Metabolic pathways visualisation

mzueva commented 2 years ago

Background

Metabolic pathways are series of chemical reactions that start with a substrate and finish with an end product. These pathways are being displayed as certain kind of infographics, often called "maps". Maps can be as public ones received from different sources like BioCyc database and as well as internal, produced by pathway modelling software. NGB shall support visualization of both types of pathway maps.

Approach

Pathways panel
- Databases sub-tab
- Pathways sub-tab
Internal pathways
External database integration
Pathways annotation
- Annotation file
- Manual colorization
Additional details

Pathways panel

A new Pathways panel shall be added. This panel shall be available:

from the VIEWS item of the main menu - to open an empty Pathways panel, e.g.:
from the context menu at the "Browser" panel when clicks the certain gene/feature - to open the Pathways panel with search results by the feature name, e.g.:
from the context menu at the "Genes" panel when clicks the certain gene/feature - to open the Pathways panel with search results by the feature name, e.g.:

In all described cases, a new Pathways panel should be opened that is placed as other side panels - at the right side of the page. This panel should contain:

pathway search input field
button to start the search
two sub-tabs:
- "Databases" (opened by default) - for displaying search results over pathways from external pathway databases
- "Pathways" - for displaying search results over internal pathways (inner NGB storing)

Example of view:

Notes:

if the Pathways panel was opened from the VIEWS item of the main menu - this panel should be empty as shown on the image above (search field is empty, sub-tabs are empty too)

if the Pathways panel was opened from the context menu when clicking any gene/feature - the name of that gene/feature should be specified to search field and the search should be performed over external pathways database by selected gene/feature name (example of the Pathways panel view in this case see below)

Databases sub-tab

After user has specified the search keyword and click the Search button or just opened the Pathways panel from the context menu when clicking any gene/feature, the search should be performed over external pathways databases by the keyword/gene or feature name. Results of the search should be displayed in the "Databases" sub-tab, e.g.:

Search results should contain a list of found maps from external pathways database. Each record should contain the following fields:

Map - map ID
Thumbnail - thumbnail image of the map
Name - map name
Description - map description. Note: as often that descriptions are rather long, there should be only short part of the description is shown, e.g. first 150 symbols

Note: list of found records should support pagination

The "Map" column should contain hyperlinks - user can click any record in this list to open details of the specific metabolic pathways map. The new form with map details should be opened in the same sub-tab instead previous list, e.g.:

This form shall contain:

button to return to the previous table (with all found maps)
map name label
"Info" button near the map name label - by click this button a tooltip should appear with the full map description
panel with additional capabilities that can be applied to the opened map:
- search control - for the search over the current pathway objects
- annotation section - for adding annotation file(s) to the current pathway
full map image:
- the map image should be shown (PNG-format image received from KEGG)
- by default, image should be autoscaled - fitted by width
- there should be "Zoom-in"/"Zoom-out" buttons - to change scale
- there should be the ability to change scale by mouse wheel
- there should be the ability to move over the image on large scales by mouse hold+move

Search over the pathway User shall have the ability to search over pathway objects - via the search control at the additional capabilities panel:

search results should be highlighted at the map image
no auto-scaling to the search results are required
each new search should highlight only new found objects, previous search results should be hide

Add annotation to the pathway User shall have the ability to add annotation(s) to the displayed map. This annotation should allow to colorize the map. The following annotations shall be supported:

heatmap file, previously registered in NGB
variation file, previously registered in NGB (TBD)
data in TSV/CSV format, uploaded from the local workstation
manually specified annotation in NGB GUI

To add an annotation, user shall click the "Add+" control at the additional capabilities panel. A pop-up shall appear, e.g.:

This pop-up shall contain:

text input field for specifying annotation name (optional)
dropdown list with heatmap and variation files registered in NGB, multiselect is disabled - only one file from the list can be selected
button to load annotation file from the local workstation (in TSV/CSV format)
text input field for specifying annotation in plain text format
controls to switch between options from which the annotation will be received. There shall be the ability to use only one option at the moment - load from the dropdown/upload from the local workstation/manual configuration
button to save the annotation

