Test report
ClinSight traceability matrix and test report
today
Source:vignettes/test_report.Rmd
test_report.RmdTraceability matrix
| Requirement | Feature | Validation | |
|---|---|---|---|
| 1 | Secure Authentication and Authorization | Restrict access (using Shinymanager. Not applicable for internal deployment; for use in production, authentication and authorization is validated in the deployment validation document). | app_authentication |
| 2 | File Integration/loading data | Create app user database | fct_SQLite |
| Create credentials database | app_authentication | ||
| Display database synchronization information | mod_db_synch_info | ||
| Ensure data in memory remains in synch with the database | mod_review_forms | ||
| Explore data | app_feature_01 | ||
| Load application module in isolation | tested in all modules | ||
| Load data from CSV files, merge with custom metadata, and start the application | app_feature_04 | ||
| Merge raw data with metadata | fct_appdata | ||
| Only allow to add query with valid user name and role | mod_query_add | ||
| Save a query | app_feature_03 | ||
| Save review of a form | app_feature_02 | ||
| Select correct data to review | get_review_data | ||
| Select rows with latest time stamp | db_slice_rows | ||
| Start application | app_server | ||
| Update user data database | fct_SQLite | ||
| Warn if database synchronization is outdated | mod_db_synch_info | ||
| Warn if no user role or user name is provided | app_server | ||
| 3 | Data Visualization Tools | Explore data | app_feature_01 |
| Get overview statistics of selected patient | mod_header_widgets | ||
| Highlight data that is not yet reviewed | mod_study_forms | ||
| Save a query | app_feature_3 | ||
| Save review of a form | app_feature_02 | ||
| View common form | mod_common_forms | ||
| View forms with study-specific data | mod_study_forms | ||
| View interactive timeline | mod_timeline | ||
| 4 | Data highlighting | Explore data | app_feature_01 |
| Get overview statistics of selected patient | mod_header_widgets | ||
| Highlight data that is not yet reviewed | mod_study_forms | ||
| Save a query | app_feature_03 | ||
| Save review of a form | app_feature_02 | ||
| View common form | mod_common_forms | ||
| View forms with study-specific data | mod_study_forms | ||
| View interactive timeline | mod_timeline | ||
| 5 | Navigation functionality | Explore data | app_feature_01 |
| Navigate through forms with study data | mod_navigate_forms | ||
| Navigate through participants | mod_navigate_participants | ||
| Navigate to patient selected in a table | mod_go_to_form | ||
| Save a query | app_feature_03 | ||
| Save review of a form | app_feature_02 | ||
| Select user configuration | mod_review_config | ||
| Show overview tables of data to review | mod_navigate_review | ||
| View sidebar containing controls of application | mod_main_sidebar | ||
| 6 | Query Management System | Add follow-up query, mark query as resolved | mod_query_follow_up |
| Create and save a query | mod_query_add | ||
| Create follow-up query | mod_query_follow_up | ||
| Error if query entry in app does not match database | mod_query_add | ||
| Only allow to add query with valid user name and role | mod_query_add | ||
| Only allow to write follow-up query if query id matches to one in database | mod_query_follow_up | ||
| Only allow to write follow-up query with valid user name and user role | mod_query_follow_up | ||
| Save a query | app_feature_03 | ||
| Verify follow-up query correctly being written in database | mod_query_follow_up | ||
| View follow-up messages of a query | mod_queries | ||
| View queries | mod_queries | ||
| Write multiple query follow-up messages | mod_query_follow_up | ||
| 7 | Reviewing functionality | Disable review buttons if review not applicable or not allowed, and give feedback why. | mod_review_forms |
| Only allow to save review with valid user name and role | mod_review_forms | ||
| Restrict right to review forms to roles specified in the app configuration | mod_review_forms | ||
| Save review of a form | app_feature_02 | ||
| Save review of a form | mod_review_forms | ||
| 8 | Reporting functionality | Create PDF report | mod_report_fct_helpers |
| Create PDF report of review actions | mod_report |
Application Test report
Created on: 2024-11-15 14:11:02 UTC.
Test Summary
Acceptance criteria according to test plan are met. Validation successful.
| N | Passed | Failed | Warnings | Errors | Skipped |
|---|---|---|---|---|---|
| 784 | 784 | 0 | 0 | 0 | 0 |
Test environment
Tests were run in the following environment:
#> R version 4.4.1 (2024-06-14)
#> Platform: x86_64-pc-linux-musl
#> Running under: Alpine Linux v3.20
#>
#> Matrix products: default
#> BLAS: /usr/local/lib/R/lib/libRblas.so
#> LAPACK: /usr/local/lib/R/lib/libRlapack.so; LAPACK version 3.12.0
#>
#> locale:
#> [1] C.UTF-8 C C C C C
#>
#> time zone: UTC
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] ggplot2_3.5.1 shiny_1.9.1 shinytest2_0.3.2 clinsight_0.1.1
#> [5] testthat_3.2.1.1
#>
#> loaded via a namespace (and not attached):
#> [1] DBI_1.2.3 attempt_0.3.1 rlang_1.1.4
#> [4] magrittr_2.0.3 timevis_2.1.0 compiler_4.4.1
#> [7] RSQLite_2.3.7 systemfonts_1.1.0 callr_3.7.6
#> [10] vctrs_0.6.5 pkgconfig_2.0.3 crayon_1.5.3
#> [13] billboarder_0.5.0 fastmap_1.2.0 backports_1.5.0
#> [16] dbplyr_2.5.0 labeling_0.4.3 fontawesome_0.5.2
#> [19] utf8_1.2.4 promises_1.3.0 rmarkdown_2.28
#> [22] tzdb_0.4.0 ps_1.8.0 ragg_1.3.3
#> [25] tinytex_0.53 purrr_1.0.2 bit_4.0.5
#> [28] waldo_0.5.3 xfun_0.47 cachem_1.1.0
#> [31] jsonlite_1.8.8 blob_1.2.4 later_1.3.2
#> [34] parallel_4.4.1 R6_2.5.1 golem_0.5.1
#> [37] bslib_0.8.0 brio_1.1.5 jquerylib_0.1.4
#> [40] Rcpp_1.0.13 knitr_1.48 base64enc_0.1-3
#> [43] R.utils_2.12.3 readr_2.1.5 httpuv_1.6.15
#> [46] tidyselect_1.2.1 rstudioapi_0.16.0 yaml_2.3.10
#> [49] codetools_0.2-20 websocket_1.4.2 curl_5.2.2
#> [52] processx_3.8.4 tibble_3.2.1 withr_3.0.1
#> [55] askpass_1.2.0 evaluate_0.24.0 desc_1.4.3
#> [58] scrypt_0.1.6 pillar_1.9.0 shinycssloaders_1.1.0
#> [61] checkmate_2.3.2 DT_0.33 shinyjs_2.1.0
#> [64] pingr_2.0.3 plotly_4.10.4 generics_0.1.3
#> [67] vroom_1.6.5 chromote_0.3.1 hms_1.1.3
#> [70] commonmark_1.9.1 munsell_0.5.1 scales_1.3.0
#> [73] globals_0.16.3 xtable_1.8-4 glue_1.7.0
#> [76] lazyeval_0.2.2 tools_4.4.1 diffobj_0.3.5
#> [79] data.table_1.16.0 fs_1.6.4 Cairo_1.6-2
#> [82] grid_4.4.1 tidyr_1.3.1 crosstalk_1.2.1
#> [85] colorspace_2.1-1 shinymanager_1.0.410 cli_3.6.3
#> [88] config_0.3.2 textshaping_0.4.0 fansi_1.0.6
#> [91] viridisLite_0.4.2 dplyr_1.1.4 gtable_0.3.5
#> [94] R.methodsS3_1.8.2 sass_0.4.9 digest_0.6.37
#> [97] htmlwidgets_1.6.4 farver_2.1.2 memoise_2.0.1
#> [100] htmltools_0.5.8.1 R.oo_1.26.0 lifecycle_1.0.4
#> [103] httr_1.4.7 shinyWidgets_0.8.6 mime_0.12
#> [106] openssl_2.2.1 bit64_4.0.5End-to-end tests
These are the tests and test results of testing the entire application end-to-end.
