diff --git a/docs/test-cases/Pathways/Pathways/Annotations/Heatmap_files.md b/docs/test-cases/Pathways/Pathways/Annotations/Heatmap_files.md new file mode 100644 index 000000000..115c64bcd --- /dev/null +++ b/docs/test-cases/Pathways/Pathways/Annotations/Heatmap_files.md @@ -0,0 +1,39 @@ +#Annotations with heatmap files + +Test verifies +- applying colorization to Pathway's map nodes using a heatmap files, previously registered in NGB + +**Prerequisites**: +1. Go to NGB +2. Close **PATHWAYS** panel if it is opened + +dataset = **SV_Sample1**, heatmap = **pathway-annotation3.tsv** +``` +Gene Tetm Tetp +Tetm 0.55 0.98 +Tetp 0.04 1.0 +Laclm 0.45 +Clp 0.29 +``` + +| Steps | Actions | Expected results | +|-------|------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| 1 | Login to NGB | | +| 2 | Go to DATASETS panel | | +| 3 | Select **pathway-annotation3** dataset in **SV_Sample1** dataset | | +| 4 | Open **PATHWAYS** panel from **VIEWS** menu | **PATHWAYS** panel is displayed first at the right side in the additional panels and consists of the following elements:
  • **Search keyword**(mandatory) - empty field
  • **SEARCH** button - disabled by default
  • "**Type keyword to start search.**" phrase displays in the panel | +| 5 | Enter **BRCA1** into **Search keyword** field | | +| 6 | Click **SEARCH** button | A table with corresponding search results are displayed in the PATHWAYS panel:
    - **Map** (*hyperlink, sortable*) - map name
    - **Description** - map description
    - **Source** - map source

    Search results are displayed in the table:
    MapDescriptionSource
    BRCA1BRCA1 testCustom
    | +| 7 | Click on the **BRCA1** hyperlink in the **Map** column | The new form with map details is opened in the same window instead previous list and contains from:

  • **<** (**Return**) - button to return to the previous table (with all found maps) displays at the top of sub-tab
  • **Map name label** (*BRCA1*) - displays to the right of **Return** button
  • **i** (**Info**) - label near the map name (by navigate this button a tooltip appears with the full map description)
  • *Additional capabilities section* displays below map label:
    - **Search** field (*empty by default*)
    - **Loupe** button
    - **Annotation** button
  • *Map* image | | | +| 8 | Click **Annotation** button | **Add annotation** modal window is opened with following values inside:
  • **Annotation name** - text input field for specifying annotation name (optional)
  • **Select heatmap file** checkbox - *to load heatmap file registered in NGB*
  • **Select VCF file** checkbox - *to load variation file registered in NGB (disabled by default)*
  • **Upload TSV/CSV** checkbox - *to load annotation file from the local workstation (in TSV/CSV format)*
  • **Manual colors config** checkbox - *for specifying annotation in plain text format*

