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[genomic_browser] Minor edits to the test plan (#9198)
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This modifies the test plan for the genomic browser module. The changes are mostly cosmetics but also include corrections of the permission names and table headers mentioned in the plan.

Resolves #9151
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@nicolasbrossard
nicolasbrossard committed Apr 23, 2024
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Showing 1 changed file with 26 additions and 89 deletions.
115 changes: 26 additions & 89 deletions modules/genomic_browser/test/TestPlan.md
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Expand Up @@ -23,7 +23,7 @@ The following permissions should be available in the database
| :---: | --- |
| genomic_browser_view_site | View Genomic Browser data from own site |
| genomic_browser_view_allsites | View Genomic Browser data across all sites |
| genomic_data_manager | Manage the genomic files |
| genomic_data_manager | Upload genomic files |


#### For a user without neither genomic_browser_view_allsites nor genomic_browser_view_site
Expand All @@ -44,12 +44,12 @@ The following permissions should be available in the database

- There should be a *Genomic Browser* item in the Loris Menu under tools.
- Accessing the http://your-base-url/genomic_browser/ should load the Genomic Browser Profile tab.
- The only candidate's data that should appear in the Datatable of the Profile, CNV, SNP and Methylation tabs should be those of the same site as this user's site.
- The Datatable that appears in the Profiles, CNV, SNP and Methylation tabs should only contain data having the same site(s) as this user's site(s).

***
#### For a user with genomic_data_manager and one of genomic_data_manager or genomic_browser_view_allsites
#### For a user with genomic_data_manager and one of genomic_browser_view_site or genomic_browser_view_allsites

- In the File tab of the Genomic Browser, there should be a *Upload File* button
- In the File tab of the Genomic Browser, there should be a *Upload File* button. For users with permission genomic_data_manager, this button will allow a file to be uploaded. For users that do not have this permission, a message saying that the user does not have sufficient privileges is displayed when the button is clicked.

***

Expand All @@ -72,151 +72,88 @@ The following permissions should be available in the database
### Data Filtering

#### Profile tab
- Clicking on the *Candidate filters* block header should hide its content.
- Clicking on the *Genomic filters* block header should hide its content.
- Filters should filter data presented in the Datatable according to the selected values after clicking on the *Show Data* button.
- Candidate filters
- Filters should filter data presented in the Datatable according to the selected/entered values on the fly (i.e as values are selected or characters are typed).
- *Site* dropdown should present all sites for a user with the genomic_browser_view_allsites permission
- *Site* dropdown should present only the user's own site for a user with the genomic_browser_view_site permission
- *DCCID* filter is an exact filter (Shows only the record with this exact value)
- *External ID* and *PSCID* are contains filters (Shows all records that contains this value)
- Genomic filters
* For the four filters, selecting 'Any' should only present record that have at least one, and selecting 'None' should present only record that don't have Files, SNP, CNV or CPG accordingly.

- The datatable should display the following columns (Summary fields)
- The datatable should display the following columns:

| No. | PSCID | Sex | Cohort | Files | SNPs | CNVs | CPGs |
| ---| --- | ---| --- | ---| --- | ---| ---|
| | | | | | | | |

- Setting the Display filter to All fields and click in the *Show Data* button should present the following columns in the Datatable

No.|PSC|DCCID|PSCID|Sex|Cohort|DoB|ExternalID|Files|SNPs|CNVs|CPGs|
| ---| --- | --- | ---| --- | ---| --- | ---| ---| --- | ---| ---|
| | | | | | | | | | | |

- Clicking the *Clear Form* button should reset the filters and the Datatable should prensent the Summary fields columns only.
- Clicking the *Clear Form* button should reset the filter.
- Clicking on column headers should sort data in ascending order on the first click then descending order on the second click.


***

#### GWAS tab

- Clicking on the *GWAS filters* block header should hide its content.
- Filters should filter data presented in the Datatable according to the selected values after clicking on the *Show Data* button.
- GWAS filters
- *Chromosome* filter is an exact filter (Shows only the record with this exact value)
- All other filters are contains filters (Shows all records that contains this value)

- Filters should filter data presented in the Datatable on the fly (i.e as values are selected or characters are typed).
- Clicking the *Clear Form* button should reset the filters.
- Clicking on column headers should sort data in ascending order on the first click then descending order on the second click.