app_authentication
initialize_credentials(). Feature 1 | (only applicable for shinymanager deployments) Restrict access. As a user, I want to be able to create a credentials database if there is none yet. The database should be accessible by a common admin account and password combination, with the requirement set in the database that the password needs to be changed after first login.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Existing credentials database. Given an existing a database named ‘credentials.db’ containing a test data frame, stored in a temporary folder, I expect that no new database will be created, and that the test data frame within the existing database still exists and is unchaged | 2 | Passed |
| Scenario 2 - Create credentials database. Create a new credentials database. Given that [credentials_db] leads to a non-existing database, and [credentials_pwd] is set to ‘test_password’, I expect that a new credentials database will be created, with the columns [user], [password], [start], [expire], [admin], [name], [mail], [role], and [sites], [is_hashed_password], and with the only existing [user] being ‘admin’, and the user named ‘admin’ having [admin] set to ‘TRUE’, and the [password] being hashed with the hased vector being different from the initialization password (‘1234’), and that the value (password) [must_change] is set to TRUE. | 7 | Passed |
| Scenario 3 - Create a new credentials database in a non-existent folder. Given that [credentials_db] leads to a non-existing .sqlite database in a nont-existent folder, and [credentials_pwd] is set to ‘test_password’, I expect that a new credentials database will be created in the specified folder. | 1 | Passed |
authenticate_ui() and authenticate_server(). (only applicable for shinymanager deployments). Feature 1 | As a user, I want to be able to enter user name and password at the login screen of the application. If the user name and password are incorrect, I want to see an error message, and remain on the login screen.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Access restricted. Given a credentials database containing the user ‘test_user_normal’ with password ‘1234’, and the [credentials_db] does not yet exist, and [credentials_pwd] is set to ‘1234’, and [credentials_folder] is set to an existing folder, and I start the application, I expect that I can only see the login screen, and that, when I try to log in with an incorrect password, I will not be granted access. | 3 | Passed |
app_feature_01
Feature 1 | Explore data. As a user, I want to be able to explore data in both common forms and study-specific forms of multiple participants in the application, so that I can appropriately assess whether there is a risk for the patient’s safety.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Data visualization. Given a fixed random test data set, with all data being marked as ‘new’/not yet reviewed, and being logged in as test user, and setting the subject id to ‘BEL_04_772’, I expect that I can see the start page, and that, by clicking on clicking on [common events], I can see the adverse event page of the selected patient with all data shown in bold (indicating the need for review), and that, by clicking on [Study data], I can see the Vital signs page of the selected patient, with all data shown in large dots (indicating the need for review), and that, after clicking on table view, the same vital signs data will be shown in a table, with all data in bold (indicating the need for review). | 4 | Passed |
app_feature_02
Feature 2 | Save review. As a user, I want to be able to save a review of a specific item of a patient successfully, and store a comment with the review.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Save review. Given a fixed fixed random test data set with all data marked as not yet reviewed, and being logged in as test user, and patient 45 selected as active patient, and the ‘Vital signs’ tab selected as the first tab in the [Study data] tabs, and clicking on [Study data] to browse to the ‘Vital signs’ tab, and clicking on [Reviewed], and adding a comment ‘test comment’ in the comment field, and clicking on [Save] to save the review, I expect that the data will be displayed as being reviewed, and that all data of the selected patient and form (Vital signs) is marked as being reviewed with the reviewer name being ‘test user’, and that the comment ‘test comment’ is saved successfully. | 4 | Passed |
app_feature_03
Feature 3 | Save a query. As a user, I want to be able to save a query based on a specific item of a patient sucessfully, and store the query in the app database
| Test | N | Result |
|---|---|---|
| Scenario 1 - Save normal query. Given a fixed fixed random test data set with all data marked as not yet reviewed, and being logged in as ‘test user’ with the user role ‘Administrator’, and patient BEL_08_45 selected as active patient, and the ‘Vital signs’ tab selected as the first tab in the [Study data] tabs, and clicking on [Study data] to browse to the ‘Vital signs’ tab, and clicking on [Create query], I expect that I see a window to write a query, and after selecting the time point [Screening], and selecting the item [Weight], and adding a query text ‘test query’ in the query field, and clicking on [Add query] to save the query, I expect that a new query has been successfully added to the database, with the query text being ‘test query’, and the user name ‘test_query’, and the subject id BEL_08_45’, and the form name ‘Vital Signs, and the item name ’Weight’, and the event label ‘Screening, and the reviewer name ’test user (Administrator)’ | 7 | Passed |
| Scenario 2 - Browse to patient and save major query. Given a fixed fixed random test data set with all data marked as not yet reviewed, and being logged in as ‘test user’ with the user role ‘Administrator’, and browsing to patient BEL_04_772 with tab ‘Adverse events’, and clicking on [Create query], I expect that I see a window to write a query, and after selecting the item [Tachycardia], and adding a query text ‘Major test query’ in the query field, and marking the query as ‘Major’, and clicking on [Add query] to save the query, I expect that a new query has been successfully added to the database, with the query text being ‘Major test query’, and the subject id BEL_08_45’, and the form name ‘Adverse events’, and the item name ‘Tachycardia’, and the query type being ‘Major’, and the event label ‘Any event’, and the reviewer name ‘test user (Administrator)’ | 8 | Passed |
| Scenario 3 - Viewing of and responding to a query. Given two queries being created as in the previous scenarios, and clicking on the queries tab, I expect that I can see the saved queries. After clicking on the first query in the table, I expect that I can see the details of this query, and that I can write a response message which will be saved after clicking ‘respond to query’. | 3 | Passed |
| Scenario 4 - responding to a query and closing it. Given two queries being created as in the previous scenarios, and viewing the queries tab, and clicking on the pre-existing query of subject [BEL_08_45], I expect that I can write a response to this query, and that I can mark the query as resolved, and that, after saving the response, the results are stored accurately. | 3 | Passed |
app_feature_04
Feature 4 | Load data from CSV files, merge with custom metadata, and start the application.As a user, I want to be able to load data from the raw csv file output from the EDC system and use a different metadata file to customize the application.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Load raw data with custom metadata. Given raw CSV data exported from the EDC system from patient [9600-002], and with metadata in which total visits is restricted to V0-V10, and with only the study_forms ‘Response’ and ‘Vitals adjusted’ in the metadataand with, at both Screening and Visit 2 the [Systolic blood pressure] being 99, [Diastolic Blood Pressure] 77, [Pulse] 77, [Resp] 9, and [Temperature] 37.5, and (only at screening) [Weight] 70kg, and that I browse to the ‘Study data’ tabI expect that I see the Vital signs page of patient [9600-002]’, and that the compact header timeline shows visits V0-V10 and that I see a figure with the data displayed, and that I see a table with the data displayed after clicking on the table view, and that the data for the figure and table in the app is the same as the raw data in the CSV files. | 5 | Passed |
Module tests
These are the tests and test results of the application’s modules.
mod_common_forms
mod_common_forms. Feature 1 | Load application module in isolation.
| Test | N | Result |
|---|---|---|
| Can load the module UI, with functioning internal parameters. | 2 | Passed |
| Can load the module server, with functioning internal parameters. | 3 | Passed |
mod_common_forms. Feature 2 | View common forms. As a user, I want to be able to view common forms in the application, which includes at least the adverse events forms (with timeline view), but can also include forms such as (concomitant) medication, and medical history.
| Test | N | Result |
|---|---|---|
| Scenario 1 - View Adverse events table. Given a list of appdata in [filtered_tables], and the active subject_id set to the existing subject with ID ‘DEU_02_482’, and a data frame with current review_data in [review_data], and the active form set to ‘Adverse events’, and the subject having an adverse event ‘Allergic Reaction’ that has not yet been reviewed, I expect that the active data set [data_active] is a data frame object, and that this data frame contains only data of subject DEU_02_482, and that the output table is a valid JSON object, and that the Adverse event ‘Allergic Reaction’ exists in the active table for subject DEU_02_482, and that the name of the Adverse event ‘Allergic Reaction’ is shown in bold. | 5 | Passed |
| Scenario 2 - View timeline. Given a list of appdata in [filtered_tables], and a data frame with current review_data in [review_data], and the active subject_id set to the existing subject with ID ‘DEU_02_482’, and the selected [form] is ‘Adverse events’, I expect that a timeline (a valid JSON object) is shown in the timeline output | 1 | Passed |
| Scenario 3 - View Medication. Given a list of appdata in [filtered_tables], and the active subject_id set to the existing subject with ID ‘NLD_06_755’, and the active form set to ‘Medication’, and the subject having the medication ‘Pantoprazole’ that has not yet been reviewed, I expect that the active data set [data_active] is a data frame object, and that this data frame contains only data of subject NLD_06_755, and that the medication ‘Pantoprazole’ exists in the active table, and that the medication name is shown in bold, and that the output table is a valid JSON object | 5 | Passed |
mod_db_synch_info
mod_db_synch_info. Feature 1 | Load application module in isolation.
| Test | N | Result |
|---|---|---|
| Can load the module UI, with functioning internal parameters. | 2 | Passed |
| Can load the module server, with functioning internal parameters. | 3 | Passed |
mod_db_synch_info. Feature 2 | Display database synchronization information. As a user, I want to be able to see the latest date at which the database is updated and at which new data was entered in the EDC.
