Metabolomics"]}
+{"_id":{"$oid":"5c99063ed5928f3d4502a9b4"},"iconType":"Imaging","packageTypes":["3-D Tissue Imaging","Multiplex ISH","CODEX","Whole Slide Images"]}
+{"_id":{"$oid":"5c99063ed5928f3d4502a9b5"},"iconType":"Proteomics","packageTypes":["Bulk Proteomics","Sub-segmental Proteomics","Near-single-cell Proteomics"]}
+{"_id":{"$oid":"5c99063ed5928f3d4502a9b6"},"iconType":"Transcriptomics","packageTypes":["Bulk total/mRNA","Bulk microRNA","Segmental miRNA","Sub-segmental RNA-Seq","Single-cell RNA-Seq","Single-nucleus RNA-Seq"]}
+{"_id":{"$oid":"5c99063ed5928f3d4502a9b7"},"iconType":"Pilot 3","packageTypes":["Pilot 3 Receipt Picture"]}
+{"_id":{"$oid":"5c99063ed5928f3d4502a9b8"},"iconType":"Other","packageTypes":["DNA Methylation","Other"]}

data/packages-template.json

@@ -0,0 +1,37 @@
+{
+    "_id": "c207526f-e02d-42c9-ad75-13a412fa41ec",
+    "packageType": "Multiplex ISH",
+    "protocol": "Other",
+    "createdAt": {
+        "$date": {
+            "$numberLong": "1582133806448"
+        }
+    },
+    "subjectId": "Smoke Testing on FF",
+    "description": "Smoke Testing on FF",
+    "submitter": {
+        "$id": {
+            "$oid": "5c49b80acb5e71004965b0f9"
+        }
+    },
+    "version": {
+        "$numberInt": "1"
+    },
+    "tisName": "UCSD/WashU",
+    "largeFilesChecked": false,
+    "tisInternalExperimentID": "Smoke Testing on FF",
+    "dataGenerators": "Smoke Testing on FF",
+    "files": [{
+        "fileName": "Data Map v3.png",
+        "size": {
+            "$numberInt": "307790"
+        },
+        "_id": "090d6835-3d96-4781-ab8c-1d6dd85aef36"
+    }, {
+        "fileName": "MiKTMC-Template.pptx",
+        "size": {
+            "$numberInt": "131571"
+        },
+        "_id": "247238c0-2ad9-42b6-957c-74cbd9dac553"
+    }],
+}

data/releases-template.json

@@ -0,0 +1,5 @@
+{
+    "version": "0",
+    "date": "May 2018",
+    "desc": "Minimal metadata collected."
+}

data/state-template.json

@@ -0,0 +1,9 @@
+{
+    "packageId": "f082ce48-e468-4be3-acfb-868d6330b5c0",
+    "state": "UPLOAD_STARTED",
+    "stateChangeDate": {
+        "$date": {
+            "$numberLong": "1568042551419"
+        }
+    },
+}

data/stateDisplay.json

@@ -0,0 +1,129 @@
+[{
+  "_id": {
+    "$oid": "5eb2d66880412d1b368962a4"
+  },
+  "state": "FILES_RECEIVED",
+  "apps": {
+    "dlu": {
+      "text": "Finishing upload",
+      "alertType": "success"
+    }
+  }
+},{
+  "_id": {
+    "$oid": "5eb2d79c80412d1b368962a5"
+  },
+  "state": "METADATA_RECEIVED",
+  "apps": {
+    "dlu": {
+      "text": "Waiting for files...",
+      "alertType": "primary"
+    }
+  }
+},{
+  "_id": {
+    "$oid": "5eb2d7f380412d1b368962a6"
+  },
+  "state": "UPLOAD_FAILED",
+  "apps": {
+    "dlu": {
+      "text": "Upload failed",
+      "alertType": "danger"
+    }
+  }
+},{
+  "_id": {
+    "$oid": "5ecd77052e72d5a73904dce2"
+  },
+  "state": "INITIAL_METADATA_RECEIVED",
+  "apps": {
+    "dlu": {
+      "text": "Waiting for files...",
+      "alertType": "primary"
+    }
+  }
+},{
+  "_id": {
+    "$oid": "5ecd77622e72d5a73904dce3"
+  },
+  "state": "UPLOAD_SUCCEEDED",
+  "apps": {
+    "dlu": {
+      "text": "DVC QC Pending",
+      "alertType": "warning",
+      "showDownload": true
+    }
+  }
+},{
+  "_id": {
+    "$oid": "5ecd777c2e72d5a73904dce4"
+  },
+  "state": "PACKAGE_LEVEL_REVIEW_STARTED",
+  "apps": {
+    "dlu": {
+      "text": "DVC QC Pending",
+      "alertType": "warning",
+      "showDownload": true
+    }
+  }
+},{
+  "_id": {
+    "$oid": "5ecd778f2e72d5a73904dce5"
+  },
+  "state": "PACKAGE_LEVEL_REVIEW_SUCCEEDED",
+  "apps": {
+    "dlu": {
+      "text": "DVC QC Pending",
+      "alertType": "warning",
+      "showDownload": true
+    }
+  }
+},{
+  "_id": {
+    "$oid": "5ecd77a42e72d5a73904dce6"
+  },
+  "state": "PACKAGE_LEVEL_REVIEW_FAILED",
+  "apps": {
+    "dlu": {
+      "text": "DVC QC Rejected",
+      "alertType": "danger",
+      "showDownload": true
+    }
+  }
+},{
+  "_id": {
+    "$oid": "5ecd78882e72d5a73904dce7"
+  },
+  "state": "PROPERTY_LEVEL_REVIEW_STARTED",
+  "apps": {
+    "dlu": {
+      "text": "DVC QC Pending",
+      "alertType": "warning",
+      "showDownload": true
+    }
+  }
+},{
+  "_id": {
+    "$oid": "5ecd78ab2e72d5a73904dce8"
+  },
+  "state": "PROPERTY_LEVEL_REVIEW_FAILED",
+  "apps": {
+    "dlu": {
+      "text": "DVC QC Rejected",
+      "alertType": "danger",
+      "showDownload": true
+    }
+  }
+},{
+  "_id": {
+    "$oid": "5ecd78c32e72d5a73904dce9"
+  },
+  "state": "PROPERTY_LEVEL_REVIEW_SUCCEEDED",
+  "apps": {
+    "dlu": {
+      "text": "DVC QC Approved",
+      "alertType": "success",
+      "showDownload": true
+    }
+  }
+}]

data/users-template.json

@@ -0,0 +1,7 @@
+{
+    "firstName": "Michael",
+    "lastName": "Rosebud",
+    "displayName": "Michael Rosebud",
+    "email": "[email protected]"
+    "shibId": "[email protected]",
+}

scripts/processLargeFileUpload/README.md

@@ -0,0 +1,9 @@
+#Process Large File Upload
+
+If installing this on a new server, first you will need to run npm install in order to get the appropriate packages to update mongo.
+
+Since this process could take a long time to complete, you will likely want to run it in screen.
+
+Then, just run processLargeFileUpload and provide the packageId you want to process when it prompts you.
+
+Pay attention to the output to see if it was sucessful.