***

#### SNP tab
- Clicking on the *Candidate filters* block header should hide its content.
- Clicking on the *Genomic Range filters* block header should hide its content.
- Clicking on the *SNP filters* block header should hide its content.
- Filters should filter data presented in the Datatable according to the selected values after clicking on the *Show Data* button.
- Filters should filter data presented in the Datatable on the fly (i.e as values are selected or characters are typed).
- Candidate filters
- *Site* dropdown should present all sites for a user with the genomic_browser_view_allsites permission
- *Site* dropdown should present only the user's own site for a user with the genomic_browser_view_site permission
- *DCCID* filter is an exact filter (Shows only the record with this exact value)
- *External ID* and *PSCID* are contains filters (Shows all records that contains this value)
- Genomic Range filters
- *Genomic Range* filter should filter SNP to prensent only SNP that *StartLoc* is contain within the range (i.e. chr14:100000-200000 should prensent all the SNP on the chromosome 14 between position 1000000 and 2000000 inclusively.
- *Genomic Range* filter should filter SNP to present only SNP for which *StartLoc* is contained within the range (i.e. chr14:100000-200000 should present all the SNP on the chromosome 14 between position 1000000 and 2000000 inclusively.
- By entering only the chromosome name in the *Genomic Range*, all the SNP on that chromosome should appear.
- SNP filters
- All the filters are contains filters (Shows all records that contains this value)
- The datatable should display the following columns (Summary fields)

|No.|PSCID|Sex|RsID|Allele A|Allele B|Reference Base|Minor Allele|Function Prediction|Damaging|Exonic Function|
| ---| --- | ---| --- | ---| --- | ---| ---| ---| ---| ---|
| | | | | | | | | | | | |

- Setting the Display filter to All fields and click in the *Show Data* button should present the following columns in the Datatable
- The datatable should display the following columns (Summary fields)

|No.|PSC|DCCID|PSCID|Sex|Cohort|DoB|ExternalID|Chromosome|Strand|StartLoc|EndLoc|Gene Symbol|Gene Name|Platform|RsID|SNP Name|SNP Description|External Source|Allele A|Allele B|Reference Base|Minor Allele|Array Report|Markers|Validation Method|Validated|Function Prediction|Damaging|Genotype Quality|Exonic Function|
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
|No.|PSCID|Sex|Cohort|Build|Platform|Allele A|Allele B|Reference Base|Minor Allele|Function Prediction|Damaging|Genotype Quality|
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---|
| | | | | | | | | | | | | |

- Clicking the *Clear Form* button should reset the filters and the Datatable should prensent the Summary fields columns only.
- Clicking the *Clear Form* button should reset the filter.
- Clicking on column headers should sort data in ascending order on the first click then descending order on the second click.

***

#### CNV tab

- Clicking on the *Candidate Filters* block header should hide its content.
- Clicking on the *Genomic Range Filters* block header should hide its content.
- Clicking on the *CNV Filters* block header should hide its content.
- Filters should filter data presented in the Datatable according to the selected values after clicking on the *Show Data* button.
- Candidate filters
- Filters should filter data presented in the Datatable on the fly (i.e as values are selected or characters are typed).
- *Site* dropdown should present all sites for a user with the genomic_browser_view_allsites permission
- *Site* dropdown should present only the user's own site for a user with the genomic_browser_view_site permission
- *DCCID* filter is an exact filter (Shows only the record with this exact value)
- *External ID* and *PSCID* are contains filters (Shows all records that contains this value)
- Genomic Range filters
- *Genomic Range* filter should filter SNP to prensent only SNP that *StartLoc* is contain within the range (i.e. chr14:100000-200000 should prensent all the SNP on the chromosome 14 between position 1000000 and 2000000 inclusively.
- By entering only the chromosome name in the *Genomic Range*, all the SNP on that chromosome should appear.
- CNV filters
- All the filters are contains filters (Shows all records that contains this value)
- The datatable should display the following columns (Summary fields)

|No.|PSCID|Sex|Location|CNV Description|CNV Type|Copy Num Change|Common CNV|Characteristics|Inheritance|
- The datatable should display the following columns:

|No.|PSCID|Sex|Cohort|Location|Type|Common|Characteristics|Inheritance|Platform|
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| | | | | | | | | | |

