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- Script for exporting data from Tools Catalog to BD Transformations
- Code to talk to NCSA LDAP for authentication
- Clusterman endpoint to read from BD Transformations database
- Flask Services
- POST <extractors/converters>_info.json to MongoDB
- GET <extractors/converters>_info.json for a specific transformation
- GET all transformations
- GET all transformations that uses a specific software
JSON Document Example
Mapping Table
Note: Changing to camel case notation for field names as MongoDB documents follow JSON.
Sl. No. | Tools Catalog Field | Transformations Catalog Field | Type | Remarks |
---|---|---|---|---|
1. | status | N/A | Integer | |
2. | creationDate | dateCreated | Date | |
3. | updateDate | dateUpdated | Date | |
4. | downloads | N/A | Integer | |
5. | license | N/A | String | |
6. | whatsnew | description | String | |
7. | compatibility | N/A | String | |
8. | url | url | String | URL |
9. | sample_input | N/A | String | URL |
10. | sample_output | N/A | String | URL |
11. | interfaceLevel | N/A | Integer | |
12. | dockerimageName | dockerImageName | String | |
13. | vmImageName | N/A | String | |
14. | dockerfile | N/A | String | Email ID |
15. | author | author | String | |
16. | dependencies | dependencies | Array | Array of Strings |
17. | transformation_type | transformationType | String | Originally this field type was an integrer with values 1 for converter and 2 for extractor |
18. | transformation_id | transformationId | String | Extractor name / converter name |
19. | title | title | String |
Transformations Catalog Example
Code Block | ||||
---|---|---|---|---|
| ||||
{
"_id" : ObjectId("53864aee7400009900ec8d22"),
"dateCreated" : ISODate("2014-05-28T20:45:34.412Z"),
"dateUpdated" : ISODate("2016-11-21T04:09:47.836Z"),
"description" : "Identify tumors in microscopy images.",
"url" : "https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-cv/browse/cellprofiler/cellprofiler-tumor?raw",
"dockerImageName" : "",
"author" : "ruiliu@illinois.edu",
"dependencies" : [
"Cell Profiler"
],
"externalServices" : [
],
"transformationType" : "extractor",
"transformationId" : "",
"title" : "Tumors",
"status" : "submitted"
} |
Extractor Info Example
Code Block | ||||
---|---|---|---|---|
| ||||
{ "@context": "http://clowder.ncsa.illinois.edu/contexts/extractors.jsonld", "name": "ncsa.csvheaders", "version": "1.0", "description": "Extracts the headers of CSV file. Only looks at the first row.", "author": "Yan Zhao <yanzhao3@illinois.edu>", "contributors": ["Luigi Marini <lmarini@illinois.edu>"], "contexts": [ { "csv_headers": "http://clowder.ncsa.illinois.edu/metadata/ncsa.csvheaders#csv_headers" } ], "repository": [ { "repType": "git", "repUrl": "https://opensource.ncsa.illinois.edu/bitbucket/scm/iarp/extractors.git" }, { "repType": "docker", "repUrl": "clowder/extractors-csvheaders" } ], "process": { "file": [ "text/csv" ] }, "external_services":[], "dependencies": [], "bibtex": [] } |
...
Converter Info Example
Code Block | ||||
---|---|---|---|---|
| ||||
{ "_idname" : ObjectId("53864aee7400009900ec8d22ImageMagick"), "statusversion" : 4"1.0", "creationDatedescription" : ISODate("2014-05-28T20:45:34.412Z")"Converts images from one format to another", "updateDateauthor" : ISODate("2016-11-21T04:09:47.836Z")"Kenton McHenry <mchenry@illinois.edu>", "contributors"downloads: ["Bing : 2Zhang <bing@illinois.edu>"], "licenserepository": : "UIUC/NCSA Open Source License.\r\nhttp://otm.illinois.edu/uiuc_openSource", "whatsnew" : "Identify tumors in microscopy images.", [ { "compatibilityrepType" : "git", "url" "repUrl": "https://opensource.ncsa.illinois.edu/bitbucket/projectsscm/CATSpol/repos/extractors-cv/browse/cellprofiler/cellprofiler-tumor?raw", "sample_input" : "converters-imagemagick.git" }, { "repType": "docker", "sample_output" "repUrl": "ncsapolyglot/converters-imagemagick", } "interfaceLevel" : 2], "dockerimageNameinput_formats" : "",[ "vmImageName" : "", "dockerfilepng" :, "bmp", "author" : "ruiliu@illinois.edu"], "dependenciesoutput_formats" : [ "jpeg", "Cell Profilerjpg", "pdf" ], "transformationexternal_typeservices" : "extractor":[], "transformation_iddependencies" : ["ImageMagick"], "titlebibtex" : "Tumors"[] } |
Mapping Table
...
status
...
creationDate
...
dateCreated
...
updateDate
...
dateUpdated
...
downloads
...
license
...
whatsnew
...
description
...
compatibility
...
url
...
url
...
sample_input
...
sample_output
...
interfaceLevel
...
dockerimageName
...
dockerImageName
...
vmImageName
...
dockerfile
...
author
...
author
...
dependencies
...
dependencies
...
transformation_type
...
transformationType
...
transformation_id
...
transformationId
...
title
...
title
...
Current Tools Catalog Example
Code Block | ||||
---|---|---|---|---|
| ||||
{ "_id" : ObjectId("53864aee7400009900ec8d22"), "dateCreated"status" : 4, "creationDate" : ISODate("2014-05-28T20:45:34.412Z"), "dateUpdatedupdateDate" : ISODate("2016-11-21T04:09:47.836Z"), "downloads" : 2, "descriptionlicense" : "UIUC/NCSA Open Source License.\r\nhttp://otm.illinois.edu/uiuc_openSource", "whatsnew" : "Identify tumors in microscopy images.", "compatibility" : "", "url" : "https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-cv/browse/cellprofiler/cellprofiler-tumor?raw", "sample_input" : "", "sample_output" : "", "dockerImageName"interfaceLevel" : 2, "dockerimageName" : "", "vmImageName" : "", "dockerfile" : "", "author" : "ruiliu@illinois.edu", "dependencies" : [ "Cell Profiler" ], "transformationTypetransformation_type" : "extractor", "transformation_id" : "", "title" : "Tumors" } |
...