Development Decisions

Changes in SEEK

Connecting SEEK - MaSyMoS Morre

• Decision made on 03.09.2020 by SO, RH, BW

• Description

  • RH wrote code in 2016(±) - maybe parts of it could still work
  • visual: insert third blue source button
  • decide later: add as "external" search?

Changes in MaSyMoS Morre

Reference Model via SEEK-ID

• Decision made on 04.12.2020 by RH, BW

• Description

  • in the MaSyMoS-database inside the document root is the following meta data

    • FILENAME original filename
    • UID - generated unique Morre-ID
    • URI - internal URI
    • VERSION_ID - internal version
    • VERSION - used by dokument (i.e. sbml)
    • LEVEL - used by dokument (i.e. sbml)
    • FILEID - used by dokument (i.e. sbml)

  • the used ID (URL to model.content) is stored in FILEID - this is the main ID

• impact

  • Morre needs a function to find model.contents by FILEID (i.e. https://fairdomhub.org/models/196/content_blobs/8745)
  • Morre needs a function to find model.contents by short FILEID with only the model id for DELETE and UPDATE (i.e. https://fairdomhub.org/models/196)

General Concept Middleware

SEEK is the leading project

• Decision made on 03.09.2020 by SO, RH, BW

• Description

  • SEEK pushes to middleware (i.e. hook)
  • the middleware will not do things autonomous

MaSyMoS indexes only the latest version

• Decision made on 03.09.2020 by SO, RH, BW

• Description

  • for now MaSyMoS has no versioning of the models in relation with SEEK

Middleware and MaSyMoS-Morre will not unpack archives

• Decision made on 17.09.2020 by RH, BW

• Description

  • models packed in archives cannot be added

Allowed Content MIME Types

• Decision made on 18.09.2020 by RH, BW

• Description

  • application/sbml+xml
  • application/xml
  • text/xml

Checks in MaSeMiWa before sending anything to MaSyMoS Morre

• Decision made on 19.10.2020 by RH, BW

• Description

  1. MIME (from JSON-Metadata)

  2. namespace, level, version (from file)

     • if level/version in namespace differ from level/version from attributes, ignore file

Connection SEEK - Middleware

What ID to use between SEEK and MaSeMiWa to reference a Model?

• Decision made on 16.09.2020 by SO, RH, BW

• Description

  • use the full URL
  • optional .json
  • ignore ?version=*
  • i.e. https://fairdomhub.org/models/196.json, https://fairdomhub.org/models/196, https://fairdomhub.org/models/196.json?version=3

Restricted access rights for the middleware

• Decision made on 03.09.2020 by SO, RH, BW

• Description

  • middleware uses public API → only public models are used
  • SEEK needs another hook: when model-visibility is switched to private → delete model in MaSyMoS

Get data on activation of hook in seek pushing to the Middleware

• Decision made on 03.09.2020 by SO, RH, BW

• Description

  • question was: WHEN to get data

  • other options

    • ❌ B: cron job - request a list of all ID, optional filtered by timestamp every x minutes

      • feels bad and brings some unpredictable behaviour

call Seek API to get all necessary data

• Decision made on 03.09.2020 by SO, RH, BW

• Description

  • question was, HOW to get data for id

Multiple contents for one model ID in the content_blobs

• Decision made on 03.09.2020 by SO, RH, BW

• Description

  • check file type
  • check for validity in middleware/MaSyMoS
  • import all valid contents

Batch/Bulk-import/reset is forced by SEEK

• Decision made on 03.09.2020 by SO, RH, BW

• Description

  • other options

    • ❌ B: PULL by middleware → MaSyMoS can reset database; create a trigger to start the procedure from outside/SEEK

      • SEEK is leading, MaSyMoS makes no decisions

Connection Middleware - MaSyMoS

What ID to use between MaSeMiWa and MaSyMoS Morre to reference a Content?

• Decision made on 24.09.2020 by RH, BW

• Description

  • one SEEK model can have several valid entries inside the content_blobs field
  • to have all these entries inside Morre, we use the full URL to the Blobs instead the link to the model, i.e. https://fairdomhub.org/models/196/content_blobs/8745
  • if any user uploaded an external linked model (with the external url in the content_blob-field url), the field link will also reference that file as a copy from the time the model was created
  • the SEEK model ID is included; it's human readable

Deleting a model will not delete any annotations

• Decision made on 17.09.2020 by RH, BW

• Description

  • deleting annotations can lead to unexpected behaviour

Update - if deleting fails the insert is done anyway

• Decision made on 04.12.2020 by RH, BW

• Description

  • update is delete + insert
  • if for whatever reason the delete fails, the insert is done with the enforceUniqueFileId==true fag, because there is no risk on having an inconsistent state

Annotation-Scanning in the background

• Decision made on 17.09.2020 by RH, BW

• Description

  • getting all Annotations for all models can be difficult because this is highly depending on the network and the servers with the data
  • the middleware run automatically once or twice a day the create_annotation_index job

Response on INSERT an Batch/Bulk-import/reset after Check

• Decision made on 20.10.2020 by RH, BW

• Description

  • after checking the import-request and adding valid models to the Queue, MaSeMiWa will response with 200 - SUCCESS
  • if there is nothing to import, the return code will differ