| Test | N | Result |
|---|---|---|
| Scenario 1 - DB synch date and EDC update date. Given current date set to 2024-01-10, and db_synch_time to 2024-01-10, and edc_latest_date to 2024-01-10, I expect that [‘synch_warning’] is empty, and that [edc_latest_date] is ‘2024-01-10’, and that [synch_time] is ‘2024-01-10’, and that the output [‘db_synch_info’] contains ‘EDC Sync date 2024-01-10’ and ‘EDC latest data 2024-01-10’ | 4 | Passed |
mod_db_synch_info. Feature 3 | Warn if database synchronization is outdated. As a user, I want to get a warning if the database synchronization did not happen on the same day as the data review.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Old synchronization. Given the current date set to 2024-01-10, and the latest DB synch date set to ‘2024-01-08’, and the latest EDC udpate date to ‘2024-01-01’, I expect that a pop-up window will be shown with a warning ‘Latest update was 2 days ago (2024-01-08)’, synchronization was more than a day old | 1 | Passed |
| Scenario 2 - Synchronization date or EDC update date missing. Given the current date set to 2024-01-10, and the latest DB synch date is either missing or ‘NULL’, and the latest EDC update date is set to ‘2024-01-01’, I expect that a pop-up window will be shown with the warning ‘The latest database synchronization date is unknown’, and the warning ‘the most recent EDC data entry is Unknown’ | 1 | Passed |
mod_go_to_form
mod_go_to_form. Feature 1 | Load application module in isolation.
| Test | N | Result |
|---|---|---|
| Can load the module UI, with functioning internal parameters. | 2 | Passed |
| Can load the module server, with functioning internal parameters. | 3 | Passed |
mod_go_to_form. Feature 2 | Navigate to patient selected in a table. As a user, I want to be able to navigate to the patient in the selected table row.If the table row contains a form name, I want to navigate to that form of theapplicable patient directly
| Test | N | Result |
|---|---|---|
| Scenario 1 - Browse to a dedicated patient and form. | 8 | Passed |
| Scenario 2 - Ignores form_name if form_name is null and browses to the first form of the patient | 3 | Passed |
| Scenario 3 - Multiple rows selected. I expect that it warns that only the first row will be used if multiple tablerows are selected | 1 | Passed |
| Scenario 4 - form_name missing. I expect that it warns and aborts if form_name is not found in the table | 1 | Passed |
| Scenario 5 - subject_id column missing. I expect that it warns and aborts if subject_id column is not found in the table | 1 | Passed |
| Scenario 6 - Empty subject id row. I expect that it warns and aborts if the selected subject id row is NULL | 1 | Passed |
| Scenario 7 - Unknown subject_id. I expect that it warns and aborts if an unknowwn subject_id was selected in the table | 1 | Passed |
| Scenario 8 - Form name missing. Warns and aborts if the form name is missing in the selected table row | 1 | Passed |
mod_header_widgets
mod_header_widgets. Feature 1 | Load application module in isolation.
| Test | N | Result |
|---|---|---|
| Can load the module UI, with functioning internal parameters. | 2 | Passed |
| Can load the module server, with functioning internal parameters. | 3 | Passed |
mod_header_widgets. Feature 2 | Get overview statistics of selected patient. As a user, I want to be able to get an overview of the selected, active patient’s data in the header. The information should show the patient ID, the number of adverse events (including a color code showing if new/updated adverse events are available), the number of forms that need a review, and a timeline figure showing the number of visits that the patient performed.
| Test | N | Result |
|---|---|---|
Scenario 1 - Subject 1, with Adverse Events and a Serious Adverse Event.
Given data sets [rev_data] and [nav_info] and
[r$filtered_tables$Adverse events] set with test data, and
the active subject ID [r$subject_id] set to [‘Subj01’] , and the active
subject having two adverse events and one severe adverse event, and the
data frame [rev_data$summary()] containing data of ‘Subj01’ with the
column ‘reviewed’ containing at least one ‘No’, I expect [AEvals_active]
to be a data frame with the adverse events of [‘Subj01’], and
[SAEvalue.individual] to be the value one, and [AEvalue.individual] to
be the value two, and [all_AEs_reviewed] to be the value ‘FALSE’, and
the output [ae_box] to contain a html element, and the ouput
[visit_figure] to contain a plot object.
|
6 | Passed |
Scenario 2 - Subject 2, no AEs recorded. Given data sets [rev_data] and
[nav_info] and [r$filtered_data$Adverse events] set with
test data, and the active subject ID [r$subject_id] set to [‘Subj02’],
and the active subject having no adverse event data available, and the
data frame [rev_data$summary()] containing no data of [‘Subj02’], I
expect SAEvalue.individual() to be zero, and AEvalue.individual() to be
zero, and the AEvals_active() table to be a data frame with zero rows,
and all_AEs_reviewed() to being set to ‘TRUE’, and output$ae_box to
contain a html element, and ouput$visit_figure to contain a plot object.
|
6 | Passed |
mod_main_sidebar
mod_main_sidebar. Feature 1 | Load application module in isolation.
| Test | N | Result |
|---|---|---|
| Can load the module UI, with functioning internal parameters. | 2 | Passed |
| Can load the module server, with functioning internal parameters. | 3 | Passed |
mod_main_sidebar. Feature 2 | View sidebar containing controls of application. As a user, I want to be able to view the main sidebar that contains buttons to save review actions, including comments, to the selected worksheet. In addition, I want to be able to navigate to the next/previous form by clicking on the next or previous button. The sidebar should also contain a button to configure review, and a button to open a modal in which I can raise a query for the selected active form and participant.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Open ‘create query’ modal. I expect that I can open a modal for creating a query after clicking the ‘create query’ button | 1 | Passed |
| Scenario 2 - Hide review panel. Given test a data frame with random data, and active_tab set to ‘Start’ (not ‘Common events’ or ‘Study data’), I expect that the review panel will be hidden. | 1 | Passed |
mod_navigate_forms
mod_navigate_forms. Feature 1 | Load application module in isolation.
| Test | N | Result |
|---|---|---|
| Can load the module UI, with functioning internal parameters. | 2 | Passed |
| Can load the module server, with functioning internal parameters. | 3 | Passed |
mod_navigate_forms. Feature 2 | Navigate through forms with study data. As a user, I want to be able to navigate forms in the application, using the back and forward buttons in the application. When clicking on the forward button, I should navigate to the next form of the same patient.
| Test | N | Result |
|---|---|---|
| Scenario 1 - New data is displayed in bold font face. I expect that a bold form name will be displayed if the form is in the vector review_forms (which contains all form names of the forms with new/updated data) | 1 | Passed |
| Scenario 2 - Already reviewed data is shown in normal font face. I expect that the form_name is shown in a non-bold font face | 1 | Passed |
| Scenario 3 - Navigating to next form. I expect that I can navigate to the next form if requested | 2 | Passed |
| Scenario 4 - Navigating to previous form. I expect that I can navigate to the previous form if requested | 2 | Passed |
| Scenario 5 - Navigation to previous form when first form is active. I expect that I navigate to the last form if the first form is active and the previous button is pressed | 2 | Passed |
| Scenario 6 - Navigation to next form when last form is active. I expect that I navigate to the first form if the last form is active and the next button is pressed | 2 | Passed |
| Scenario 7 - Uncommon change of tabs. I expect that the module does not error if a change in tabs is requested and the main tab is named other than ‘Common events’ or ‘Study data’. | 2 | Passed |
| Scenario 8 - Using non-existing forms or empty forms numbers. I expect that there will be a warning when a non-existing form is used or an empty form number is given, and that the page change is aborted, and that the module does not crash | 3 | Passed |
mod_navigate_participants
mod_navigate_participants. Feature 1 | Load application module in isolation.
| Test | N | Result |
|---|---|---|
| Can load the module UI, with functioning internal parameters. | 2 | Passed |
| Can load the module server, with functioning internal parameters. | 3 | Passed |
mod_navigate_participants. Feature 2 | Navigate through participants. As a user, I want to be able to browse through the study participants by means of a back and forward button, or with a drop-down menu. I want to be able to see some summary information of the selected patient. After pressing save, the patient should be selected as active patient in the app.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Given a table with general information in reactiveValues [r], and the selected participant set to ‘Subj2’, and pressing the apply button (setting [subj_apply] to 2), I expect that the global active subject_id in reactivevalues [r] is set to ‘Subj2’ | 3 | Passed |
| Scenario 2 - Given a table with general information in reactiveValues [r], and the selected participant set to ‘Subj2’, and pressing the next or previous button, I expect that the selected subject will be the nex or previous subject. | 2 | Passed |
| Scenario 3 - Given a table with general information in reactiveValues [r], and the selected participant set to the FIRST subject in the table, and pressing the back button, I expect that the active subject ID does not change | 1 | Passed |
| Scenario 4 - Given a table with general information in reactiveValues [r], and the selected participant set to the LAST subject in the table, and pressing the next button, I expect that the active subject ID does not change | 1 | Passed |
| Scenario 5 - Given a table with general information in reactiveValues [r], and the active global subject in [r] is set to a non-existent one, I expect that [pt_info] contains a message with the text ‘Data missing’ | 1 | Passed |
| Scenario 6 - Given a table with general information in reactiveValues [r], and the active [subject_id] set to ‘Subj1’, and the actions and clicking the subject tile in the header, I expect that a module will be shown with participant information, and with options to change the current participant. | 4 | Passed |
mod_navigate_review
mod_navigate_review. Feature 1 | Load application module in isolation.
