biolab-unige / xtens-app Goto Github PK

Return 400 ValidationError if other fields beside "identifier" and "password" are sent

To support projects

Error while opening data details view:

Uncaught TypeError: Cannot read property 'group' of undefined

On data-details.ejs (https://github.com/biolab-unige/xtens-app/blob/master/views/templates/data-details.ejs):
if (index === fields.length-1 || groupname !== metadata[fields[index+1].formattedName].group ) {

"details" is not allowed

PUT http://10.116.13.60:1337/data/3 400 (Bad Request)send @ jquery.js:9664
undefined utils.js:24

Subjects delete API is missing

To keep track of data creation and changes:

There are three complementary approaches to be considered

1. Email report to a supervisor / a number of admins
2. Historical tables on db (administrator level, return to a previous state (operator, date, old data, changes))
3. Double control (supervisor, data list with check boxes: "confirmed"/"quality assured" true - false) for Quality Assurance (QA)

There are various reasons for a rewrite of the front-end.

• Backbone and stickit are not really that popular anymore
• Many fragmented templates used here and there
• No clear way to test properly the view

At the moment possible alternatives are:

1. React + Redux
2. Vue + Vuex (?)
3. Angular

I would uniform the group privileges to the BSD nomenclature, therefore:

• wheel = superuser
• admin = manager

No error response.
Update of all other attributes works properly.

Set up an identifier into data types model to associate data types between different projects ( i.e. type fluid in projects A is the same in project B) allowing users to perform advanced searches getting results from multiple projects.

Historical tables on db (administrator level, return to a previous state (operator, date, old data, changes))

This require some thought.
At the moment only data branching is supported, i.e. a data instance can have multiple children but only one single father.
replacing the one-to-many with a many-to-many relationship would do the trick but this should be supported by Data, Sample, and Subject as well.

Email report to a supervisor / a number of admins

How to define who recieves the mails

Add full text search feature like Google.
Add a check box to every attribute ( researchable true false) or entire datatype researchable?

When i modify or create any type of data, date keeps changing.
Example:
Date inserted: 1975-05-11
Date displayed by postgres: 1975-05-11
Date returned by node's pg: 1975-05-10T23:00:00.000Z

@gicaz: can you verify if this is the case? (maybe in your installation)?

This is the relevant line to debug, I think:

A date as 17 January 2003 should be saved as:

1. 2003-01-17 in the database
2. 2003-01-16T23:00:00.000Z as a JavaScript formatted date string in zulu time/UTC/GMT
3. 17/01/2003 when displayed according to the Italian Time Zone (using moment)

Handle projects through Groups ( many to many association).
Use the existing datatype privileges system to filter a group to a specific set of datatypes (related to a specific project).
Operators view only the filtered datatype structure.

POST http://10.116.13.60:1337/undefined//10.116.13.60:8080/irods-rest/rest/fileContents/iggRiabZone/home/rods/landing/pt13mesi.MTS 404 (Not Found)

dropzone.js 1347

(Download a file works fine)

Handle different level of permission ( no privilege, view, details,download, edit):

• no privilege: No datatype in List selection (queryBuilder and Create)
  -Overview: No datatype in List selection (Create). Searchable in queryBuilder, but no details, download and edit functions
• Details: No datatype in List selection (Create). Searchable in queryBuilder with details, but no download and edit method
• Download: No datatype in List selection (Create). Searchable in queryBuilder with details and download, but no edit method
• Edit: datatype in List selection (Create) and Searchable in queryBuilder with details, download and edit methods

should correct recursive query in xtens-pg module, to retrive right number links without loop.
node_modules/xtens-pg/lib/other/recursiveQueries.js

Also D3 package not support loop node, have to cancel loop nodes in links array.
assets/js/modules/DataType.js

Associate data with operator / project / group.
Map who inserts the data.
Map who downloads / searches the data

Handle contact information: if name, surname and email already exist, new biobank will be associate to existing contact.

When you edit data with loop values, edit form does not show the values and when you press the Save button, loop values are lost.

assets/js/modules/Data.js

Error: Group.js:106 Uncaught TypeError: Cannot read property 'destroy' of undefined

Server side: add "info" metadata field to metadata schema. Support validation with JOI
Client Side: build a tooltip (?) component to attach to metadata field input

To found a valid solution to test query stream method:

biolab-unige/xtens-waterline@a48fd03

Tests will have to be fixed beforehand.