If user selects any annotation from the dropdown list or load from the local TSV/CSV file, the view of that pop-up shall be changed:

annotation name field is automatically filled by selected file name. Then, user can manually change this name, if needs
the control shall appear - to set where the pathway object IDs (names/labels) are expected - in first column (row headers) or in first row (column headers)
for the annotation, the ability to config the colorizing shall be support. Here the same settings as for heatmaps should be:
- ability to select between continuous (default) and discrete colorizing
- for continuous colorizing, there should be the ability to set colors for max, min, average values
- for discrete colorizing, there should be the ability to set a color for each specific value or configure color(s) for values range(s)

If user selects "Manual colors config" - no additional controls appear, in this case user should manually specify the colorization scheme and annotation name if needs, e.g.:

When the annotation was saved:

the annotation pop-up shall be closed
saved annotation should appear in the additional capabilities panel. For each added annotation, there should appear:
- annotation name (as hyperlink). If it was not specified - it should be set automatically, e.g. annotation_<index_number>
- remove button near the annotation name - to remove the annotation from the list
- checkbox near the annotation name - to enable (apply) it or disable
just saved annotation should be applied to the map
when the annotation is applied to the map - objects according to the annotation should be colorized to the specified colors
- if no objects are found with the specified identifiers - nothing should be colorized
  
  Note: about annotation possible formats and colors applying see below.

Manage the annotations:

user can add and apply several annotations for the map
if any object is subject to several annotations - it should be colorized only according to the first applied annotation
user can click any annotation name to open the annotation details and change them if needs - in the annotation pop-up (similar as described above)
user can remove any annotation by the remove button near it

Pathways sub-tab

Pathways sub-tab can be opened manually. Here, the search over internal NGB pathways should be performed - by the keyword/gene or feature name. Search should be performed over the following fields of pathway maps:

name
description
map objects

Results of the search should be displayed in the same sub-tab - similar to Databases sub-tab, but without map IDs and thumbnails, e.g.:

Each record should contain the following fields:

Map - map name
Description - map description

Notes:

List of found records should support pagination

Table should supports sorting by "Map" column

The "Map" column should contain hyperlinks - user can click any record in this list to open details of the specific metabolic pathways map. The new form with map details should be opened in the same sub-tab instead previous list. Content and functionality for internal maps details should be fully similar to external database maps, the single difference - the map image should be generated and drawn from pathway map file in SBGN-xml format, e.g.:

Internal pathways

NGB shall support registration and management of pathway map files in one of the following formats: SBML, SBGN, Biopax (TBD with GUI team)
Pathway data shall not be stored in the internal database, server just stores path to the original file (same as for BAM files and similar), but some lucene index may be required to allow gene search over the pathway
NGB CLI shall provide standard register, list, delete operations for pathway map files
GUI shall support drawing of pathway maps in the selected format

BioCYC Pathways integration

NGB shall support registration of BioCYC pathway files in biopax format
NGB shall support gene search over registered BioCYC pathway files
NGB shall support visualization of BioCYC biopax pathways

Pathways annotation

Pathway annotation shall be supported for both internal and external pathways
NGB shall support annotation of pathway map based on heatmap or custom TSV/CSV (table) data like different pathway tools e.g. Pathview
NGB shall support annotation of pathway map based on variations data (TBD: how to map variation to pathway element)

Map colorizing shall be different according to the annotation source.

Annotation file

When user selects heatmap/TSV or CSV file as annotation, the matrix format of the annotation is expected. In this case:

pathway objects (their IDs, names or labels) should be placed in the first column (row headers) or the first row (column headers) of the matrix. Note: this should be specified by the user when create/edit annotation in GUI
all other matrix values should be used for colorizing pathways objects

If the continuous scheme is selected, the algorithm of the colorizing should be the following:

3 colors should be configured - for minimum value (from all matrix), for maximum value (from all matrix) and middle value (average between minimum and maximum). Colors for all other values in matrix are selected from a gradient according to these three
for each pathway object from the matrix - if this object is presented at the map, it should be colorized:
- color(s) for the object should be determined from the value corresponding to that object in the matrix and from the defined gradient
- only object background color should be changed
- if for the object, there are several values in the matrix:
- for each value, the color should be determined
- object should be colorized in all these colors equally (from left to right in the order as values are specified in matrix)