| Test | N | Result |
|---|---|---|
| Can load the module UI, with functioning internal parameters. | 2 | Passed |
| Can load the module server, with functioning internal parameters. | 3 | Passed |
mod_navigate_review. Feature 2 | Show overview tables of data to review. As a user, I want to be able to see detailed information about which forms need to be reviewed, and which queries are already queried. This can be shown in tables. I want to be able to switch view so that I can quickly filter only the forms of the active participant, or show data of all participants of the selected sites.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Given Subject id set to ‘subject01-test’, and [input$show_all_data] set to TRUE/FALSE, I expect that the table header text will be ‘All data’/‘subject01-test’ , respectively (in bold font) | 2 | Passed |
| Scenario 2 - Given Subject id set to ‘subject01-test’, and [input$show_all_data] set to either TRUE/FALSE, and rev_data$summary (=reactiveVal()) containing summary data with at least the column subject_id, I expect that the table with review data shows either the summary review data from all subjects or only from the selected subject, and that the table with query data shows either summary review data from all subjects or only from the selected subject. | 8 | Passed |
| Scenario 3 - Given Subject id set to ‘subject01-test’, and [input$show_all_data] set to either TRUE/FALSE, and rev_data$summary() (=reactiveVal()) containing an empty data frame, and r$query_data being an empty data frame, I expect that an empty summary table and an empty summary will be shown | 5 | Passed |
| Scenario 4 - Given Subject id set to ‘subject01-test’, and the input value [show_all_data] is set to either TRUE/FALSE, and the [summary()] data frame in [rev_data] contains summary review data, and I click on an external button to open the review data modal, I expect that I can see the summary table with data of patient ‘subject01-test’, and that I can switch to data of all patients [show_all_data] to TRUE, and that I can switch to the tab with the query table | 3 | Passed |
mod_queries
mod_queries. Feature 1 | Load application module in isolation.
| Test | N | Result |
|---|---|---|
| Can load the module UI, with functioning internal parameters. | 2 | Passed |
| Can load the module server, with functioning internal parameters. | 3 | Passed |
mod_queries. Feature 2 | View queries. As a user, I want to be able to view all queries in a table if show_resolved is set to TRUE, ordered by query resolved status (open queries first), and query type (major queries on top) . If show_resolved is set to FALSE, only open queries will be shown.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Show queries. Given a data frame [query_df], and [show_resolved] is set to ‘TRUE’, I expect the initial queries to be shown in ‘initial_queries’ ordered by resolved status and query type, and if [show_resolved] is set to ‘TRUE’, I expect that only the open queries are shown in ‘initial_queries’, ordered by query type (major queries on top). | 2 | Passed |
mod_queries. Feature 3 | As a user, I want to be able to view all the follow-up messages that have been written for a selected query. I want to be able to click follow-up, to write a follow-up message to the query.
| Test | N | Result |
|---|---|---|
| Scenario 2 - Select query with follow-up messages. Given a data frame with test query data, and with the selected row [queries_row_selected] set to ‘2’, and show_resolved set to ‘TRUE’, I expect [selected_query] to be the selected [query_id] ‘ID1-unique_id’, and that the [selected_query_data] data frame shows the query and its follow-up query, as stored in the test query data, and the selected query title contains the item name, subject_id, item_group, and resolved value. | 3 | Passed |
| Scenario 3 - Selected query that is unresolved. Given a data frame [query_df], and with the selected row [queries_row_selected] set to ‘1’, and show_resolved set to ‘TRUE’, I expect [selected_query] to be the selected query_id ‘ID2-unique_id’, and that [selected_query_data] shows the correct query belonging to the selected query_id, and that the selected query title contains the item name, subject_id, item_group, and will not show that it is resolved. | 3 | Passed |
mod_query_add
mod_query_add. Feature 1 | Load application module in isolation.
| Test | N | Result |
|---|---|---|
| Can load the module UI, with functioning internal parameters. | 2 | Passed |
| Can load the module server, with functioning internal parameters. | 3 | Passed |
mod_query_add. Feature 2 | Create and save a query. As a user, I want to be able to create a query and save it to the remote database and to the internal data frame. Together with the query text, I want to be able to save other mandatory information, such as query type, the name of the reviewer, a timestamp, the ID of the participant, and the form at which the query is applicable. Optional other information that I want to be able to save with the query is the name of the item in question.
| Test | N | Result |
|---|---|---|
| Scenario 1 - The currently active form information is correct. Given [subject_id] set to ‘ID1’, and [active_form] consecutively set to ‘Vital signs’ and ‘Adverse events’, I expect that the data frame [selected_data] shows a data frame with available data of [subject_id] ‘ID1’ and [active_form] but filtered on the [subject_id] and [active_form()] | 2 | Passed |
| Scenario 2 - A query can be saved successfully. Given [subject_id] is set to ‘ID2’, and [active_form()] is set to ‘Medication’, and [query_text] is ‘Add a new test query’, and [query_select_visit] is set to ‘Visit 1’, and [query_select_item] is set to ‘Oxycodon’, and [query_major] is set to ‘FALSE’, and [query_add_input] is set to 1 (indicating a button click), I expect that one new query is saved in [query_data] for patent ‘ID1’, and that the ‘item_group’ of the query is ‘Medication’, and ‘item’ is ‘Oxycodon’, and ‘reviewer’ is ‘User 1’ with the role ‘Medical Monitor’, and ‘query’ is ‘Add a new test query’, and ‘resolved’ is ‘No’, and the remote database contains the same query as in [query_data]. | 7 | Passed |
| Scenario 3 - Save a major query. Given [subject_id] is set to ‘ID3’, and [active_form()] is set to ‘Adverse events’, and [query_text] is ‘Major query text.’, and [query_select_visit] is set to ‘Visit 1’, and [query_select_item] is set to ‘Pneumothorax’, and [query_major] is set to ‘TRUE’, and [query_add_input] is set to 1 (indicating a button click), I expect that one new query is saved in [query_data] for patent ‘ID3’, and that the ‘item_group’ of the query is ‘Adverse events’, and ‘item’ is ‘Pneumothorax’, and ‘reviewer’ is ‘User 1’ with the role ‘Medical Monitor’, and ‘query’ is ‘Major query text.’, and ‘resolved’ is ‘No’, and the remote database contains the same query as in [query_data]. | 7 | Passed |
mod_query_add. Feature 3 | Error if query entry in app does not match database. As a user, I want to be able to see an error message if the latest query entry does not match the one in the database after saving a new entry.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Database save function not working. Given a test data base, and the function ‘db_save’ being mocked (temporarily replaced) with a function that does not write to the database, and [user_name] set to ‘test user’, and [active_form] to ‘Adverse events’, and [subject_id] to ‘885’, and [query_text] set to ‘Test query’, and [query_select_visit] to ‘Any visit’, and [create_query] to 1, and [query_add_input] to 1, I expect that [save_review_error] is TRUE, and that the new query is not saved in memory, and that [query_data] remains the same as the input test query data. | 3 | Passed |
mod_query_add. Feature 4 | Only allow to add query with valid user name and role. As a user, I want that saving a query is only possible with a valid user name and role
| Test | N | Result |
|---|---|---|
| Scenario 1 - Trying to save a query without user name. Given a data frame and a database with review data with [reviewed] status set to ‘new’ (not reviewed yet), and no [user_name] available, and [subject_id] set to ‘885’, and [active_form] set to ‘Adverse events’, and no [user_role] set to ‘Medical Monitor’, and setting the value [form_review] is to ‘TRUE’ and clicking on the [save_review] button, I expect that a query_error will be shown, and that no [query_data] in the application and in the database is unchanged. | 3 | Passed |
| Scenario 2 - Trying to save a query without user role. Given the same conditions as in scenario 1, but user_name now set to ‘test user’, and no user role available, and trying to save a review, I expect that a query_error will be shown, and that no [query_data] in the application and in the database is unchanged. | 3 | Passed |
mod_query_follow_up
mod_query_follow_up. Feature 1 | Load application module in isolation.