  • **Apply** button - disabled by default
  • **Cancel** button | | +| 9 | Set checkbox in **Select heatmap file** field |
  • New empty dropdown field *(mandatory)* is displayed below checkbox
  • 2 pathway objects display below dropdown field:
    - **in first column** checkbox (set by default)
    - **first row** checkbox
  • **Annotation name** field is empty
  • **Apply** button is disabled | | +| 10 | Select **pathway-annotation3** in dropdown field |
  • Annotation name field is automatically filled by selected file name = **pathway-annotation3**
  • The following values displays below **Pathway objects** field:
  • Type = Continuous
  • Block of the colors settings: High, Middle, Low, Missing data
  • **Apply** button is enabled | | +| 11 | Click **Apply** button |
  • **Add annotation** modal window is closed
  • Saved annotation is appeared in the new **Annotations** pop-up window
  • Annotation name displays as hyperlink
  • Checkbox displays near the annotation name - *to enable (apply) it or disable*
  • The checkbox is set automatically
  • Remove button displays near the annotation name - *to remove the annotation from the list* | +| 12 | Look at the map | 3 colors is 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:
    Node nameNode color
    Tetmyellow\red
    Tetpgreen\red
    Laclpgreen
    Laclmlight-green
    Clpgreen
  • All other nodes are not colored | +| 13 | Click **pathway-annotation3** in **Annotations** pop-up |
  • **Add annotation** modal window is opened | +| 14 | Set checkbox in **first row** objects | | +| 15 | Click **Apply** button |
  • **Add annotation** modal window is closed
  • Saved annotation displays as hyperlink in **Annotations** pop-up window = **pathway-annotation3** | +| 16 | Look at the map | 3 colors is 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:
    Node nameNode color
    Tetmyellow\red
    Tetpgreen\red
    | +| 17 | Click **pathway-annotation3** in **Annotations** pop-up |
  • **Add annotation** modal window is opened | +| 18 | Select **Discrete** type and Apply changes |
  • For each specific value of the matrix the color is configured (or color(s) for value range(s)) | +| 19 | Look at the map. |
  • Each pathway object from the matrix colorized in the defined color
  • Defined color(s) for the object is determined from the value corresponding to that object in the matrix and from the defined gradient
  • Only object background color is changed
  • For the object with several values in the matrix: object is colorized in all these colors equally (from left to right in the order as values are specified in matrix) | diff --git a/docs/test-cases/Pathways/Pathways/Annotations/Manual_Annotation.md b/docs/test-cases/Pathways/Pathways/Annotations/Manual_Annotation.md new file mode 100644 index 000000000..7a8150826 --- /dev/null +++ b/docs/test-cases/Pathways/Pathways/Annotations/Manual_Annotation.md @@ -0,0 +1,23 @@ +#Manual annotations + +Test verifies +- applying manual colorization to Pathway's map nodes (custom and collage) + +**Prerequisites**: +1. Go to NGB +2. Close **PATHWAYS** panel if it is opened + + +| Steps | Actions | Expected results | +|-------|-------------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| 1 | Login to NGB | | +| 2 | Open **PATHWAYS** panel from **VIEWS** menu | **PATHWAYS** panel is displayed first at the right side in the additional panels and consists of the following elements:
  • **Search keyword**(mandatory) - empty field
  • **SEARCH** button - disabled by default
  • "**Type keyword to start search.**" phrase displays in the panel | +| 3 | Enter **BRCA1** into **Search keyword** field | | +| 4 | Click **SEARCH** button | A table with corresponding search results are displayed in the PATHWAYS panel:
    - **Map** (*hyperlink, sortable*) - map name
    - **Description** - map description
    - **Source** - map source

    Search results are displayed in the table:
    MapDescriptionSource
    BRCA1BRCA1 testCustom
    | +| 5 | Click on the **BRCA1** hyperlink in the **Map** column | The new form with map details is opened in the same window instead previous list and contains from:

  • **<** (**Return**) - button to return to the previous table (with all found maps) displays at the top of sub-tab
  • **Map name label** (*BRCA1*) - displays to the right of **Return** button
  • **i** (**Info**) - label near the map name (by navigate this button a tooltip appears with the full map description)
  • *Additional capabilities section* displays below map label:
    - **Search** field (*empty by default*)
    - **Loupe** button
    - **Annotation** button
  • *Map* image | | | +| 6 | Click **Annotation** button | **Add annotation** modal window is opened with following values inside:
  • **Annotation name** - text input field for specifying annotation name (optional)
  • **Select heatmap file** checkbox - *to load heatmap file registered in NGB*
  • **Select VCF file checkbox** - *to load variation file registered in NGB (disabled by default)*
  • **Upload TSV/CSV** checkbox - *to load annotation file from the local workstation (in TSV/CSV format)*
  • **Manual colors config** checkbox - *for specifying annotation in plain text format*