For example, if the annotation file looks like:

          Sample1
Gene1     -0.87
Gene2     0.1
Gene3     0.93
Gene4     0.99
Gene5     -0.8

Then, the following example map with applied annotation shall be colorized in the way (if the gradient colors were selected correspondingly):

For example, if the annotation file looks like:

          Sample1       Sample2
Gene1     -0.87         0.02
Gene2     0.1           -0.45
Gene3     0.93          0.88
Gene4     0.99
Gene5     -0.8          -0.9

Then, the following example map with applied annotation shall be colorized in the way (if the gradient colors were selected correspondingly):

If the discrete scheme is selected, the algorithm of the colorizing should be the following:

for each specific value of the matrix the color should be configured (or color(s) for value range(s))
for each pathway object from the matrix - if this object is presented at the map, it should be colorized in the defined color
- defined color(s) for the object should be determined from the value corresponding to that object in the matrix and from the defined gradient
- only object background color should be changed
- if for the object, there are several values in the matrix:
- object should be colorized in all these colors equally (from left to right in the order as values are specified in matrix)

For example, if the annotation file looks like:

          Sample1       Sample2
Gene1     -0.87         0.02
Gene2     0.1           -0.45
Gene3     0.93          0.88
Gene4     0.99
Gene5     -0.8          -0.9

Then, the following example map with applied annotation shall be colorized in the way (if colors were selected correspondingly):

Manual colorization

Manual colorization annotation is expected in the following format:

<object_identifier_1>    <background_color1>[,<foreground_color1>]
<object_identifier_2>    <background_color2>[,<foreground_color2>]
...

Note: color can be specified in HEX format (in this case, it should start with # symbol, e.g. #ffffff) or as HTML color name (e.g. White)

The algorithm of the colorizing should be the following:

for each pathway object from the list - if this object is presented at the map, it should be colorized in the defined color:
- <background_color> (if specified) should be used as background color
- <foreground_color> (if specified) should be used as border color and text color

For example, if the manual annotation config looks like:

Gene1     #121212
Gene2     Yellow,#ffab00
Gene3     Green,#cca837
Gene4     Red
Gene5     #000000,White

Then, the following example map with applied annotation shall be colorized in the way:

Additional details

Created annotations should be stored globally
Users shall have the ability to save an opened map with applied annotation(s) in the session

Tatyana2022 commented 2 years ago

Bug was found: Missing pathway map for 'Glycolysis 2'

To reproduce:

Go to NGB
Open VIEWS->PATHWAYS
Go to PATHWAYS panel
Enter 1 value in Search keyword field
Click on Glycolysis2 hyperlink in 'Name' column
Look at PATHWAYS sub-tab

Expected result: Specific pathways map should be displayed in the PATHWAYS sub-tab

Actual result: Text data outside of root node. Line: 0 Column: 63 Char: } text displays instead Glycolysis2 pathways map

@mzueva @okolesn

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: 400 error appears after applying sorting in the PATHWAYS search result table

Prerequisites: Open console (F12)

To reproduce:

Go to NGB
Open VIEWS->PATHWAYS
Go to PATHWAYS panel
Enter 1 value in Search keyword field
Sort by 'Map' column
Look at PATHWAYS sub-tab

Expected result: The results in the table are displayed according to the applied sorting No errors in the console

Actual result: Sorting is applied. No values in the search results table 400 error displays in the console

Extra details: Infinite loader is displayed in the PATHWAYS sub-tab when trying to search again The results are displayed in the table after reloading the page

@mzueva @DmitriiKrasnov

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: The map scale is reset to default after switching to another panel

To reproduce:

Go to NGB
Go to PATHWAYS panel
Search by any pathway in Search keyword field (e.g. Repressilator)
Click on result in the Map column (e.g. Repressilator)
Zoom in/out the map
Remember scale of the map
Go to any another panel (e.g. DATASETS)
Go back to PATHWAYS panel