| Test | N | Result |
|---|---|---|
| Can load the module UI, with functioning internal parameters. | 2 | Passed |
| Can load the module server, with functioning internal parameters. | 3 | Passed |
mod_query_follow_up. Feature 2 | Create follow-up query. As a user, I want to be able to create a follow-up message on a selected query. The follow-up message should be saved in the review database and should be the same as the message in-memory.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Add query follow-up message. Given a query database containing a row with [query] set to ‘Query text test.’ and [query_id] set to ‘ID1-unique_id’, and [selected_query] set to ‘ID1-unique_id’, and the input [query_follow_up_text] set to ‘Test Follow-up message’, and [user_name] set to ‘Admin test’ and [user_role] to ‘Medical Monitor’, and the input value [resolved] set to ‘FALSE’, and the input [query_add_follow_up] incremented to 1 to save the query, I expect that the follow-up message will be written in the remote and in-memory database | 4 | Passed |
mod_query_follow_up. Feature 3 | Add follow-up query, mark query as resolved. As a user, I want to be able to add a follow-up query and mark a query as resolved. The information should be saved in the query database.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Add query follow-up and resolve query. Given a query database containing a row with [query] set to ‘Query text test.’ and [query_id] set to ‘ID1-unique_id’, and [selected_query] set to ‘ID1-unique_id’, and the input [query_follow_up_text] set to ‘Test Follow-up message’, and [user_name] set to ‘Admin test’ and [user_role] to ‘Medical Monitor’, and the input value [resolved] set to ‘TRUE’, and the input [query_add_follow_up] incremented to 1 to save the query, I expect that the value [query] with query_id ‘ID1-unique_id’ is a vector with the two strings ‘Query text test.’ and ‘Test Follow-up message’, and that the follow-up number [n] of the same query_id is a vector with ‘1’ and ‘2’, and that the [resolved] value is ‘Yes’, and that a valid date is written in the [resolved_date], and that the in-memory [query_data] data frame contains the same query timestamp, and the same query text, and the same query reviewer name and reviewer role as in the query database, and that the database [resolved] values are ‘No’ for the row with the initial query and ‘Yes’ for the follow-up query. | 8 | Passed |
mod_query_follow_up. Feature 4 | Write multiple query follow-up messages. As a user, I want that multiple follow-up messages for a query can be written and saved in the query database, and that the order of the follow-up messages remains as expected.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Saving multiple query follow-up messages. Given a query database containing a row with [query] set to ‘Query text test.’ and [query_id] set to ‘ID1-unique_id’, and [selected_query] set to ‘ID1-unique_id’, and [user_name] set to ‘Admin test’ and [user_role] to ‘Medical Monitor’, and the input [query_follow_up_text] set to ‘FU message 1’, and [resolved] set to ‘FALSE’, and the input [query_add_follow_up] incremented to 1 to save the query, and the input [query_follow_up_text] set to ‘FU message 2’ , and [resolved] set to ‘TRUE’, I expect that the value [query] with query_id ‘ID1-unique_id’ is a vector with three strings (‘Query text test.’ ‘FU message 1’ and ‘FU message 2’), and that the follow-up number [n] of the same query_id is a vector with ‘1’, ‘2’, and ‘3’, and that the in-memory [resolved] value is ‘Yes’, and that a valid date is written in the [resolved_date], and that both the in-memory [query_data] data frame and the query database contain the same query timestamp, and the same query text, and the same query reviewer name and reviewer role, and that the database [resolved] values are ‘No’ for the first two rose and ‘Yes’ for the final follow-up query. | 8 | Passed |
mod_query_follow_up. Feature 5 | Only allow to write follow-up query if query id matches to one in database. As a user, I want that no follow-up query will be written to the database and that the in-memory query information remains the same if it is unclear which query the follow-up message concerns.
| Test | N | Result |
|---|---|---|
| Scenario 1 - No follow-up query without selected query id. Given a specific [query_follow_up_text], and no query id set in [selected_query], I expect that the query database and internal query data frame remain the same. | 4 | Passed |
| Scenario 2 - No follow-up query with an unknown query id. Given a specific [query_follow_up_text], and the query id in [selected_query()] is set to an unknown query_id which is not in the database, I expect that no data will be written to the database, and that a warning will be given | 3 | Passed |
mod_query_follow_up. Feature 6 | Only allow to write follow-up query with valid user name and user role. As a user, I want that no follow-up query will be written to the database if no valid user name or user role is available.
| Test | N | Result |
|---|---|---|
| Scenario 1 - No user name available. follow-up query without selected query id. Given no user name is available, and [query_follow_up_text] contains a specific follow-up text, and [selected_query] is set to ‘ID1-unique_id’, and trying to save a follow-up query by pressing [query_add_follow_up], I expect that [query_error] shows an informative error, and I expect that the query database and internal query data frame remain the same. | 3 | Passed |
| Scenario 2 - No user role available. Given the same a conditions as in Scenario 1, but now with [user_name] set to ‘test user’ and no [user_role] available, and trying to save a follow-up query by pressing [query_add_follow_up], I expect that no data will be written to the database, and that a warning will be given | 3 | Passed |
mod_query_follow_up. Feature 7 | Verify follow-up query correctly being written in database. As a user, I want to be able to see an error message if the latest query entry does not match the one in the database after saving a new entry.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Database save function not working. Given a test data base, and the function ‘db_save’ being mocked (temporarily replaced) with a function that does not write to the database, and [user_name] set to ‘Admin test’, and [active_form] to ‘Adverse events’, and [subject_id] to ‘ID1’, and [query_follow_up_text] set to ‘Test Follow-up message’, and [query_add_follow_up] to 1, I expect that [save_review_error] is TRUE, and that the new query is not save in memory, and that [query_data] remains the same as the input test query data. | 4 | Passed |
mod_report
mod_report. Feature 1 | Load application module in isolation.
| Test | N | Result |
|---|---|---|
| Can load the module UI, with functioning base paramneters and internals. | 2 | Passed |
| Can load the module server, with functioning internal parameters. | 3 | Passed |
mod_report. Feature 2 | Create PDF report of review actions. As a user, I want to be able to create a PDF report that contains my review activities of that session.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Report data preparation. Given data frames [query_data] and [review_data], and all values in column ‘Reviewed’ in [review_data] are ‘Yes’, and the get_review_data is set to 1, I expect that the internal data frames are correctly prepared for reporting. | 3 | Passed |
| Scenario 2 - Warn for missing reviews. Given data frames [query_data] and [review_data], and some values in column ‘Reviewed’ in [review_data] are ‘No’, and the get_review_data is set to 1, and check_missing_data is set to 1, I expect that opening the missing data modal is trigggered, by incrementing the rev_data$open_modal counter with one. | 6 | Passed |
| Scenario 3 - Download report. Given data frames [query_data] and [review_data], and all values in column ‘Reviewed’ in [review_data] are ‘Yes’, and the get_review_data is set to 1, and the user is set to ‘Test user (Medical Monitor)’, I expect that I can successfully download a PDF report containing the review activities. | 3 | Passed |
mod_report_fct_helpers
create_report() Feature 1 | Create PDF report. As a user, I want to be able to create a PDF report showing either, depending on the user settings, the activities of the reviewer during a session, or an overview of the review status at a certain date, showing all data of a patient.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Create report. Given a Report template at inst/app/Report.Rmd, and input of a reactiveValue r containing the user name and the review data with all sites reviewed, and a data frame [review_df] with the review information, and a data frame [query_df] with the queries raised, and fileinput set to the location at which the file should be saved, I expect that a PDF report will be created at the location of [fileinput]. | 1 | Passed |
mod_review_config
mod_report. Feature 1 | Load application module in isolation.
| Test | N | Result |
|---|---|---|
| Can load the module UI, with functioning internal parameters. | 2 | Passed |
| Can load the module server, with functioning internal parameters. | 3 | Passed |
mod_review_config. Feature 2 | Select user configuration. As a user, I want to be able to select my user configuration before I start to perform a review. I want to be able to configure the regions and the sites that I will review. After selecting these, the data should be filtered so that only data from the filtered regions/sites will be shown.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Warn for missing sites. Given a test data set with random data, and and a site name was provided that is not available in the test data set, I expect that a warning will be given with the text ‘Not all sites are found in the appdata’. | 1 | Passed |
| Scenario 2 - Filters data and subject ids as expected. Given a test data set with random data containing the regions ‘BEL’, ‘NLD’, and ‘DEU’, I expect that the regions are initially set to ‘BEL’, ‘NLD’, and ‘DEU’, and given that I select the region ‘NLD’ and press the [Save] button, I expect that the app regions are now set to ‘NLD’, and that the data frame is filtered to contain only the SubjectIds from region ‘NLD’. | 4 | Passed |
| Scenario 3 - Warns if only sites are selected that are not in the app data set. Given a test data set with random data, and region is set to ‘NLD’, and site selection is set only to the non-existent ‘Site x’, and the button [Save] is pressed, I expect that the filtering will be aborted, and that a warning will be shown. | 2 | Passed |
| Scenario 4 - Apply review configuration. Given a test data set containing regions ‘NLD’, ‘DEU’, and ‘BEL’, and sites ‘Site 01’ and ‘Site 02’ belonging to region ‘DEU’, and clicking on [settings], I expect to see the modal to select regions and sites to review, and given that I deselect all regions and click on [Save], I expect that I will get the message ‘You must select at least one site/region to review.’, and that the data within the app will not be updated with the empty selection, and given that I select region ‘DEU’, I expect that only the sites ‘Site 01’ and ‘Site 02’ will be selected, and given that I click on [Save], I expect that a confirmation will be shown with the text ‘Review configuration applied successfully’, and that the data within the app only contains data of ‘Site 01’ and ‘Site 02’, and I expect that the selected configuration is shown correctly when opening the configuration panel again. | 9 | Passed |
mod_review_config. Feature 3 | Allow to change roles if multiple are assigned. As a user, I want to be able to change my role, if there are multiple roles allocated.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Change user role. Given a user named ‘test user’ with the user_role set to ‘Administrator’, and the available roles set to ‘Administrator’ and ‘Medical Monitor’, and a test data set with random data, and after setting the ‘active_role’ to ‘Medical Monitor’ and clicking ‘save changes’, I expect that the user role is changed to ‘Medical Monitor’. | 3 | Passed |
mod_review_forms
mod_review_forms. Feature 1 | Load application module in isolation.
