| Oracle® Health Sciences Data Management Workbench User's Guide Release 2.3.1 Part Number E35217-02 |
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View PDF |
| Oracle® Health Sciences Data Management Workbench User's Guide Release 2.3.1 Part Number E35217-02 |
|
|
View PDF |
This section covers the Home page and ways to change the columns and records displayed in many pages of the user interface:
You must first select a study in the Home page before you can work in it in Oracle Health Sciences Data Management Workbench (Oracle DMW).
Select the study you want to view or work on from the Studies list and then click the link to the page you want to work in.
Or, if the list is too long:
In field above the list, type all or part of the name of the study.
Press Enter.
Select the study you want in the list. The system displays links to all the user interface pages you can access.
Note:
The next time you log in, the system automatically loads the last study you were working in. To change to a different study, delete the study name in the field above the list and type all or part of the name of the study you want to work in.You must select a study lifecycle mode before you can work in a study. You may have security privileges for only one or two modes of the three:
Development is for studies being set up and modified.
Quality Control is for studies being tested.
Production is for live studies and also for viewing completed studies.
In the Home page, Data Loads tab, you can view information on past data loads for the selected study, including:
Note:
You can query on most column to filter the data loads displayed; see "Querying By Example".Data Model: The Input clinical data model that is the target of the load.
Type:
FILEWATCHER for data loaded from a file by File Watcher.
INFORM for data loaded from InForm.
File Name/InForm Load Process: The system displays different information depending on the data load type:
For files, the full path of the file loaded.
For InForm, the type of data load: INFORM_DEFINITION, INFORM_METADATA, INFORM_MANUAL_DATA or INFORM_SCHEDULED_DATA.
Last Job: The job ID of the most recent load for the clinical data model.
Last Load: The date and time of the most recent execution.
Last Load Results: Success, Warnings, or Failure for completed jobs. Click the icon to view or download the log file generated by Oracle DMW.
There are other statuses for incomplete jobs; see "Statuses for Uncompleted Jobs".
View Output (File loads only): Click the icon to view or download the Oracle SQL Loader log file.
View Error Report (File loads only): Click the icon to view or download the error file, if any.
See "Changing User Interface Display" and "Querying By Example".
You set up data loading when you define input clinical data models. See "Configuring the InForm Connector" and "Configuring File Watcher" for more information.
The system uses the following statuses in addition to Success, Warnings, and Failure for completed jobs:
Pending: The job has not yet started running.
Started: The job has begun pre-processing.
Executing: The Program has connected to database and is running.
Finalizing: The job has begun post-processing.
Aborted: The job has been manually stopped while underway.
On Hold: The job is waiting for the quiesce process to complete.
Expired: The system removed the job from the queue after the timeout interval passed.
Duplicate: The job is a duplicate of another job; the currency of the source data, parameter values, and executable instance version are the same. Therefore the system does not rerun the job unless the person submitting the job chooses to force reexecution. To view the job that this one would duplicate, paste the Duplicate Job ID in the search window and locate the job.
This section contains the following topics:
Transformations are displayed by the name of their target data model. The upper pane lists each transformation once and displays information about it and the most recent execution and installation of it.
View Table Transformations Click a transformation's triangular node to see all the target tables and information on the most recent execution of the transformation of the specific table.
View Run History Select a transformation in the upper pane and the system displays information on all past executions in the Run History pane.
View Log Files The following columns are for different types of jobs. Click the icon to view the log file.
Log: The most recent manually submitted job
Triggered Job Log: The most recent triggered job
Install Job Log: The most recent installation of the transformation
You can run transformations manually and, if they are set up to support it, they can be triggered by a job that writes data to any of their source tables; see "Automatically Triggering Transformations and Validation Checks by Upstream Processes".
To run a transformation manually, Select the Transformation and Submit the Job.
Select the transformation you want to run and click Submit.
The Submit button does not appear if:
You have not selected a transformation.
The selected transformation has not been installed; check the Install Status column.
To execute a transformation:
Enter values in the following fields:
Submission Mode: Select one:
Full mode normally takes longer and includes data deletion.
Incremental normally is faster and does not include data deletion.
If you are submitting a transformation for a single table and the table is defined with Unit of Work processing, you can also select:
Full UOW mode normally takes longer and includes data deletion.
Incremental UOW normally is faster and does not include data deletion
See "Data Processing Types and Modes" for more information.
Note:
You may want to set up regular Incremental loads at frequent intervals and regular Full loads at longer intervals. See "Data Processing Types and Modes" for more information.Force Execution: Before running a job, the system checks the source data currency, parameter values, and the version number of the programs. If none of these has changed since the last run, the results would be unchanged if the job ran again, so the system does not execute the job and returns a status of Success.
If you want to run the job anyway, select Force Execution. The system then uses Full mode, regardless of the Submission Mode setting.
Submission Type: Select:
Immediate to run the job once, as soon as possible
Scheduled to set up a regular schedule
Deferred to run the job once, at a future time
Frequency: If you selected Scheduled, enter a number of minutes, hours, or days that you want to elapse between runs, and select the time unit.
Start and End Date:
If you selected Scheduled, select a date and time to begin running on schedule and a date and time to stop.
If you selected Deferred, select a date and time to run the job.
Trigger Downstream Transformations and Validation Checks: Select this check box if you want this job (or each job if you are setting up regularly scheduled runs) to trigger validation checks in the target model and transformations from the target model to all others that come after it, in sequence. This can happen only if the source models in the affected transformations are set up to trigger downstream processes; see "Creating Model Mappings".
Click Refresh at any time for an update.