  • **Apply** button - disabled by default
  • **Cancel** button | | +| 7 | Set checkbox in **Manual colors config** field |
  • New empty text input field is displayed below checkbox
  • **Annotation name** field is empty
  • **Apply** button is disabled | | +| 8 | Enter following values into text input field: *
    Laclp green yellow
    Laclm #45abff #b22222
    Clp red #45abff* |
  • Values and colors are entered
  • **Apply** button is enabled | | +| 9 | Click **Apply** button |
  • **Add annotation** modal window is closed
  • Saved annotation is appeared in the new **Annotations** pop-up window
  • Annotation name displays as hyperlink *(If it was not specified - it should be set automatically, e.g. annotation_)*
  • Checkbox displays near the annotation name - *to enable (apply) it or disable*
  • The checkbox is set automatically
  • Remove button displays near the annotation name - *to remove the annotation from the list* | +| 10 | Look at the map | All nodes according to the annotation is colorized to the specified colors:
    Node nameNode colorText/Border
    Laclpgreenyellow
    Laclmbluered
    Clpredblue
  • All other nodes are not colored | +| 11 | Repeat 2-10 steps for **Pwycollage human** pathway with following values: *
    F6P green yellow
    DHAP #45abff #b22222
    13-DPG red #45abff* | All nodes according to the annotation is colorized to the specified colors:
    Node nameNode colorText/Border
    F6Pgreenyellow
    DHAPbluered
    13-DPGredblue
  • All other nodes are not colored. | diff --git a/docs/test-cases/Pathways/Pathways/Annotations/TSV_CSV_uploading.md b/docs/test-cases/Pathways/Pathways/Annotations/TSV_CSV_uploading.md new file mode 100644 index 000000000..4b85d4341 --- /dev/null +++ b/docs/test-cases/Pathways/Pathways/Annotations/TSV_CSV_uploading.md @@ -0,0 +1,39 @@ +#Annotations with uploading TSV/CSV files + +Test verifies +- applying colorization to Pathway's map nodes using a CSV/TSV file + +**Prerequisites**: +1. Go to NGB +2. Close **PATHWAYS** panel if it is opened + +Create .csv file = **pathway-ann.csv** +``` +Gene,Tetm,Clp +Tetm,0.55,0.98 +Tetp,0.04,1 +Laclm,0.33,0.45 +Clp,0.29,0.89 +f6p,0.29,0.89 +``` + +| Steps | Actions | Expected results | +|-------|--------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| 1 | Login to NGB | | +| 2 | Go to DATASETS panel | | +| 3 | Open **PATHWAYS** panel from **VIEWS** menu | **PATHWAYS** panel is displayed first at the right side in the additional panels and consists of the following elements:
  • **Search keyword**(mandatory) - empty field
  • **SEARCH** button - disabled by default
  • "**Type keyword to start search.**" phrase displays in the panel | +| 4 | Enter **BRCA1** into **Search keyword** field | | +| 5 | Click **SEARCH** button | A table with corresponding search results are displayed in the PATHWAYS panel:
    - **Map** (*hyperlink, sortable*) - map name
    - **Description** - map description
    - **Source** - map source

    Search results are displayed in the table:
    MapDescriptionSource
    BRCA1BRCA1 testCustom
    | +| 6 | Click on the **BRCA1** hyperlink in the **Map** column | The new form with map details is opened in the same window instead previous list and contains from:

  • **<** (**Return**) - button to return to the previous table (with all found maps) displays at the top of sub-tab
  • **Map name label** (*BRCA1*) - displays to the right of **Return** button
  • **i** (**Info**) - label near the map name (by navigate this button a tooltip appears with the full map description)
  • *Additional capabilities section* displays below map label:
    - **Search** field (*empty by default*)
    - **Loupe** button
    - **Annotation** button
  • *Map* image | | | +| 7 | Click **Annotation** button | **Add annotation** modal window is opened with following values inside:
  • **Annotation name** - text input field for specifying annotation name (optional)
  • **Select heatmap file** checkbox - *to load heatmap file registered in NGB*
  • **Select VCF file** checkbox - *to load variation file registered in NGB (disabled by default)*
  • **Upload TSV/CSV** checkbox - *to load annotation file from the local workstation (in TSV/CSV format)*
  • **Manual colors config** checkbox - *for specifying annotation in plain text format*

