This page is under construction.
Tools Catalog is the main web application that the tool contributors of Brown Dog will interact with. Current version of Tools Catalog (0.4.0) needs to be simplified and made more user friendly, in order for that to happen. Tools Catalog 0.4.0 is written in Scala using the Play framework, which is less popular than languages like Python, JavaScript, etc. There are also many features in Tools Catalog 0.4.0, which are either not needed or not clearly understood by the users. This will be an opportunity to re-design and re-implement Tools Catalog with only the required set of functionalities, which are user friendly as well.
We have this ongoing task and will tentatively use the name "Brown Dog Transformations" (previously suggested by Ben) or "BD Transformations" in short as we describe Tools Catalog "2.0" on this page. For the remaining part of this document we will use BD Transformations in place of Tools Catalog 2.0. This will help clarify thoughts related to Tool vs Software.
This section will define the main concepts that will need to be clearly understood for easily interacting with BD Transformations. An example can be Software vs Transformation or any new terminology that will be used in BD Transformations.
Converter: Program that does data format conversion.
Extractor: Program that process and extract metadata from data.
Transformation: Any converter or extractor or extractor program.
Software: Software tool / library that is used by an extractor or converter to do data transformation.
converters_info.json: A JSON file that describes a converter.
extractors_info.json: A JSON file that describes an extractor.
Minimum Viable Product (MVP): Version of BD Transformations with only a few basic features. This will be developed through some kind of a hackathon.
The user roles in BD Transformations will be:
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 |
{
"_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"
} |
{
"@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": []
} |
{
"name": "ImageMagick",
"version": "1.0",
"description": "Converts images from one format to another",
"author": "Kenton McHenry <mchenry@illinois.edu>",
"contributors": ["Bing Zhang <bing@illinois.edu>"],
"repository": [
{
"repType": "git",
"repUrl": "opensource.ncsa.illinois.edu/bitbucket/scm/pol/converters-imagemagick.git"
},
{
"repType": "docker",
"repUrl": "ncsapolyglot/converters-imagemagick"
}
],
"input_formats": [
"png", "bmp"
],
"output_formats": [
"jpeg", "jpg", "pdf"
],
"external_services":[],
"dependencies": ["ImageMagick"],
"bibtex": []
} |
{
"_id" : ObjectId("53864aee7400009900ec8d22"),
"status" : 4,
"creationDate" : ISODate("2014-05-28T20:45:34.412Z"),
"updateDate" : ISODate("2016-11-21T04:09:47.836Z"),
"downloads" : 2,
"license" : "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" : "",
"interfaceLevel" : 2,
"dockerimageName" : "",
"vmImageName" : "",
"dockerfile" : "",
"author" : "ruiliu@illinois.edu",
"dependencies" : [
"Cell Profiler"
],
"transformation_type" : "extractor",
"transformation_id" : "",
"title" : "Tumors"
} |