| Test | N | Result |
|---|---|---|
| Can load the module UI, with functioning internal parameters. | 2 | Passed |
| Can load the module server, with functioning internal parameters. | 3 | Passed |
mod_review_forms. Feature 2 | Save review of a form. As a user, I want to be able to save a review of a form in the database. After saving the review, all items of that form that are not yet reviewed should get a tag that the value was reviewed.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Save a review. Given test review data with at least an ‘Adverse event’ form with patient ‘885’,and [user_name] set to ‘test_name’ and [user_role] to ‘Medical Monitor’and [active_patient] set to ’885’, and [active_form] set to ‘Adverse events’, and [active_tab] set to ‘Common forms’, and [form_reviewed] set to FALSE, I expect that I can save a new review properly, with the result saved in the application being the same as the one saved in the database. | 8 | Passed |
| Scenario 2 - Save a review. Given a data frame and a database with review data with [reviewed] status set to ‘new’ (not reviewed yet), and [user_name] set to ‘test_name’ and [user_role] to ‘Medical Monitor’, and [subject_id] set to ‘885’, and [active_form] set to ‘Adverse events’, and first (1) No input is given, then (2) the [form_reviewed] tick box is ticked and the comment field enabled, and then (3) the [save_review] button is clicked, I expect that, after each action, the save review button and the option to add a comment will be (1) disabled, (2) enabled, and (3) disabled, and that, after the aforementioned input actions, the review status of the active form and active subject in the database is set to ‘old’ (reviewed), and the reviewer is set to ‘test_name’. | 14 | Passed |
mod_review_forms. Feature 3 | Disable review buttons if review not applicable or not allowed, and give feedback why. As a user, I want to get feedback on whether a review is needed or not for an active form. The review controls should only be enabled when there is data to review.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Review needed. Given test review data with at least an ‘Adverse event’ form with patient ‘885’, and [active_patient] set to ‘885’, and [active_form] set to ‘Adverse events’, and [active_tab] set to ‘Common forms’, and [form_reviewed] set to FALSE, I expect that the data frame [active_review_data] contains one row with data of participant ‘885’, and with the [item_group] set to ‘Adverse events’, and that a message will be displayed containing the text ‘Requires review’ | 4 | Passed |
| Scenario 2 - Saving with unchanged review status. Given the same conditions as in Scenario 1, and setting comment to ‘test comment’, and attempting to save a review ‘save review’, I expect that [enable_save_review()] is set to ‘FALSE’, and that the review database remains unchanged. | 3 | Passed |
| Scenario 3 - No data to review. Given [active_form] set to a form of which no data is available named [no_data_form], and that I try to save a review by setting [save_review] to 1, I expect that a warning message will be displayed with the text [Nothing to review], and that no new information is saved to the database, and that no new information is saved to the app data frame. | 3 | Passed |
mod_review_forms. Feature 4 | Only allow to save review with valid user name and role. As a user, I want that saving data is only possible with a valid user name
| Test | N | Result |
|---|---|---|
| Scenario 1 - Trying to save data without user name. Given a data frame and a database with review data with [reviewed] status set to ‘new’ (not reviewed yet), and [subject_id] set to ‘885’, and [active_form] set to ‘Adverse events’, and no [user_name] available, and setting the value [form_review] is to ‘TRUE’ and clicking on the [save_review] button, I expect that an error message will be displayed, and that the review data of the selected subject and form is unaltered. | 2 | Passed |
Feature 5 | Ensure data in memory remains in synch with the database. As a user, I want that data in memory remains the same as the one in the database, even if an error occurs when saving data to the database
| Test | N | Result |
|---|---|---|
| Scenario 1 - Database save function not working. Given test review data, and the function ‘db_save_review’ being mocked (temporarily replaced) with a function that does not write to the database, and [user_name] set to ‘885’, and [active_form] to ‘Adverse events’, and [active_tab] to ‘Common forms’, and [form_reviewed] to ‘TRUE’, and [save_review] to ‘1’, I expect that [save_review_error] is TRUE, and that the new review data is not saved in memory, and that the rows of [review_data] in the database of subject 885 are still marked as not reviewed | 3 | Passed |
mod_review_forms. Feature 6 | Restrict right to review forms to roles specified in the app configuration. As an admin, I want to be able to restrict the right to review forms to the roles specified in the config file.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Role without review privileges. Given the [user_name] ‘test_user’, and the unprivileged user_role ‘restricted_role’, I expect that all the review options are disabled, and that in the review_error output a message is shown that review is not allowed for the user’s active role. | 5 | Passed |
mod_study_forms
mod_study_forms. Feature 1 | Load application module in isolation.
| Test | N | Result |
|---|---|---|
| Can load the module UI, with functioning internal parameters. | 2 | Passed |
| Can load the module server, with functioning internal parameters. | 3 | Passed |
mod_study_forms. Feature 2 | View forms with study-specific data. As a user, I want to be able to view a form with study-specific data. The forms will be specified with a study-specific metadata file.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Given subject id is set to NLD_05_561, and form filter set to ‘pulse’ and ‘bmi’, I expect that [fig_data] contains a data frame with only items ‘BMI’ and ‘Pulse’, and that a plotly [dynamic_figure] contains a plotly htmlwidget figure, and that the figure outputcontains a valid JSON object | 4 | Passed |
| Scenario 3 - ‘show_all’ set to FALSE. Given subject id NLD_05_561, and input value ‘show_all’ is set to ‘FALSE’, I expect that a table with only review data of subject NLD_05_561 will be shown, and that a valid JSON output table will be created | 5 | Passed |
| Scenario 4 - Given subject id NLD_05_561, and the input value [show_all] is set to ‘TRUE’, I expect that a table with review data of everyone will be shown, and that a valid JSON output table will be created | 4 | Passed |
Feature 4 | Highlight data that is not yet reviewed. As a user, I want to be able to see data that has not yet been reviewed highlighted
| Test | N | Result |
|---|---|---|
| Scenario 1 - Review status information. Given subject id is set to ‘885’, and the form set to ‘Vital signs’, and the filter set to ‘pulse’ and ‘bmi’, I expect that [fig_data] contains a column named ‘reviewed’, and that the ‘reviewed’ column contains the values ‘Yes’ or ‘No’. | 3 | Passed |
| Scenario 2 - Showing review status. Given a test data set with random test data, and [subject_id] is set to ‘NLD_06_755’, and form is set to ‘Vital signs’, and the filter is set to ‘temperature’, I expect that in the [fig_data] only temperature data is shown, with the first measurement being old and the new one not yet reviewed, and that in the figure the data of subject ‘NLD_06_755’ is highlighted, with both the last data point being shown as a bigger dot indicating it needs to be reviewed, and that, after switching to table view, it shows the table with not yet reviewed data highlighted. | 4 | Passed |
mod_timeline
mod_timeline. Feature 1 | Load application module in isolation.
| Test | N | Result |
|---|---|---|
| Can load the module UI, with functioning internal parameters. | 2 | Passed |
| Can load the module server, with functioning internal parameters. | 3 | Passed |
mod_timeline. Feature 1 | As a user, I want to be able to view an interactive timeline that displays study events, such as visits and study drug administration, together with data related to patient monitoring stuch as adverse events.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Given a Form ‘Adverse events’, I expect two internal dataframes (timeline_data_active() and timeline_data()) and a JSON timeline object timeline as output | 5 | Passed |
| Scenario 2 - Given a Form other than ‘Adverse events’, I expect two empty internal dataframes (timeline_data_active() and timeline_data()) and an empty timeline object as output | 3 | Passed |
Function tests
These are tests and test results of lower-level functions (units) that are used within the application modules.
add_missing_columns
add_missing_columns() makes implicitly missing columns in a dataframe explicitly missing. It adds all columns with columns names in a character vector of choice to the dataset if the column is missing.