  • **Apply** button - disabled by default
  • **Cancel** button | | +| 8 | Set checkbox in **Upload TSV/CSV** field |
  • **Choose TSV/CSV file** button is appeared
  • 2 pathway objects display below dropdown field:
    - **in first column** checkbox (set by default)
    - **first row** checkbox
  • **Annotation name** field is empty
  • **Apply** button is disabled | | +| 9 | Click **Choose CSV/TSV file** and select file |
  • Annotation name field is automatically filled by selected file name = **pathway-ann.csv**
  • The following values displays below **Pathway objects** field:
  • Type = Continuous
  • Block of the colors settings: High, Middle, Low, Missing data
  • **Apply** button is enabled | | +| 10 | Click **Apply** button |
  • **Add annotation** modal window is closed
  • Saved annotation is appeared in the new **Annotations** pop-up window
  • Annotation name displays as hyperlink
  • Checkbox displays near the annotation name - *to enable (apply) it or disable*
  • The checkbox is set automatically
  • Remove button displays near the annotation name - *to remove the annotation from the list* | +| 11 | Look at the map | 3 colors is 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:
    Node nameNode color
    Tetmyellow\red
    Tetpgreen\red
    Laclpgreen
    Laclmgreen/light-green
    Clpgreen/red
  • All other nodes are not colored | +| 12 | Click **pathway-ann** in **Annotations** pop-up |
  • **Add annotation** modal window is opened | +| 13 | Set checkbox in **first row** objects | | +| 14 | Click **Apply** button |
  • **Add annotation** modal window is closed
  • Saved annotation displays as hyperlink in **Annotations** pop-up window = **pathway-ann** | +| 15 | Look at the map | 3 colors is 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:
    Node nameNode color
    Tetmgreen/red\red
    Clpgreen\light-green
    | +| 16 | Click **pathway-ann** in **Annotations** pop-up |
  • **Add annotation** modal window is opened | +| 17 | Select **Discrete** type and Apply changes |
  • For each specific value of the matrix the color is configured (or color(s) for value range(s)) | +| 18 | Look at the map. |
  • Each pathway object from the matrix colorized in the defined color
  • Defined color(s) for the object is determined from the value corresponding to that object in the matrix and from the defined gradient
  • Only object background color is changed
  • For the object with several values in the matrix: object is colorized in all these colors equally (from left to right in the order as values are specified in matrix) | diff --git a/docs/test-cases/Pathways/Pathways/Annotations/Variation_file.md b/docs/test-cases/Pathways/Pathways/Annotations/Variation_file.md new file mode 100644 index 000000000..e69de29bb diff --git a/docs/test-cases/Pathways/Pathways/Launch_Pathways_from_Track.md b/docs/test-cases/Pathways/Pathways/Launch_Pathways_from_Track.md new file mode 100644 index 000000000..4f708550c --- /dev/null +++ b/docs/test-cases/Pathways/Pathways/Launch_Pathways_from_Track.md @@ -0,0 +1,29 @@ +#Launch pathways panel from GENES (track and panel) + +Test verifies +- launching pathways panel from track and GENES panel + +**Prerequisites**: +1. Go to NGB +2. Close **PATHWAYS** panel if it is opened + +1. dataset = **SV_Sample1**, .gtf = **Homo_sapiens.GRCh38.gtf.gz** + +| Steps | Actions | Expected results | +|-------|----------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| 1 | Login to NGB | | +| 2 | Go to **Datasets** tab | | +| 3 | Select dataset from Prerequisites | **SV_Sample1** dataset is selected | +| 4 | Go to **Browser header** | | +| 5 | Set checkbox **GRCh38_Genes** in the **GRCH38** dropdown list (if it is not set) | | +| 6 | Open **GENES** panel in **VIEWS** menu (if not opened) | **GENES** panel is opened | +| 7 | Find **BRCA1** gene by **Name** column using filter | **BRCA1** gene displays in the panel | +| 8 | Right click by **BRCA1** gene |
  • Context menu is displayed
  • **Show pathways** display below **Show similar genes** | +| 9 | Click on **Show pathways** in the context menu | **PATHWAYS** panel is displayed first at the right side in the additional panels and consists of the following elements:
  • **Search keyword**(mandatory) - filled by name of selected gene (**BRCA1**)
  • **SEARCH** button is enabled
  • A table with 3 columns is displayed below "Search keyword" field:
    - **Map** (*hyperlink, sortable*) - map name
    - **Description** - map description
    - **Source** - map source