- Setting the Display filter to All fields and click in the *Show Data* button should present the following columns in the Datatable

|No.|PSC|DCCID|PSCID|Sex|Cohort|DoB|ExternalID|Chromosome|Strand|StartLoc|EndLoc|Size|Location|Gene Symbol|Gene Name|CNV Description|CNV Type|Copy Num Change|Event Name|Common CNV|Characteristics|Inheritance|Array Report|Markers|Validation Method|Platform|
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| | | | | | | | | | | | | | | | | | | | | | | | | | | |

- Clicking the *Clear Form* button should reset the filters and the Datatable should prensent the Summary fields columns only.
- Clicking the *Clear Form* button should reset the filter.
- Clicking on column headers should sort data in ascending order on the first click then descending order on the second click.

***

#### Methylation tab

- Clicking on the *Candidate filters* block header should hide its content.
- Clicking on the *Genomic Range filters* block header should hide its content.
- Clicking on the *CpG filters* block header should hide its content.
- Filters should filter data presented in the Datatable according to the selected values after clicking on the *Show Data* button.
- Candidate filters
- Filters should filter data presented in the Datatable on the fly (i.e as values are selected or characters are typed).
- *Site* dropdown should present all sites for a user with the genomic_browser_view_allsites permission
- *Site* dropdown should present only the user's own site for a user with the genomic_browser_view_site permission
- *DCCID* filter is an exact filter (Shows only the record with this exact value)
- *External ID* and *PSCID* are contains filters (Shows all records that contains this value)
- Genomic Range filters
- *Genomic Range* filter should filter SNP to prensent only SNP that *StartLoc* is contain within the range (i.e. chr14:100000-200000 should prensent all the SNP on the chromosome 14 between position 1000000 and 2000000 inclusively.
- By entering only the chromosome name in the *Genomic Range*, all the SNP on that chromosome should appear.
- CpG filters
- *CPG namer* filter is an exact filter (Shows only the record with this exact value)
- All other filters are contains filters (Shows all records that contains this value)
- The datatable should display the following columns (Summary fields)

|No.|PSCID|Sex|Cpg Name|Beta Value|Chromosome|Strand|Gene|
| --- | --- | --- | --- | --- | --- | --- | --- |
| | | | | | | | |

- Setting the Display filter to All fields and click in the *Show Data* button should present the following columns in the Datatable

|No.|PSC|DCCID|PSCID|Sex|Cohort|DoB|Sample|Cpg Name|Beta Value|Chromosome|Strand|StartLoc|Probe Loc A|Probe Seq A|Probe Loc B|Probe Seq B|Design|Color|Assembly|SNP 10|Gene|Accession Number|Gene Grp|Island Loc|Context|Fantom Prom|DMR|Enhancer|HMM Island|Reg Feature Loc|Reg Feature Grp|DHS|Platform|
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
|No.|PSCID|Sex|Sample|Probe Seq A|Probe Loc B|Probe Seq B|Infinium Design|Color|Gene|Accession Number|Position|DMR|DHS|
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| | | | | | | | | | | | | | |

- Clicking the *Clear Form* button should reset the filters and the Datatable should prensent the Summary fields columns only.
- Clicking the *Clear Form* button should reset the filter.
- Clicking on column headers should sort data in ascending order on the first click then descending order on the second click.

***

#### Files tab

- *Type* filter is an exact filter (Shows only the record with this exact value)
- All other filters are contains filters (Shows all records that contains this value)
- Filters should filter data presented in the Datatable on the fly (i.e as values are selected or characters are typed).

The following columns should be presented

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