Actual result: Zoom of the mao should be the same as it was remembered in 6 step

Expected result: The zoom is reset to default after switching to another panel

@mzueva @rodichenko @DmitriiKrasnov

Tatyana2022 commented 2 years ago

Bug was found: Node highlighting disappears after applying the 'Reset to default' button

To reproduce:

Go to NGB
Go to PATHWAYS panel
Search by any pathway in Search keyword field (e.g. Repressilator)
Click on search result in the Map column (e.g. Repressilator)
Add annotation (e.g. Laclp LimeGreen,#45abff) and click Apply button
Click Reset Default view button
Take a look at the node specified in the annotation (e.g. Laclp)

Expected result: Node specified in the annotation (e.g. Laclp) should be highlighted (e.g. LimeGreen,#45abff)

Actual result: All nodes do not have a highlight after clicking the Reset Default view button

@mzueva @DmitriiKrasnov

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: Apply button is active in annotations if <Enter> set between conditions

To reproduce:

Go to NGB
Go to PATHWAYS panel
Search by any pathway in Search keyword field (e.g. Repressilator)
Click on search result in the Map column (e.g. Repressilator)
Click + button in the Annotation window
Mark Manual colors config checkbox
Enter the following conditions below checkbox:
```
Laclp   LimeGreen
<Enter>
Tetm    Red
```
Look at Apply button

Expected result: Apply button should be disabled

Actual result: Apply button is active

@mzueva @DmitriiKrasnov

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: Server error is displayed when searching for some keywords

To reproduce:

Go to NGB
Go to PATHWAYS panel
Enter 'and' keword in Search keyword field
Click Search button
Look at results below search field

Expected result: 1) Matched search result should be displayed in the table 2) Nothing found. Try to search another gene. phrase should be displayed if there are no matches in the search results

Actual result: An error displays in the panel:

Extra details: The same behavior for 'or' keyword And for uppercase (AND,OR)

@mzueva @okolesn

Tatyana2022 commented 2 years ago

Bug was found: Server errors are displayed when searching for some special characters

To reproduce:

Go to NGB
Go to PATHWAYS panel
Enter '*^' value in Search keyword field
Click Search button
Look at results below search field

Expected result: Nothing found. Try to search another gene. phrase should be displayed if there are no matches in the search results

Actual result: An error displays in the panel:

Extra details: The same behavior for following values: !, (,),-,+,[

@okolesn

Tatyana2022 commented 2 years ago

Some notes after conversation with @DmitriiKrasnov

Each map should have its own annotations. Verified
Heatmaps and manual annotations should be saved, CSV files - not.

Tatyana2022 commented 2 years ago

Bug was found: Map scale remains the same after applying the Restore default view button

To reproduce:

Go to NGB
Open PATHWAYS panel
Apply search by any pathway (e.g. Repressilator)
Open search result (e.g. Repressilator)
Zoom in (or zoom out) the map
Click Restore default view button
Look at the map

Expected result: The map should be autoscaled - fitted by width

Actual result: Scale of the map stays the same does not fit to the width

@mzueva @DmitriiKrasnov Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: Previously selected node remains selected when revisiting the map page

To reproduce:

Go to NGB
Open PATHWAYS panel
Apply search by value Glycolysis1
Open search result Glycolysis1
Look at D-Glyceraldehyde 3-phosphate node in the map

Expected result: The whole map should be without highlights

Actual result: D-Glyceraldehyde 3-phosphate node is highlighted as selected node (in brown)

Extra details: The same behavior for Glycolysis

@DmitriiKrasnov

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: The Apply button is enabled if no heatmaps are selected or added to annotations.

Prerequisites: Open Console (F12)

To reproduce:

Go to NGB
Go to Pathways
Select BRCA1 pathway in the Search keyword field and apply Search
Click BRCA1 pathway
Click A button (annotations)
Set checkbox in Select heatmap file field
Click Apply button

Expected result: Apply button shouldn't be clickable for fields without added heatmaps. Errors shouldn't be displayed in the console

