System Testing

[remstef]

This issue for testing system

• Mainnav

  • [x] Start with collapsed services in Mainnav
  • [x] Settings Button is without function
  • [x] Header in Mainnav takes too much space -> reduce
  • [x] Order available annotation types alphabetically
  • [x] Order documents alphabetically
  • [x] reduce space between documents in list

• Grid Controller

  • [x] remove buttons without function: delete, add, edit

• Upload

  • [x] Uploading of empty documents gives error
  • [x] Whats the filter for uploading documents? (.txt, .py, .sh seem possible, no suffix is impossible to select, either allow only txt, or remove filter, document should be rejected by the backend then)

• Visualization:

  • [x] sentence indicator overlays the sentence for log sentences #sentence indicator position below text
  • [x] sometimes navigating through sentences is not possible anymore (only first sentence stays visible)
  • [x] connecting nodes is not working (drawing a relation)
  • [x] moving nodes into another compound node is not possible
  • [x] collapsing a compound node is sometimes not possible (button is not available)
  • [x] collapsing / uncollapsing changes zooms in / out (user losses focus)
  • [x] searching for new terms/ clicking on an annotation opens new graph at random positions (zooms in / out + user losses focus)
  • [x] after clicking on an annotation source of a node, clicking on an underlined text doesn't resolve to its annotations but only queries the services. #calling annotation resources after clicking one of sources.
  • [x] selecting an annotation from the second sentence onwards gives wrong text -> offset is calculated only from the first sentence

• Resource properies view (on the right)

  • [x] when metadata is collapsed, the respective Buttons should also be collapsed
  • [x] make sources unique (no duplicates)

• Minor things:

  • [ ] Circlenav changes symbol when clicking -> unnecessary (the one with one wheel is visually clearer, why?)
  • [ ] Opening/ Closing of search bar is not necessary, it can always be there

• Probably related:

  • [ ] while playing around, I received the following error messages

TypeError: Cannot read property 'name' of undefined
    at module.exports (/opt/project/frontendserver/api/service/call.js:2:21)
    at call (/opt/project/frontendserver/api/service/serviceEndpoint.js:35:21)
    at Layer.handle [as handle_request] (/opt/project/frontendserver/node_modules/express/lib/router/layer.js:95:5)
    at next (/opt/project/frontendserver/node_modules/express/lib/router/route.js:137:13)
    at Route.dispatch (/opt/project/frontendserver/node_modules/express/lib/router/route.js:112:3)
    at Layer.handle [as handle_request] (/opt/project/frontendserver/node_modules/express/lib/router/layer.js:95:5)
    at /opt/project/frontendserver/node_modules/express/lib/router/index.js:281:22
    at Function.process_params (/opt/project/frontendserver/node_modules/express/lib/router/index.js:335:12)
    at next (/opt/project/frontendserver/node_modules/express/lib/router/index.js:275:10)
    at Function.handle (/opt/project/frontendserver/node_modules/express/lib/router/index.js:174:3)

TypeError: Cannot read property 'mv' of undefined
    at postDocuments (/opt/project/frontendserver/api/storage/storageEndpoint.js:63:10)
    at Layer.handle [as handle_request] (/opt/project/frontendserver/node_modules/express/lib/router/layer.js:95:5)
    at next (/opt/project/frontendserver/node_modules/express/lib/router/route.js:137:13)
    at Route.dispatch (/opt/project/frontendserver/node_modules/express/lib/router/route.js:112:3)
    at Layer.handle [as handle_request] (/opt/project/frontendserver/node_modules/express/lib/router/layer.js:95:5)
    at /opt/project/frontendserver/node_modules/express/lib/router/index.js:281:22
    at Function.process_params (/opt/project/frontendserver/node_modules/express/lib/router/index.js:335:12)
    at next (/opt/project/frontendserver/node_modules/express/lib/router/index.js:275:10)
    at Function.handle (/opt/project/frontendserver/node_modules/express/lib/router/index.js:174:3)
    at router (/opt/project/frontendserver/node_modules/express/lib/router/index.js:47:12)

TypeError: Cannot read property 'name' of undefined
    at module.exports (/opt/project/frontendserver/api/service/call.js:2:21)
    at call (/opt/project/frontendserver/api/service/serviceEndpoint.js:35:21)
    at Layer.handle [as handle_request] (/opt/project/frontendserver/node_modules/express/lib/router/layer.js:95:5)
    at next (/opt/project/frontendserver/node_modules/express/lib/router/route.js:137:13)
    at Route.dispatch (/opt/project/frontendserver/node_modules/express/lib/router/route.js:112:3)
    at Layer.handle [as handle_request] (/opt/project/frontendserver/node_modules/express/lib/router/layer.js:95:5)
    at /opt/project/frontendserver/node_modules/express/lib/router/index.js:281:22
    at Function.process_params (/opt/project/frontendserver/node_modules/express/lib/router/index.js:335:12)
    at next (/opt/project/frontendserver/node_modules/express/lib/router/index.js:275:10)
    at Function.handle (/opt/project/frontendserver/node_modules/express/lib/router/index.js:174:3)

[remstef]

See also https://github.com/uhh-lt/autolinks/wiki/System-Testing-Workflow

[alvinrindra]

Hi @remstef, my current commits and merges to the master fix some bugs, and add new feature 'merge Nodes To Compound'. At the moment it works in the frontend, but unfortunately, it only saves one node in the backend. What I mean here, if we create new nodes with one compound, the backend only saves the compound one, not with its children. We can discuss further later when I come to the office.

