stateDiagram
[*] --> Pending
Pending --> Draft
Draft --> MetadataValidating
MetadataValidating --> MetadataValid
MetadataValid --> Draft
MetadataValidating --> MetadataInvalid
MetadataInvalid --> Draft
MetadataValid-->GraphValidationRequested
GraphValidationRequested--> GraphValidating
GraphValidating-->GraphValid
GraphValidationRequested--> GraphValidating
GraphValidating-->GraphInvalid
GraphInvalid-->GraphValidationRequested
GraphValid --> Submitted : submit to hca?
GraphValid --> Submitted : submit to archives and get accessions?
Submitted --> Processing
Submitted --> Exporting
Processing --> Archiving
Archiving --> Archived
Archived --> Exporting : submit to hca?
Exporting --> Exported
Exported --> Draft : when a metadata is updated
Exported --> Cleanup : delete data files?
Cleanup --> Completed
Completed --> [*]

sequenceDiagram
  participant User
  participant UI
  participant Broker
  participant Core
  participant State as State Tracker
  participant Validator
  participant Staging Manager
  participant Upload
  participant Upload Area

  User->>UI: uploads test spreadsheet
  UI-->>Broker: request import
  Broker-->>Broker: parse spreadsheet <br/>and converts rows to json's 
  Broker-->>Core: creates submission entity

  Core-->>Core: creates submission entity
  Core-->>State: sends message new submission is created <br/> and it inits submissionState to PENDING
  State-->>State: creates a state machine object for submission<br/> and it inits its state to PENDING
  
  Core-->>Staging Manager: sends message to request for an upload area from Upload Service
  Staging Manager-->>Upload: requests to create and upload area directory
  Upload-->>Staging Manager: responds with upload area location
  Staging Manager-->>Core: sends message which contains upload area location
  Core-->>Core: stores upload area location to submission envelope entity

  Broker-->>Core: creates metadata entities <br/> and links them to submission and project
  Core-->>Core: creates metadata entities with initial validationState DRAFT
  Core-->>State: sends message that there new metadata in DRAFT

  Core-->>Validator: sends messages for each metadata added
  Validator-->>Core: sets metadata validationState to VALIDATING
  Core-->>State: sends a message that a metadata is set to VALIDATING

  Validator-->>Validator: validates metadata json against json schema and ontology api
  Validator-->>Core: sets metadata validationState as VALID or INVALID + validation error
  Validator-->>Core: for file metadata, sets metadata validationState as INVALID if data is not uploaded yet
  Core-->>State: sends a message that a metadata is set to VALID/INVALID

  State-->>State: checks if submission should be set to DRAFT/VALIDATING/VALID/INVALID
  State-->>Core: sets submission state to DRAFT/VALIDATING/VALID/INVALID <br/> PUT /commitValidating or <br/> PUT /commitValid ...
  
  User->>Upload Area: using hca-util cli, <br/> syncs test files from hca-util to Upload Service's upload area
  Upload Area-->>Upload: notifies that a data file is uploaded
  Upload-->>Upload: checksums the data file
  Upload-->>Core: sends message that the data file is uploaded and checksummed
  Core-->>Core: stores cloudUrl and checksum from Upload Service in file metadata 
  Core-->>Validator: sends message for file metadata that that was updated with cloudUrl
  Validator-->>Upload: for file metadata, once metadata is set to VALID and has cloudUrl,<br/> it requests for data file validation
  Upload-->>Upload: does file validation
  Upload-->>Core: sends core the file validation job result
  Core-->>Core: sets file metadata validation state to VALID/INVALID
  Core-->>State: sends a message that a file metadata is set to VALID/INVALID

  State-->>State: checks if submission should be set to DRAFT/VALIDATING/VALID/INVALID
  State-->>Core: if all metadata are VALID, sets submission state to VALID <br/> PUT /commitValid

sequenceDiagram
  participant User
  participant UI
  participant Broker
  participant Core
  participant State as State Tracker
  participant GV as Graph Validator