Actual result: Apply button is clickable. An error displays in the console:

app.bundle.9705ab3038a4620f71e0.js:60 TypeError: Cannot read properties of null (reading 'rows')
    at app.bundle.9705ab3038a4620f71e0.js:1064:95514
    at ngbPathwaysAnnotationService.value (app.bundle.9705ab3038a4620f71e0.js:1064:95664)
    at ngbPathwaysAnnotationAddDlgController.value (app.bundle.9705ab3038a4620f71e0.js:1049:398255)
    at fn (eval at compile (app.bundle.9705ab3038a4620f71e0.js:60:155706), <anonymous>:4:738)
    at expensiveCheckFn (app.bundle.9705ab3038a4620f71e0.js:60:178880)
    at callback (app.bundle.9705ab3038a4620f71e0.js:60:249496)
    at Scope.$eval (app.bundle.9705ab3038a4620f71e0.js:60:195953)
    at Scope.$apply (app.bundle.9705ab3038a4620f71e0.js:60:196292)
    at HTMLButtonElement.<anonymous> (app.bundle.9705ab3038a4620f71e0.js:60:249603)
    at HTMLButtonElement.dispatch (app.bundle.9705ab3038a4620f71e0.js:39:58996)

Extra details: The same behavior with checkbox Upload TSV/CSV :

TypeError: Cannot read properties of null (reading 'columnLabels')
    at app.bundle.9705ab3038a4620f71e0.js:1064:95198
    at ngbPathwaysAnnotationService.value (app.bundle.9705ab3038a4620f71e0.js:1064:95372)
    at ngbPathwaysAnnotationAddDlgController.value (app.bundle.9705ab3038a4620f71e0.js:1049:398255)
    at fn (eval at compile (app.bundle.9705ab3038a4620f71e0.js:60:155706), <anonymous>:4:738)
    at expensiveCheckFn (app.bundle.9705ab3038a4620f71e0.js:60:178880)
    at callback (app.bundle.9705ab3038a4620f71e0.js:60:249496)
    at Scope.$eval (app.bundle.9705ab3038a4620f71e0.js:60:195953)
    at Scope.$apply (app.bundle.9705ab3038a4620f71e0.js:60:196292)
    at HTMLButtonElement.<anonymous> (app.bundle.9705ab3038a4620f71e0.js:60:249603)
    at HTMLButtonElement.dispatch (app.bundle.9705ab3038a4620f71e0.js:39:58996)
    at HTMLButtonElement.elemData.handle (app.bundle.9705ab3038a4620f71e0.js:39:55827)

@DmitriiKrasnov @mzueva @rodichenko

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: The values specified in the heatmap and displayed in the annotations are different

Prerequisites: Open Console (F12)

To reproduce:

Go to NGB
Go to Pathways
Select BRCA1 pathway in the Search keyword field and apply Search
Click BRCA1 pathway
Click A button (annotations)
Set checkbox in Select heatmap file field
Select BRCA1-annotation heatmap in dropdown menu
Select Discrete type
Look at colored values

Expected result: Heatmap values should be displayed

Actual result: The following values displays in the discrete type:

@DmitriiKrasnov @mzueva @rodichenko

Not reproducible

Tatyana2022 commented 2 years ago

Bug was found: The second search is performed not for the entire phrase

To reproduce:

Go to NGB
Open PATHWAYS
Find and open pwycollage.graph
Apply search with following values: bisphosphatase: ybhA
Look at pathway

Expected result: Only one node should be highlighted: fructose 1,6-bisphosphatase: ybhA

Actual result: Almost all nodes are highlighted

Extra details: Only one match is found in console:

@rodichenko @DmitriiKrasnov @mzueva

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: Nodes remain highlighted after applying search with an empty field

To reproduce:

Go to NGB
Open PATHWAYS
Find and open pwycollage.graph
Apply search with following values: bisphosphatase: ybhA
Сlear the Search field
Apply search with empty Search field
Look at pathway

Expected result: Nodes are not highlighted

Actual result: Previously highlighted nodes remain highlighted

@rodichenko @DmitriiKrasnov @mzueva

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: Pathway display does not change to default after clicking Restore default view button (for collages only)

To reproduce:

Go to NGB
Open PATHWAYS panel
Find and open pwycollage.graph
Go to pathway
Remember the location of nodes and edges
Change location of any node or edge
Click Reset to default view button
Look at Pathway