SOLUTION: create a new resource with a list of resources.value: [] first with cid: -1 example: { "before": {"rid":1534,"value":[ {"rid":153456}, {"rid":153345} ], "metadata":{}}, "after": {"cid": 46, "rid":1534,"value":"djzjdt","metadata":{ "label": "asdasf"}} }

[remstef]

@alvinrindra whats the status on the open issues?

[remstef]

• Document Handling:
  • [x] Document deletion should also remove the currently active sentences (document lense)
  • [ ] re-uploading fails (its uploaded but server chrashes) see error message:
    • show loading indicator! #alvin: I think, this one occurs due to server crash

      
      fs.js:1081
      return binding.unlink(pathModule.toNamespacedPath(path));                                            
           ^

Error: ENOENT: no such file or directory, unlink './uploads/Tcell.txt'
at Object.fs.unlinkSync (fs.js:1081:18) at Request._callback (/opt/project/frontendserver/api/storage/storageEndpoint.js:95:12)
at Request.self.callback (/opt/project/frontendserver/node_modules/request/request.js:185:22)
at Request.emit (events.js:159:13) at Request. (/opt/project/frontendserver/node_modules/request/request.js:1157:10)
at Request.emit (events.js:159:13) at IncomingMessage. (/opt/project/frontendserver/node_modules/request/request.js:1079:12) at Object.onceWrapper (events.js:254:19) at IncomingMessage.emit (events.js:164:20) at endReadableNT (_stream_readable.js:1054:12) npm ERR! code ELIFECYCLE npm ERR! errno 1 npm ERR! autolinks@1.0.0 start: node server.js npm ERR! Exit status 1 npm ERR! npm ERR! Failed at the autolinks@1.0.0 start script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

╭─────────────────────────────────────╮ │ │ │ Update available 5.5.1 → 6.2.0 │ │ Run npm i -g npm to update │ │ │ ╰─────────────────────────────────────╯

npm ERR! A complete log of this run can be found in:
npm ERR! /root/.npm/_logs/2018-07-19T13_32_23_445Z-debug.log

- Visualiztion test (search)
   - [x] include loading indicator
   - [x] cancel invoked relation adding
   - [x] use rid as "label" for compound nodes without metadata label
   - [x] adding a relation from a node outside of a compund node to a node which is inside a compound node creates a new node outside of the compound node after refreshing ---> expected behavior, show immediately
    - [x] merge rename to "move into", make button on node itself
    - [x] Compound rename to "create new comound" 
    - [x] clear -> also clear any temporary variables 
    - [ ] creating compound from nodes which are within compounds should not move them out of the first compound, #new compound node is created inside the previous parent of current children nodes

[alvinrindra]

• [ ] Add how to / guides inside app?
• [ ] Interpreting a document takes too long. :( -> documents? :((

Hi @remstef, we still need to keep "CreateCompound" feature, since you said that we cannot change value type of resources. As we know, to create a compound node, we need to have resource values as array [ ] by default. If we create a compound node from an existing node by using "Move Into" feature to another nonparent target node, it means that we are going to change the value of that nonparent target node from "string" to [array], which is not possible by the backend.

• [x] warning / rejects for creating a single node to another single / non parent target node.
• [x] adding edge to different parent "B cell" compound with "New" children node, end up with "New" Compound with "New" children Node ---> Problem first index array for the compound element

-> SOLUTION: Make the compound to be the rid / metadata label if any for the compound, not the first index array anymore!!!!.

• [x] inconsistency for compound creation: first index array of children or the resource itself?
• [x] filter based on active listServices
• [ ] annotation resources from interpretDid and localSearch should be inside one annotation container. ISSUES: interpretDid returns fix / same offsets of annotationResources, meanwhile, localSearch returns everything / different offsets of annotation Resources.
• [x] delete new compound and moveInto from the grid controller. and New compound node sidenav will appear in the merging nodes scenario.
• [x] Prevent creating connection to parent: warning message
• [x] Interpreting document empty focus parameter: {}
• [x] clicking source also enables the annotation type
• [x] highlight annotation offsets according to annotation resources
• [ ] discontinuous annotations
• [ ] merging nodes to another nodes which have relations --> create a duplicate in frontend
• [ ] sync localSearch annotationResources with active annotationType, so not all of annotationResources will be appeared

[alvinrindra]

Hi @remstef , I have some issues from the backend. You now change every same label node with different rids.

• [x] This is what 'B cell' demo looks like if the rids are different.

• [ ] Another issue is that I think we still need an annotation container provided by the backend. If the annotation container is generated in the frontend, it means that annotation container is not editable since it doesnt have rid, cid and metadata and it's only a temporary annotation container.

What if a user wants to edit that annotation container? such update its label or even move to another compound nodes?

• [ ] Only demo endpoint that only works in Demo Service. bar / baz{username} / foo are not working anymore.

• [x] creating two compound nodes, that have different labels, under same parents give the same rid compounds. E.g: I want to merge a single node "A" to a single node "B" under "Z" compound. With our scenario, this will create another compound right? for "A" to "B". Now it's fine, compound "AB" is created for node "A" and "B" under "Z" with rid "149". Then I want to merge node "C" to "D" with compound name "CD", but I get the same rid which is "149". When I refresh the app, I got "CD" compound with children "A", "B", "C", and "D".

• [ ] no sources/provenances in annotationResouces after interpreting the documents, it is only triggered when I call localSearch

• [ ] Deploy to live

• [ ] annotations problem ==> alt + a , to annotation mode