@gicaz Apparently xtens waterline depends still on the old versions of bluebird and loadash. This needs to be fixed
Could you investigate on this?

npm WARN saveError Problems were encountered
npm WARN saveError Please correct and try again.
npm WARN saveError invalid: have [email protected] (expected: git+https://github.com/biolab-unige/xtens-waterline.git) /Users/massi/Projects/unige/xtens-app/node_modules/xtens-waterline
npm WARN saveError extraneous: [email protected] /Users/massi/Projects/unige/xtens-app/node_modules/xtens-waterline
npm WARN saveError extraneous: [email protected] /Users/massi/Projects/unige/xtens-app/node_modules/xtens-waterline/node_modules/bluebird
npm WARN saveError extraneous: [email protected] /Users/massi/Projects/unige/xtens-app/node_modules/xtens-waterline/node_modules/lodash

Data, Sample, Subject lists and Xtenstable rendering is too slow.
Find a way to improve performance and give a better user experience.
Pagination? Stream data?

PUT http://10.116.13.60:1337/subject/1 500 (Internal Server Error)send @ jquery.js:9664
jQuery.extend.ajax @ jquery.js:9215
Backbone.ajax @ backbone.js:1428
Backbone.sync @ backbone.js:1411
Backbone.sync @ utils.js:39_.extend.sync @ backbone.js:436_.extend.save @ backbone.js:647
Subject.Views.Edit.Data.Views.Edit.fullExtend.saveData @ Subject.js:135
bound @ lodash.js:729
jQuery.event.dispatch @ jquery.js:4670
elemData.handle @ jquery.js:4338
utils.js:18 undefined

TERMINAL
error: Sent 500 ("Server Error") response
error: ValidationError: child "personalInfo" fails because ["createdAt" is not allowed, "updatedAt" is not allowed]

Double control (supervisor, data list with check boxes: "confirmed"/"quality assured" true - false) for Quality Assurance (QA)

• XTENS PG:
  conditional search leafSearch - if true set RIGHT OUTER JOIN and remove DISTINCT
  Remove all NULL Rows produced by RIGHT OUTER JOIN?

• Server side:
  preprocessQueryParams - handle array of data types in content of QueryArgs
  filter getMetadata variable through privileges (if overview set getMetadata to false)

• Client side:
  getMetadata radio button on every NestedCondition
  set queryArgs Object with the new info: getMetadata, leafSearch, label DataType
  handle metadata visualization thorugh datatable ( groups of columns, filter, etc)

I would suggest to implement this a HTTP PATCH method

PATCH /operator/password (or PATCH /password?)

{
"oldPasswoed" ..,
"newPassword": ...,
"confirmedNewPassword: ...
}

Verify oldPassword and test equality between newPassword and confirmedNewPassword.

Uncaught TypeError: this.template is not a function DataFile.js :49

DataFile.Views.List.Backbone.View.extend.render @ DataFile.js:49
data.fetch.success @ XtensTable.js:339
options.success @ backbone.js:594fire @ jquery.js:3148
self.fireWith @ jquery.js:3260done @ jquery.js:9314
callback @ jquery.js:9718

In /datatypes delete a datatype parents of a datatype, not work.
No error in console.
The datatype 3 had 1 and 8 as parent. I deleted 8 from edit form and then i save but datatype 8 remains. This is what returned on console:
KnexStrategy.updateDataType - child-parent association found: 3-1
{ parents: [ 1 ],
name: 'Report RM',
schema:
{ body:
[ [Object],
[Object],
[Object],
[Object],
[Object],
[Object],
[Object] ],
header:
{ name: 'Report RM',
model: 'Data',
version: '0.0.1',
ontology: '',
fileUpload: false,
description: 'Analysis RM' } },
model: 'Data',
id: 3,
createdAt: Tue Sep 15 2015 11:45:11 GMT+0200 (CEST),
updatedAt: Thu Jan 28 2016 17:36:17 GMT+0100 (CET) }
{ id: 1,
isWheel: true,
isManager: true,
canAccessPersonalData: true,
canAccessSensitiveData: true }

After changing a metadata field the associated value is not removed.
This create an issue when putting fields that allow controlled lists (the previous value get attached to the list)

The Data types are saved correctly and do also show up in the PostgreSQL database, but they don't show up in the web application and it is not possible to select them and create a graph.

Write explicitly the allowed routes in XTENS

@gicaz The size of selectors should be harmonized
See select2 library