| Test | N | Result |
|---|---|---|
| Returns a data frame with the same number of rows as the input data frame, and adds the columns in the [column] argument to the data frame if these are not yet present, and errors if not a data frame is provided. | 4 | Passed |
| Returns the input data frame if the columns in the [column] argument are already present in the data frame | 1 | Passed |
| Returns the original data frame and gives a warning if all column names are missing (NA_character_) | 2 | Passed |
Removes missing values from the columns argument and
displays a warning when doing so.
|
2 | Passed |
| Can add a missing column if the provided data frame has zero rows | 4 | Passed |
adjust_colnames
adjust_colnames() can adjust column names by replacing a pattern with a replacement string.
| Test | N | Result |
|---|---|---|
| Outputs a valid data frame | 1 | Passed |
| Errors with a missing input data frame object [data] | 1 | Passed |
| Errors with a missing input [pattern] | 1 | Passed |
| Errors with a missing [replacement] pattern | 1 | Passed |
| Adjusts names as intended, with the column name [pattern] being replaced by the provided [replacement] string | 1 | Passed |
app_server
collapse_column_vals
collapse_column_vals() can collapse values in a column in a data frame into a string with a given separator, for example a comma. The values to collapse are all the values in a group (defined by the grouping columns). Values excluded from the collapse can also be defined.
| Test | N | Result |
|---|---|---|
| can collapse all the unique values of a character variable in a data frame with a given separator. | 1 | Passed |
| can exclude variables from the collapse | 5 | Passed |
| returns an empty data frame if an empty data frame is provided as input | 1 | Passed |
| errors if the data frame is missing | 1 | Passed |
| produces the expected snapshot | 1 | Passed |
collect_query_data
collect_query_data() works
| Test | N | Result |
|---|---|---|
| collects data from a database without errors | 1 | Passed |
| Selects the latest timestamp by the required groups (query_id and n (n= number showing follow-up message) ). This ensures that a query can be edited, and that only the latest (edited) result will be returned. | 2 | Passed |
| set all colums to resolved with the equivalent resolved date | 1 | Passed |
datatable_custom
datatable_custom() works
| Test | N | Result |
|---|---|---|
| creates a datatable | 1 | Passed |
| creates a datatable and can change column names | 2 | Passed |
| creates a datatable and can add a title to the table | 2 | Passed |
| Produces a valid datatable with zero rows if no rows provided in the input table | 2 | Passed |
| Errors if not a valid data frame is provided | 1 | Passed |
| Errors if rename_vars is not a character vector | 1 | Passed |
| Errors if title is not a character vector | 1 | Passed |
db_slice_rows
db_slice_rows. Feature 1 | Select rows with latest time stamp. As a user, I want to be able to select rows in a database or data frame, that have the lastest timestamp per selection group. This way, I can select (for example) the latest data point with the latest review activity. I want to be able to at least filter using two timestamp variables, so that the data can be filtered on the latest edit of the study site (as captured in the external EDC system), as well as on the latest edit of the review data by the reviewer in the application.
| Test | N | Result |
|---|---|---|
| Scenario 1 - Given a data frame with review data with one date-time variable [review_dttm] and grouping variables [ID] and [group], I expect that I can slice the database with the output being a data frame, and with the output data frame containing the rows with the latest data point per group | 2 | Passed |
| Scenario 2 - Given a data frame with review data with and two date-time variables, that is stored in a database, I expect that I can slice the data frame based on both date-time variables, selecting the rows with the latest date-time values. | 2 | Passed |
| Scenario 3 - Given a data frame with the same date time values in the same group, and the data frame being saved in a database, I expect a warning if I try to slice the database, and that the last entry per group is selected, which is the most recent entry. | 2 | Passed |
fct_SQLite
db_create(). Feature 1 | Create app user database. As a user, I want to be able to create an app database that contains the necessary tables for the application to function.
| Test | N | Result |
|---|---|---|
| Can create an app database | 6 | Passed |
| Can create a .sqlite app database if the database folder does not exist, with the required tables named [all_review_data], db_synch_time, and query_data | 2 | Passed |
db_update(). Feature 2 | Update user data database.
| Test | N | Result |
|---|---|---|
| Never changes original entries in the database | 1 | Passed |
| Adds a new row to a database if there are new rows | 1 | Passed |
| Still performs an update if synch_time is not available | 1 | Passed |
| Adds a new row for each data point with a new/updated EditdateTime. | 1 | Passed |
| Does not change the database if there are no changes (synch_time is the same) | 2 | Passed |
db_save_review() works
| Test | N | Result |
|---|---|---|
| Can update a review info row | 1 | Passed |
| Updates all items from a item_group as reviewed | 4 | Passed |
| warns with multiple rows in the review_row object | 1 | Passed |
fct_app_role_helpers
get_roles_from_config() works
| Test | N | Result |
|---|---|---|
| retrieves app roles, and errors with incorrect input | 2 | Passed |
get_valid_roles() works
| Test | N | Result |
|---|---|---|
| select roles out of available ones, in the order as described in the config file | 1 | Passed |
| allows list-type input | 1 | Passed |
| errors with incorrect input | 2 | Passed |
| sanitizes role input by converting everything to lowercase, by splitting up strings when commas are detected, and by removing white spaces if applicable | 2 | Passed |
| warns, but does not error, if input is empty or if no valid roles are available, and outputs an empty named character vector | 6 | Passed |
fct_appdata
merge_meta_with_data. Feature 1 | Merge raw data with metadata. As a user, I want to be able to merge raw data with metadata. Furthermore, I want to be able to fix suffixes and rename the limits and significance values to the standard names used in the app.
| Test | N | Result |
|---|---|---|
| Produces a data frame without errors | 3 | Passed |
| Scenario 1 - Given a data frame with raw data,I expect that the output will be the same as recorded in a snapshot. | 2 | Passed |
fct_figure_helpers
remove_boxplot_outliers() removes boxplot outliers from plotlyggplotly() boxplots.
| Test | N | Result |
|---|---|---|
| creates a valid plotly object | 1 | Passed |
| has all markers in boxplot layers set to zero | 1 | Passed |
fct_tables
Create_table.default() works and creates a table in wide format.
| Test | N | Result |
|---|---|---|
| Creates expected table output | 3 | Passed |
| produces the same output using the S3 method | 1 | Passed |
| Outputs an empty table if an empty table is provided | 2 | Passed |
create_table.continuous() works.
| Test | N | Result |
|---|---|---|
| Produces the expected output | 3 | Passed |
| Produces the same output with the S3 method | 1 | Passed |
| Ignores explanation_column and unit_column if they are NULL | 2 | Passed |
| does not error with a zero-row data frame input | 2 | Passed |
create_table.general() works
| Test | N | Result |
|---|---|---|
| creates a table with S3 method | 2 | Passed |
| creates expected table | 1 | Passed |
| does not error with a zero-row data frame input | 2 | Passed |
create_table.adverse_events() works
| Test | N | Result |
|---|---|---|
| creates a table with S3 method for adverse events | 2 | Passed |
| creates expected AE table | 1 | Passed |
| does not error with a zero-row data frame input | 2 | Passed |
create_table.medication() works
| Test | N | Result |
|---|---|---|
| creates a table with S3 method for medication | 2 | Passed |
| creates expected medication table | 1 | Passed |
| does not error with a zero-row data frame input | 2 | Passed |
create_table.medical_history() works
| Test | N | Result |
|---|---|---|
| creates a table with S3 method for medical history | 2 | Passed |
| creates expected medical history table | 1 | Passed |
| does not error with a zero-row data frame input | 2 | Passed |
fct_utils
time_stamp() should give the timestamp of the current time.
| Test | N | Result |
|---|---|---|
| gives a character value as output that can be converted to a date value. | 3 | Passed |
errors when format or timezone are not recognized by internal formats
(see OlsonNames() for timezones and strptime()
for correct date formats.
|
2 | Passed |
timestamp() function creates a timestamp of the current time, in the expected format (form) and timezone.
| Test | N | Result |
|---|---|---|
| Gives a character output that can be converted to a date format without error | 3 | Passed |
| errors if date-time or timezone format is unknown | 2 | Passed |
get_max_time() gives the maximum date/time in a column provided in a data set or a list of data sets
| Test | N | Result |
|---|---|---|
| gives expected output if either a list or a data frame is provided as input | 3 | Passed |
| errors if a data frame with zero rows is provided and if all values are missing (which might happen if the wrong date format is provided) | 2 | Passed |
expand_columns() will expand one or more list columns in a data frame into additional rows.
