CZO: Geostreaming Data Framework Integration

Goals

• CSV files uploaded to Clowder are annotated with information about the variables contained within the file using standard vocabularies.
• This metadata, together with metadata about the location or sensor attached to a dataset is used to automatically ingest data into the Geostreaming API.

Components

• Clowder
• Dataset is annotated with sensor information
• Reuse existing relationship between dataset and sensor
• Or... add metadata to dataset
• Variable Annotation Extractor (VAE)  BD-2315 - Getting issue details... STATUS
• Annotate files with entries from standard vocabularies
• Col. 3 contains term http://odm2/precipitation
• Multiple mappings can be provided, each with their own likelihood
• For example, if only 9 out of 10 columns match a prior mapping, likelihood is 90%
• Or percentage of files seen with this type of mapping
• Variables Mapping Service (VMS) BD-2310 - Getting issue details... STATUS
  
  • POST/GET/PUT/DELETE mappings
  • The collection in MongoDB contains documents that represent mappings
    
    • Each mapping is a collection of mappings between strings (column headers) and standard vocabularies (uri terms)
    • How many times have seen a particular mapping (how many unique files)
    • When a mapping is not complete, i.e. we can only identify a subset of the columns, we should keep track of how many we columns we successfully identified
      • let's say a csv file has 10 columns, but we can only tag 4, we would have 40% accuracy
  • Maybe keep a collection of what files match what mapping
  • SEARCH for mappings that match a set of CSV headers and return them in order of accuracy
    • Client submits one list of CSV column names, service returns a list of potential mappings including accuracies.
  • Dockerize the service:
    • BD-2318 - Getting issue details... STATUS
• Semantic Annotation Service (SAS)
  • http://ecgs.ncsa.illinois.edu/SAS.html
  • We should build a simpler version of this as a Flask application storing info in MongoDB
• Datapoints Extractor (DPE)
• Creates datapoints in the Geostreaming API based on rows in the CSV input file
• Requires mapping from Variable Annotation Extractor
• Site information as metadata on dataset
• Geostreaming Data Framework
  • Store and visualize datapoints
  • https://geodashboard.ncsa.illinois.edu/
  • Geostreaming API (GSAPI)

Workflow

• File F1 (CSV) uploaded to dataset D1
• VAE reads headers in
• VAE requests matching mappings from mapping service VMS
• VAE adds metadata entries to file F1
• DPE extracts datapoints from CSV and adds them to GSAPI

Tasks

• Update https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-csv to store more information (Decided as Won't Do.)
  • which column has which header
  • include column number and label, for example (3, "temperature)
• Develop Variables Mapping Service (VMS)
  • Simple flask app with mongodb back end
• Variable Annotation Extractor (VAE)
  • En extension of the extractor-csv that queries the VMS and stores standard names in metadata
    • We should support multiple mappings added to metadata
• Figure out where the frontend should be
  • Standalone client
  • Clowder add metadata widget