  User->>UI: submission is Valid, requests to validate Graph
  UI-->>Core: requests for graph validation
  Core-->> GV: sends message to validate graph
  GV-->>Core: request to set to GRAPH VALIDATING
  Core-->>State: notifies of state transition to GRAPH VALIDATING
  State-->>State: checks if valid transition
  State-->>Core: requests to set submission to GRAPH VALIDATING
  Core-->>Core: sets submission to GRAPH VALIDATING

  GV-->>Core: if there are errors, sets the graph validation errors in the metadata
  GV-->>Core: sends GRAPH INVALID event
  Core-->>State: sends GRAPH INVALID event
  State-->>State: checks if valid transition
  State-->>Core: requests to set submission to GRAPH INVALID
  Core-->>Core: sets submission to GRAPH INVALID
  
  GV-->>Core: if there no errors, sends GRAPH VALID event
  Core-->>State: sends GRAPH VALID event
  State-->>State: checks if valid transition
  State-->>Core: requests to set submission to GRAPH VALID
  Core-->>Core: sets submission to GRAPH VALID

sequenceDiagram
  participant User
  participant UI
  participant Core
  participant State as State Tracker
  participant Exporter
  participant Archiver
  participant DSP
  
  User->>UI: chooses to submit to the EBI archives and clicks Submit
  UI-->>Core: request to submit to the archives
  Core-->>Core: gets assay process
  Core-->>Exporter: sends messages per assay
  
  Exporter-->>Exporter: receives message for an assay
  Exporter-->>State: sends messages when a message is processing <br/> and when it's finished.
  State-->>Core: sets submission state to PROCESSING
  Exporter-->>Exporter: generates bundle manifests for an assay
  Exporter-->>State: sends a message when it finished processing an assay

  State-->>State: keeps track of all assay messages and checks if all are finished
  State-->>Core: when all assay messages finished, it sets submissionState to ARCHIVING<br/> this signals that user can start the manual process
  
  User->>Archiver: manually triggers archiving
  Archiver-->>Archiver: converts metadata
  Archiver-->>DSP: creates DSP submission and creates metadata
  User->>DSP: does manual process to upload files for sequencing runs
  User->>DSP: wait for the DSP submission to be valid and submittable
  User->>Archiver: requests to submit submission
  Archiver-->>DSP: submits submission
  Archiver-->>DSP: retrieves accessions
  Archiver-->>Core: updates metadata with retrieved accessions
  Archiver-->>Core: sets status to ARCHIVED

  Core-->>Core: generates the Export link
  UI-->>UI: displays Export button when Export links is present

sequenceDiagram
  participant User
  participant UI
  participant State as State Tracker
  participant Core
  participant Staging Manager
  participant GCPTS as GCP Transfer Service
  participant Exporter
  participant Terra
  
  User->>UI: clicks Export button to submit to HCA
  UI-->>Core: requests for export, triggers exporting
  Core-->>Exporter: sends messages per assay
  Exporter-->>State: sends a message when a message is being processed <br/> and when it's finished.
  State-->>Core: sets submission state to EXPORTING <br/>when not all messages have finished yet
 
  Exporter-->>GCPTS: if needed to export data, triggers data file transfer
  GCPTS-->>Terra: transfers data files to Terra staging area from upload area
  Exporter-->>Exporter: waits til data transfer is complete
  Exporter-->>Core: crawls graph from assay process to donor
  Exporter-->>Terra: creates all metadata files included in the graph in the Terra staging area
  Exporter-->>Terra:  creates links.json file in the Terra staging area
  State-->>State: keeps track that all messages are processed
  State-->>Core: sets submission state to EXPORTED
  
  User->> Core: waits until submission is EXPORTED
  

sequenceDiagram
  participant User
  participant UI
  participant Core
  participant State as State Tracker
  participant Staging Manager
  
  UI-->>UI: displays Delete upload area button
  User->>UI: clicks Delete upload area button
  UI-->>Core: requests for cleanup
  Core->>State: sends message for cleanup
  State->>Core: sets submission to cleanup <br/> PUT /commitCleanup
  Core-->>Staging Manager: sends message to delete upload area
  Staging Manager-->> Upload: requests to delete the upload area 
  Staging Manager-->> Core: sets the submission to COMPLETE
  Core-->>State: sends message for COMPLETE