Expected result: Pathway display changed to default view after clicking Restore default view button

Actual result: Pathway display does not change to default after clicking Restore default view button

@rodichenko @DmitriiKrasnov @mzueva

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: Values are not pulled from the added heatmap file in discrete view in annotations

Prerequisites: Create heatmap file: e.g. Pathway-ann.csv with following values:

Gene,Sample1,Sample2
Tetm,0.55,0.98
Tetp,0.04,1
Laclm,0.33,0.45
Clp,0.29,0.89
f6p,0.29,0.89

To reproduce:

Go to NGB
Open PATHWAYS panel
Find and open Repressilator_PD
Click A (annotations) button
Click + (add annotation) button
Set checkbox in Upload CSV/TSV field
Click Choose CSV/TSV file button
Add file from Prerequisites: Pathway-ann.csv
Set Discrete view

Expected result: Values should be automatically displayed from the added heatmap file in discrete view Range checkbox should be displayed near values (flag is not set by default)

Actual result: No values in the discrete view.

Extra details: Nodes are highlighted in black after clicking the Apply button

The range view is displayed when you click on the Add Color button No Range checkboxes in the Discrete view

@rodichenko @mzueva @DmitriiKrasnov

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: Canceled changes are applied to the color scheme

To reproduce:

Go to NGB
Open PATHWAYS panel
Find and open Repressilator_PD
Click A (annotations) button
Click + (add annotation) button
Set checkbox in Select heatmap file field
Select BRCA1-annotation heatmap in dropdown menu
Set Continuous type (if not set)
Change any color (e.g. LOW from Green to Pink)
Click Cancel button
Open created annotation (BRCA1-annotation)

Expected result: LOW color should be Green Pathway's nodes should be highlighted according to the set values

Actual result: LOW color is Pink

Pathway nodes are highlighted according to the values in the color scheme.

Extra details: The same behavior for Upload TSV/CSV checkbox

@rodichenko @mzueva @DmitriiKrasnov

Fixed and verified

Tatyana2022 commented 2 years ago

Need to improve:

Nice to have any validation message for heatmap files with empty or wrong data in annotations: E.g. "Wrong file format"
It would be great to have highlighting nodes and edges in light gray for collages, like in an external application
It would be great to automatically substitute annotation names every time depending on the selected checkbox - Verified

@DmitriiKrasnov @mzueva

Tatyana2022 commented 2 years ago

Bug was found: Apply button is disabled after uploading CSV/TSV filed in annotations

To reproduce:

Go to NGB
Open PATHWAYS panel
Find and open BRCA1
Click A (annotations) button
Click + (add annotation) button
Set checkbox in Upload CSV/TSV field
Click Choose CSV/TSV file button
Add any CSV/TSV file
Set checkbox in Manual colors config field
Enter any value
Repeat 6-8 steps
Look at Apply button

Expected result: Apply button should be active

Actual result: Apply button is disabled

@rodichenko @mzueva @DmitriiKrasnov

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: Manual annotations and with heatmap files are not saved in the annotation pop-up

To reproduce:

Go to NGB
Open PATHWAYS panel
Find and open BRCA1
Add any manual annotation
Add any annotation with heatmap file
Remember names of created annotations
Wait some hours (e.g. due to next day)
Repeat 1-3 steps
Open annotations window

Expected result: Manual and annotations with heatmap files should be displayed in the annotation window

Actual result: No saved annotations: manual and annotations with heatmap files

@rodichenko @mzueva @DmitriiKrasnov

Tatyana2022 commented 2 years ago

Bug was found: Nodes remain highlighted after applying search to collage pathway

To reproduce:

Go to NGB
Open PATHWAYS panel
Find and open pwycollage.graph
Enter bisphosphatase in the Search field
Apply search
Look at earlier highlighted nodes

Expected result: All matched nodes should have green text without gray highlight

Actual result: All matched nodes have light gray highlight

Extra details: Highlight nodes remains even after clearing search

@rodichenko @mzueva @DmitriiKrasnov

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: Edges move a little after clicking Restore default view button

To reproduce:

Go to NGB
Open PATHWAYS panel
Find and open BRCA1 pathway
Click Restore default view button
Look at edges on the map

Expected result: The map should be unchanged if no changes have been made before.