| Test | N | Result |
|---|---|---|
| can expand one column and gives an error if the provided column name does not exist | 4 | Passed |
| can unite expansions with existing column. The new name is the existing name united with the expansion column value, with _ separator in between. | 2 | Passed |
| can remove expansion columns if needed | 1 | Passed |
| can expand multiple columns | 4 | Passed |
title_case() works
| Test | N | Result |
|---|---|---|
| gives the expected title case output | 2 | Passed |
| works on character vectors and returns NA if a value in the vector is missing | 1 | Passed |
create_unique_id() creates a unique id every time the function is called
| Test | N | Result |
|---|---|---|
| gives a character value as output | 1 | Passed |
| produces unique ids every time it is called | 1 | Passed |
simplify_string() works
| Test | N | Result |
|---|---|---|
| gives a character output with expected clean names | 2 | Passed |
| errors if something else than a vector is provided | 2 | Passed |
| converts factors to character strings without error | 1 | Passed |
order_string() works
| Test | N | Result |
|---|---|---|
| returns a character vector, with missing values first, following with strings ordered first by letters and then by numbers | 2 | Passed |
| errors if input is not a vector | 1 | Passed |
| warns if input is not of class character, but still gives an output | 2 | Passed |
get_unique_vars() works
| Test | N | Result |
|---|---|---|
| gets all unique variables, outputs a data frame, and returns the expected results | 3 | Passed |
| returns a data frame with with the requested variables but with missing values if the variables are not available in the dataset | 2 | Passed |
| works with a data frame as input | 1 | Passed |
| handles missing var variables in a data frame | 1 | Passed |
| errors if all provided variable names in ‘var’ have zero characters | 1 | Passed |
bind_rows_custom() works
| Test | N | Result |
|---|---|---|
| errors if the input is not a list of data frames | 1 | Passed |
| returns a data frame with expected results | 2 | Passed |
| does not error with an empty data frame in the list | 2 | Passed |
| returns an empty data frame with column names preserved when all data frames in the list are empty | 1 | Passed |
| returns an empty data frame with column names preserved when all data frames in the list are empty, AND the columns that need conversion are of different type | 1 | Passed |
| does not error with if the column to be converted does not exist in one of the data frames. Instead the column will be added for that data frame with missing character values. | 2 | Passed |
collapse_fct_levels() combines factor levels.
| Test | N | Result |
|---|---|---|
| gives a factor as output with the expected levels and length | 3 | Passed |
| errors if not a factor or character vector is provided | 2 | Passed |
| warns if an empty vector is provided | 1 | Passed |
| warns for non-existent levels if warn_non_existent_levels is TRUE | 1 | Passed |
| returns an empty factor with new_levels as levels if a vector with only missing values is provided | 1 | Passed |
is_date() works
| Test | N | Result |
|---|---|---|
| gives a logical as output, which is TRUE if a date is provided and FALSE otherwise | 3 | Passed |
| errors if the input is not a vector | 1 | Passed |
cols_to_char() works
| Test | N | Result |
|---|---|---|
| converts non-numeric columns (for example factors) to character | 1 | Passed |
| errors with non-data.frame input | 2 | Passed |
date_cols_to_char() works
| Test | N | Result |
|---|---|---|
| converts date columns to character | 1 | Passed |
| errors with non-data.frame input | 2 | Passed |
clean_dates() works
| Test | N | Result |
|---|---|---|
| cleans dates as expected and returns a date vector, replacing unknown years with date columns to character | 1 | Passed |
| returns dates unaltered | 1 | Passed |
| errors with incorrect input | 2 | Passed |
vector_select() Can include or exclude values from a vector based on given regular expressions.
| Test | N | Result |
|---|---|---|
| 01 | Can include and exclude values based on a given regular expression | 1 | Passed |
| 02 | Can use multiple include statements to check for inclusion | 1 | Passed |
| 03 | Can use multiple exclude statements to check for inclusion | 1 | Passed |
| 04 | Can use multiple include and exclude statements simultaneously | 1 | Passed |
| 05 | Handles NULL inputs and errors with non-vector inputs | 5 | Passed |
format_test_results() works
| Test | N | Result |
|---|---|---|
| errors with incorrect input | 1 | Passed |
| returns a list with expected output and informs that all tests passed | 4 | Passed |
| returns a list with expected output, and prints a warning if there are failures | 4 | Passed |
all_tests_passed() provides expected output
| Test | N | Result |
|---|---|---|
| returns TRUE when all pass | 1 | Passed |
| returns TRUE with a skipped test and [include_skipped] is FALSE | 1 | Passed |
| returns FALSE with a failure | 1 | Passed |
| returns FALSE with a skipped test and [include_skipped] is TRUE | 1 | Passed |
| returns FALSE with an error | 1 | Passed |
| returns FALSE with a warning | 1 | Passed |
| returns FALSE with no tests available | 1 | Passed |
| returns NA with a warning if [var] does not exist in the results list | 2 | Passed |
get_available_data
get_available_data() creates a data frame with all available data per individual. It summarizes the available data points for each individual for each time point. For study data forms, the data points will be taken from event_name. For common forms, the Name column of the pivot table data will be used (for example, the specific adverse event or concomitant medication)
| Test | N | Result |
|---|---|---|
| Creates a data frame with the correct columns per individual. | 2 | Passed |
| Creates the expected data frame with given random appdata input | 1 | Passed |
| Adds a form_repeat number to item_name if duplicates occur within an individual, to ensure item names can be uniquely identified | 1 | Passed |
| can change the name of the form_repeat number that is written to the item_name if duplicates occur | 1 | Passed |
get_base_value
| Test | N | Result |
|---|---|---|
| get_base_value can add base values to a data frame | 1 | Passed |
| get_base_value handles zero-row data frames and errors with incorrect input values | 3 | Passed |
| get_base_value handles missing base values and missing variable names | 3 | Passed |
get_form_level_data
get_form_level_data() works
| Test | N | Result |
|---|---|---|
| adds default form-level columns to the input, sets the column types of the default correctly, and keeps the column specs of the default values | 1 | Passed |
| only updates a value to the default one if the value is missing | 1 | Passed |
| warns if not valid data input is provided and returns defaults | 4 | Passed |
| errors if the key column (form_column) is not available | 1 | Passed |
| warns if any defined forms do not match the expected ones in ‘all_forms’ | 2 | Passed |
get_review_data
get_review_data(). Feature 1 | Select correct data to review. As a user, I want to be able to extract data from a data frame, with only the required columns and, if there are duplicates in the rows, the row with the latest edit date-time is selected.
| Test | N | Result |
|---|---|---|
| returns a data frame | 1 | Passed |
| returns the expected number of columns and rows, and selects the row with latest edit date-time if there is a duplicated row | 4 | Passed |
golem-recommended
| Test | N | Result |
|---|---|---|
| app ui | 2 | Passed |
| app server | 4 | Passed |
| app_sys works | 1 | Passed |
| golem-config works | 2 | Passed |
golem_utils_server
| Test | N | Result |
|---|---|---|
| not_in works | 2 | Passed |
| not_null works | 2 | Passed |
| not_na works | 2 | Passed |
| drop_nulls works | 1 | Passed |
| %||% works | 2 | Passed |
| %|NA|% works | 2 | Passed |
summarize_review_data
summarize_review_data() works
| Test | N | Result |
|---|---|---|
| Scenario 1 - Given a random data set provided, I expect that summary dataframe snapshot will be as expected | 1 | Passed |
| Scenario 1 - Given that none of the data within a group was reviewed, and all values in the [status] column are ‘new’, I expect that, in the summarized data frame, all values in the [reviewed] column are ‘No’ and all values in the [status] column labels are ‘new’. | 1 | Passed |
| Scenario 2 - Given that all data within a group was reviewed, I expect that, in the summarized data frame, all values in the [reviewed] column are ‘Yes’ and all values in the [status] column labels are ‘old’. | 1 | Passed |
| Scenario 3 - Given that some data within a group was new and some was updated, I expect that, in the summarized data frame, all values in the [reviewed] column are ‘No’ and all values in the [status] column labels are ‘new/updated’. | 1 | Passed |
| Scenario 4 - Given that some data within a group was old and some was new, I expect that, in the summarized data frame, all values in the [reviewed] column are ‘No’ and all values in the [status] column labels are ‘new’. | 1 | Passed |
| Scenario 5 - Given that some values within a group were old and some were updated, I expect that, in the summarized data frame, all values in the [reviewed] column are ‘No’ and all values in the [status] column labels are ‘updated’. | 1 | Passed |
| Scenario 6 - Given that some values within a group were ‘old’, some ‘updated’ and some ‘new’, I expect that, in the summarized data frame, all values in the [reviewed] column are ‘No’ and all values in the [status] column labels are ‘new/updated’. | 1 | Passed |
update_review_data
update_review_data() works
| Test | N | Result |
|---|---|---|
| creates a data frame with the expected result | 2 | Passed |
| warns if the updated dataset does not contain any new data, and returns an empty data frame | 2 | Passed |
| warns if rows are not found in the updated dataset but still returns a valid data frame; might happen if entries are deleted from the source | 2 | Passed |