    All matched results are displayed in the table:
    MapDescriptionSource
    BRCA1BRCA1 testCustom
  • **Pagination** displays at the bottom right corner of table if there are more records than the window can display
  • **Vertical scroll** is displayed only if this is required according to screen size | +| 10 | Go back to **GENES** panel | | +| 11 | Click on **BRCA1** search result | Corresponding gene displays in the gene's track: **BRCA1** | +| 12 | Right click by **BRCA1** gene on the track |
  • Context menu is displayed
  • **Show pathways** display below **Show similar genes** | +| 13 | Click on **Show pathways** in the context menu | **PATHWAYS** panel is displayed first at the right side in the additional panels and consists of the following elements:
  • **Search keyword**(mandatory) - filled by name of selected gene (**BRCA1**)
  • **SEARCH** button is enabled
  • A table with 3 columns is displayed below "Search keyword" field:
    - **Map** (*hyperlink, sortable*) - map name
    - **Description** - map description
    - **Source** - map source

    All matched results are displayed in the table:
    MapDescriptionSource
    BRCA1BRCA1 testCustom
  • **Pagination** displays at the bottom right corner of table if there are more records than the window can display
  • **Vertical scroll** is displayed only if this is required according to screen size | +| 14 | Click on the **BRCA1** hyperlink in the **Map** column | The new form with map details is opened in the same window instead previous list and contains from:

  • **<** (**Return**) - button to return to the previous table (with all found maps) displays at the top of sub-tab
  • **Map name label** (*BRCA1*) - displays to the right of **Return** button
  • **i** (**Info**) - label near the map name (by navigate this button a tooltip appears with the full map description)
  • *Additional capabilities section* displays below map label:
    - **Search** field (*empty by default*)
    - **Loupe** button
    - **Annotation** button
  • *Map* image | +| 15 | Navigate to **i** label | Tooltip appears with the full map description (*BRCA1 test*) | +| 16 | Look at *Map* image. |
  • Map can consists from nodes and edges.
  • Each node and edges are clickable, dynamic and can be changed
  • Image is autoscaled by default (fitted by width)
  • Scale can be changed by mouse wheel and *Manage view buttons*
  • *Manage view buttons* should be displayed to the right of the map: | diff --git a/docs/test-cases/Pathways/Pathways/Launch_Pathways_from_VIEWS.md b/docs/test-cases/Pathways/Pathways/Launch_Pathways_from_VIEWS.md new file mode 100644 index 000000000..1b141cd93 --- /dev/null +++ b/docs/test-cases/Pathways/Pathways/Launch_Pathways_from_VIEWS.md @@ -0,0 +1,28 @@ +_#Default view of PATHWAYS panel + +Test verifies + - default view of PATHWAYS panel (custom anf collage pathways) from **VIEWS** menu + +**Prerequisites**: +1. Go to NGB +2. Close **PATHWAYS** panel if it is opened + + +| Steps | Actions | Expected results | +|-------|-------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| 1 | Login to NGB | | +| 2 | Go to **VIEWS** menu |
  • **VIEWS** menu is displayed
  • **PATHWAYS** panel is displayed after **LINEAGE** | +| 3 | Select **PATHWAYS** panel | **PATHWAYS** panel is displayed first at the right side in the additional panels and consists of the following elements:
  • **Search keyword**(mandatory) - empty field
  • **SEARCH** button - disabled by default
  • "**Type keyword to start search.**" phrase displays in the panel | +| 4 | Go to **Search keyword** field |
  • **Search keyword** field is empty if the panel is opened from **Views** menu and has light grey color of button with dark-grey text
  • Search can be done by:
    - **Map** name
    - **Description**
    - Node name in the map | +| 5 | Enter **BRCA1** into **Search keyword** field |
  • **SEARCH** button is enabled
  • **"Type keyword to start search.**" phrase displays in the panel | | | +| 6 | Click **SEARCH** button |
  • A table with 3 columns is displayed below "Search keyword" field:
    - **Map** (*hyperlink, sortable*) - map name
    - **Description** - map description
    - **Source** - map source