Actual result: Edges move a little

https://user-images.githubusercontent.com/83421565/159654130-b935f4d8-6491-4f48-905f-c4f959a42707.mov

@mzueva @rodichenko @DmitriiKrasnov

Tatyana2022 commented 2 years ago

Bug was found: Apply button is disabled after switching between checkboxes in annotations

To reproduce:

Go to NGB
Open PATHWAYS panel
Find and open BRCA1
Click A (annotations) button
Set checkbox in Upload CSV/TSV field
Unset checkbox in Upload CSV/TSV field
Set checkbox in Manual colors config field
Enter any value
Look at Apply button

Expected result: Apply button should be active

Actual result: Apply button is disabled

Extra details: Same behavior for all toggle options between checkboxes

@rodichenko @mzueva @DmitriiKrasnov

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: The map slides to the right or left when zooming in or out

To reproduce:

Go to NGB
Open PATHWAYS panel in main menu
Find and open pathway BRCA1
Click on + button
Double click on - button

Expected result: The pathway map should maximize and minimize in the center of the PATHWAYS panel

Actual result: 5) The pathway's map slides to the bottom right corner when zooming in 6) The pathway's map slides to the left upper corner when zooming out

@rodichenko @mzueva @DmitriiKrasnov

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: An error displays in the console after opening PATHWAYS panel from track

Prerequisites Open console (Ctrl+F12)

To reproduce:

Go to NGB
Open PATHWAYS panel in main menu
Find and open Pwycollage E.Coli
Search by ybha in the Search field
Click on highlighted value
Go to gene's track on BROWSER panel
Open Context menu
Click Show pathways
Look at console

Expected result: No errors in the console. Pathways panel is opened

Actual result: Pathways panel is opened An error displays in the console

app.bundle.0e08a0baaf769ff20edb.js:1049 Uncaught TypeError: Cannot read properties of null (reading 'isHeadless')
    at Core.headless (app.bundle.0e08a0baaf769ff20edb.js:1049:80163)
    at app.bundle.0e08a0baaf769ff20edb.js:1047:52662
    at cachedBoundingBoxImpl (app.bundle.0e08a0baaf769ff20edb.js:1047:56462)
    at Collection.elesfn$k.boundingBox (app.bundle.0e08a0baaf769ff20edb.js:1047:58057)
    at update (app.bundle.0e08a0baaf769ff20edb.js:1047:45276)
    at Element.elesfn$k.updateCompoundBounds (app.bundle.0e08a0baaf769ff20edb.js:1047:47584)
    at Object.beforeGet (app.bundle.0e08a0baaf769ff20edb.js:1047:40870)
    at Element.<anonymous> (app.bundle.0e08a0baaf769ff20edb.js:1047:8991)
    at Element.<anonymous> (app.bundle.0e08a0baaf769ff20edb.js:1041:33596)
    at _loop2 (app.bundle.0e08a0baaf769ff20edb.js:1047:67984)
    at app.bundle.0e08a0baaf769ff20edb.js:1047:68151
    at forEachEventObj (app.bundle.0e08a0baaf769ff20edb.js:1047:65787)
    at Emitter.p.emit.p.trigger (app.bundle.0e08a0baaf769ff20edb.js:1047:67148)
    at Core.emit (app.bundle.0e08a0baaf769ff20edb.js:1049:9858)
    at app.bundle.0e08a0baaf769ff20edb.js:1047:68248
    at forEachEventObj (app.bundle.0e08a0baaf769ff20edb.js:1047:65695)

@rodichenko @mzueva @DmitriiKrasnov

Tatyana2022 commented 2 years ago

Bug was found: Pop-up Annotations window is not displayed after creation annotation

To reproduce:

Go to NGB
Open PATHWAYS panel in main menu
Find and open pathway BRCA1
Click on A(Annotation) button
Fill any field by any values
Click Apply button

Expected result: Pop-up Annotation window with created annotation should be displayed in the right upper corner

Actual result: Pop-up Annotations window is not displayed after creation annotation