    Search results are displayed in the table:
    MapDescriptionSource
    BRCA1BRCA1 testCustom
  • **Pagination** displays at the bottom right corner of table if there are more records than the window can display
  • **Vertical scroll** is displayed only if this is required according to screen size | +| 7 | Click on the **BRCA1** hyperlink in the **Map** column | The new form with map details is opened in the same window instead previous list and contains from:

  • **<** (**Return**) - button to return to the previous table (with all found maps) displays at the top of sub-tab
  • **Map name label** (*BRCA1*) - displays to the right of **Return** button
  • **i** (**Info**) - label near the map name (by navigate this button a tooltip appears with the full map description)
  • *Additional capabilities section* displays below map label:
    - **Search** field (*empty by default*)
    - **Loupe** button
    - **Annotation** button
  • *Map* image | +| 8 | Navigate to **i** label | Tooltip appears with the full map description (*BRCA1 test*) | +| 9 | Look at *Map* image |
  • Map can consists from nodes and edges.
  • Each node and edges are clickable, dynamic and can be changed
  • Image is autoscaled by default (fitted by width)
  • Scale can be changed by mouse wheel and *Manage view buttons*
  • *Manage view buttons* should be displayed to the right of the map: | +| 10 | Look at **Search** field |
  • **Search** field is empty by default
  • Search can be done over pathway objects
  • Search results are highlighted at the map image
  • No auto-scaling to the search results
  • Each new search is highlighted only new found objects, previous search results should be hidden | +| 11 | Click **< (Return)** button |
  • The previous table (with all found maps) displays at the top of sub-tab
  • **BRCA1** value displays in the **Search keyword** field
  • **Search** button is enabled | | +| 12 | Clean **Search keyword** field |
  • **Search keyword** field is empty
  • **Search** button is disbled | +| 13 | Enter **pwycollage.graph** into **Search keyword** field |
  • **SEARCH** button is enabled
  • **Search keyword** field is filled | +| 14 | Click **Search** button | A table with 3 columns is displayed below "Search keyword" field:
    - **Map** (*hyperlink, sortable*) - map name
    - **Description** - map description
    - **Source** - map source

    Search results are displayed in the table:
    MapDescriptionSource
    pwycollage.graphCollage
  • **Pagination** displays at the bottom right corner of table if there are more records than the window can display
  • **Vertical scroll** is displayed only if this is required according to screen size | +| 15 | Click on the **pwycollage.graph** hyperlink in the **Map** column | The new form with map details is opened in the same window instead previous list and contains from:

  • **<** (**Return**) - button to return to the previous table (with all found maps) displays at the top of sub-tab
  • **Map name label** (*pwycollage.graph*) - displays to the right of **Return** button
  • **No** **i** (**Info**) label near the map name
  • *Additional capabilities section* displays below map label:
    - **Search** field
    - **Loupe** button
    - **Annotation** button
  • *Map* image | +| 16 | Look at *Map* image. |
  • Map can consists from nodes and edges.
  • Each node and edges are clickable, dynamic and can be changed
  • Image is autoscaled by default (fitted by width)
  • Scale can be changed by mouse wheel and *Manage view buttons*
  • *Manage view buttons* should be displayed to the right of the map: |_ diff --git a/docs/test-cases/Pathways/Pathways/Navigation.md b/docs/test-cases/Pathways/Pathways/Navigation.md new file mode 100644 index 000000000..1b0c8c4b2 --- /dev/null +++ b/docs/test-cases/Pathways/Pathways/Navigation.md @@ -0,0 +1,22 @@ +#Navigation + +Test verifies +- navigation between pathways panel and gene track + +**Prerequisites**: +1. Go to NGB +2. Close **PATHWAYS** panel if it is opened + +| Steps | Actions | Expected results | +|-------|-------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| 1 | Login to NGB | | +| 2 | Go to **Datasets** tab | | +| 3 | Open **PATHWAYS** panel from **VIEWS** menu | **PATHWAYS** panel is displayed first at the right side in the additional panels and consists of the following elements:
  • **Search keyword**(mandatory) - empty field
  • **SEARCH** button - disabled by default
  • "**Type keyword to start search.**" phrase displays in the panel | +| 4 | Enter **Pwycollage human** into **Search keyword** field | | +| 5 | Click **SEARCH** button | A table with corresponding search results are displayed in the PATHWAYS panel:
    - **Map** (*hyperlink, sortable*) - map name
    - **Description** - map description
    - **Source** - map source

    Search results are displayed in the table:
    MapDescriptionSource
    Pwycollage humanCollage
    | +| 6 | Click on the **Pwycollage human** hyperlink in the **Map** column | The new form with map details is opened in the same window instead previous list and contains from:

  • **<** (**Return**) - button to return to the previous table (with all found maps) displays at the top of sub-tab
  • **Map name label** (*Pwycollage human*) - displays to the right of **Return** button
  • **i** (**Info**) - label near the map name (by navigate this button a tooltip appears with the full map description)
  • *Additional capabilities section* displays below map label:
    - **Search** field (*empty by default*)
    - **Loupe** button
    - **Annotation** button
  • *Map* image | | +| 7 | Enter **enolase: eno** into **Search** field | +| 8 | Click **Search** button | **enolase: eno** node highlighted green in the map | +| 9 | Click on highlighted **enolase: eno** node |
  • Gene track is opened in the BROWSER panel
  • **Eno** gene is displayd on the track | +| 10 | Right click on **Eno** gene |
  • Context menu is displayed
  • **Show pathways** displays below **Show similar genes** | +| 11 | Click **Show pathways** in context menu |
  • **ENO** gene name displays in the **Search keyword** field in **PATHWAYS** panel
  • Search results matched with **ENO** value are displayed in the table below. | diff --git a/docs/test-cases/Pathways/Pathways/Successful_search_without_results.md b/docs/test-cases/Pathways/Pathways/Successful_search_without_results.md new file mode 100644 index 000000000..7938d8ccf --- /dev/null +++ b/docs/test-cases/Pathways/Pathways/Successful_search_without_results.md @@ -0,0 +1,18 @@ +_#Successful search without results + +Test verifies +- default view of PATHWAYS panel for search without results + +**Prerequisites**: +1. Go to NGB +2. Close **PATHWAYS** panel if it is opened + + +| Steps | Actions | Expected results | +|-------|-------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| 1 | Login to NGB | | +| 2 | Go to **VIEWS** menu |
  • **VIEWS** menu is displayed
  • **PATHWAYS** panel is displayed after **LINEAGE** | +| 3 | Select **PATHWAYS** panel | **PATHWAYS** panel is displayed first at the right side in the additional panels and consists of the following elements:
  • **Search keyword**(mandatory) - empty field
  • **SEARCH** button - disabled by default
  • "**Type keyword to start search.**" phrase displays in the panel | +| 4 | Go to **Search keyword** field |
  • **Search keyword** field is empty if the panel is opened from **Views** menu and has light grey color of button with dark-grey text
  • Search can be done by:
    - **Map** name
    - **Description**
    - Node name in the map | +| 5 | Enter **001test** into **Search keyword** field |
  • **SEARCH** button is enabled
  • **"Type keyword to start search.**" phrase displays in the panel | | | +| 6 | Click **SEARCH** button. |
  • Search is done
  • No table below **Search** field
  • The following phrase displays insread table:
    ***Nothing found. Try to search by another keywords.*** | \ No newline at end of file