@rodichenko @mzueva @DmitriiKrasnov

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: It is not possible reopen Add Annotation pop-up with manual colorization

To reproduce:

Go to NGB
Open PATHWAYS panel in main menu
Find and open pathway BRCA1
Click on A(Annotation) button
Set checkbox in Manual colors config field
Set any values (e.g. Laclp red blue)
Click Apply button
Click on A(Annotation) button
Click on link with created annotation

Expected result: Add annotation pop-up should be opened with filled Manual colors config field

Actual result: Add Annotation pop-up with manual colorization is not opened

Extra details: An error displays in the console:

app.bundle.0e08a0baaf769ff20edb.js:60 TypeError: Cannot read properties of null (reading 'copy')
    at ngbPathwaysAnnotationAddDlgController (app.bundle.0e08a0baaf769ff20edb.js:1049:399004)
    at Object.invoke (app.bundle.0e08a0baaf769ff20edb.js:60:40742)
    at extend.instance (app.bundle.0e08a0baaf769ff20edb.js:60:105109)
    at Object.link (app.bundle.0e08a0baaf769ff20edb.js:639:27641)
    at app.bundle.0e08a0baaf769ff20edb.js:639:43464
    at app.bundle.0e08a0baaf769ff20edb.js:639:44048
    at app.bundle.0e08a0baaf769ff20edb.js:60:183790
    at app.bundle.0e08a0baaf769ff20edb.js:60:183933
    at Scope.$eval (app.bundle.0e08a0baaf769ff20edb.js:60:195953)
    at Scope.$digest (app.bundle.0e08a0baaf769ff20edb.js:60:193358)
    at Scope.$apply (app.bundle.0e08a0baaf769ff20edb.js:60:196379)
    at HTMLAnchorElement.<anonymous> (app.bundle.0e08a0baaf769ff20edb.js:60:249603)
    at HTMLAnchorElement.dispatch (app.bundle.0e08a0baaf769ff20edb.js:39:58996)
    at HTMLAnchorElement.elemData.handle (app.bundle.0e08a0baaf769ff20edb.js:39:55827)

@rodichenko @mzueva @DmitriiKrasnov

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: Server error is displayed when searching for certain values

To reproduce:

Go to NGB
Open PATHWAYS panel in main menu
Enter **pw* value in the Search keyword** field
Click Search button

Expected result: All matched results started with "pw" value should be displayed in the table

Actual results: Your operation has been aborted due to NGB has encountered a server problem. text displays instead table with results

Extra details: The same behavior for: Glycolysis_Homo_sapiens, Glycolysis description...

Finds results for following pathways: pwycollage.graph, BRCA1...

@mzueva @okolesn

Fixed and verified

Tatyana2022 commented 2 years ago

Bug was found: Switching to the gene track does not match the result

To reproduce:

Go to NGB
Open PATHWAYS panel in main menu
Find and open Pwycollage human pathway
Apply search with following values: fbp
Click on found node
Go to gene's track on BROWSER panel
Look at found gene

Expected result: The gene should not have been found because there is no match

Actual result: FBP1 gene is displayed in the gene track

@rodichenko @DmitriiKrasnov @mzueva

Tatyana2022 commented 2 years ago

Bug was found: The Apply button is activated after double-clicking the checkbox in annotations

To reproduce:

Go to NGB
Open PATHWAYS panel
Find and open BRCA1
Click A (annotations) button
Set checkbox in Upload CSV/TSV field
Unset checkbox in Upload CSV/TSV field
Look at Apply button

Expected result: Apply button should be disabled

Actual result: Apply button is active

@rodichenko @mzueva @DmitriiKrasnov

Tatyana2022 commented 2 years ago

Bug was found: Incorrect coloring of nodes if the node consists of more than 1 value

To reproduce:

Go to NGB
Open PATHWAYS panel
Find and open Pwycollage human pathway
Click A (annotations) button
Set checkbox in Manual colors config field
Enter enolase: eno red blue
Click Apply button
Look at enolase: eno node

Expected result: enolase: eno node should have blue background with red text

Actual result: enolase: eno text has red text only without background

@rodichenko @mzueva @DmitriiKrasnov

epam / NGB