You can set up a chain of transformation and validation check executions beginning when you load data into the system or at any point thereafter by setting the Can Trigger attribute of a source model in a transformation to Yes. This ensures that the data in all participating models is always as up-to-date as possible.
A study has Input models called InForm, Central Lab and Local Lab that all feed data to the Review model, which feeds data to the Analysis model, which feeds data into the Submission model.
In the Review model's transformation, for which all Input models are source models, set the Can Trigger attribute to Yes for each Input model. Whenever data is loaded into any of these Input models, the transformation to the Review model is triggered, as are all the validation check batches defined in the Review model.
In the Analysis model's transformation, which has only the Review model as a source in this example, set Can Trigger to Yes for Review as a source model. Whenever data is loaded into the Review model—as the result of a data load to any of its source models or because of a manual or scheduled execution—the transformation to the Analysis model is triggered, as well as all validation check batches defined in the Analysis model.
In the Submission model's transformation, you may prefer not to set the source model's Can Trigger attribute to Yes. It may not be important to have the latest data as soon as possible if the purpose of this model is to export final data for regulatory submission, and you may prefer not to use system resources for frequent executions.
The Validation Checks tab displays validation check batches for the selected clinical data model.
When you select a batch, the system displays all its validation checks in the Validate Checks pane and information on all its past executions in the Run History pane.
To submit a batch, select it and click Submit.
The Submit button does not appear if:
You have not selected a validation check batch.
The selected batch has not been installed; check the Installed column.
You must run validation checks as a batch. It is possible to disable a validation check in the Study Configuration page so that it is not included in the batch execution. To find out if a check was included in the batch, check the log file in the Run History pane.
To run a validation check batch:
Enter values in the following fields:
Submission Mode: Select one:
Full mode takes longer and includes data deletion.
Incremental is faster and does not include data deletion.
Force Execution: Before running a job, the system checks the source data currency, parameter values, and version number of the transformation or validation check programs. If Force Execution is not selected and none of these has changed since the last run, the system does not execute the job.
If you want to run the job anyway, select Force Execution.
Submission Type: Select Immediate to execute the job once, as soon as possible. Select Scheduled to set up a regular schedule.
Frequency: If you selected Scheduled, enter a number of minutes, hours, or days that you want to elapse between runs, and select the time unit.
Start and End Date: If you selected Scheduled, select a date and time to begin execution and a date and time to end execution.
Trigger Downstream Transformations and Validation Checks: Select this check box if you want the system to detect all transformations and validation checks set up for this data model and all others that come after it, and submit them sequentially.
Click Refresh at any time for an update.
To check the log file, click the Log icon in the Run History pane.
Click a validation check batch in the upper pane to view its job history in the Run History pane. You can:
View Log File Click the icon in the Log column to view or download the log file.
Cancel Job Click to cancel a pending manually submitted job.
Cancel Triggered Job Click to cancel a pending triggered job; see "Automatically Triggering Transformations and Validation Checks by Upstream Processes".
If the File Watcher service detects a file in a watched location that cannot be loaded because no File Specification for any clinical data model in the study matches it, it displays information about the file on the Files Not Processed tab of the Home page for the selected study.
Files may not match any File Specification because:
They are misnamed, which may include case differences.
There is a mistake in the File Specification regular expression; see "Creating File Specifications".
The Files Not Processed screen displays the following information about each unloadable file:
Label: Description
File Name
Path: Full path to the file on the file system
Status: The possible statuses are:
DETECTED: The file has been detected in the watched folder but has not yet been submitted. (The scheduled submission time is in the Data Load Date column.)
MISSING: The file was detected but deleted before the scheduled deletion date.
DELETED: The file was deleted by File Watcher as scheduled.
Detection Date
Deletion Date
Data Missing
Many pages in the user interface that are laid out like tables with columns and rows allow you to change the data display in several ways:
You can sort on values in a single column or up to three columns.
Note:
The system sorts only the records that are currently displayed. For example, if there are a total of 200 rows but the page shows only 50 at a time, when you sort by column value, only the 50 currently displayed rows are sorted. To be sure you have seen all the rows, you must view and sort all four pages in this example.You can click on the up and down arrow on the right side of any column heading to sort on that column. You may need to widen the column to see the arrows.
To sort on up to three column values:
Select View, then Advanced Sort.
In the Sort By field, select the primary column to sort on and then select either:
Ascending to sort in alphabetical or numeric order (a...z or 0...9).
Descending to sort in reverse alphabetical or numeric order (z...a or 9...0).
In the first Then By field, select the secondary column to sort on and either Ascending or Descending. Within the sort order you specified in Step 1, the system sorts records in the order you specify here.
In the second Then By field, select the tertiary column to sort on and either Ascending or Descending. Within the sort order you specified in Steps 1 and 2, the system sorts records in the order you specify here.
Click OK.
To hide columns you don't need to see in order to make more room for columns you do need to see:
Select View, then Columns. The system displays all available columns, with a check next to those that are currently displayed. If you want to add or hide a single column, click the column name in the list.
To show or hide more columns, select Show More Columns.
Use the arrows to move columns from the Hidden Columns area to the Visible Columns area or the reverse. You can also reorder columns here.
Click OK.
To make it easier to see the columns you need most without scrolling or put the columns you need in a more logical order:
Select View, then Reorder Columns.
Use the arrows to move columns up or down in relation to each other. Columns at the top of the list are displayed leftmost on the page.
Click OK.
Alternatively, you can drag and drop columns directly on the page using the mouse.
You can "freeze" the leftmost column or columns so that they remain visible even when you scroll far to the right. If the columns you want to have always visible are not located farthest to the left, reorder columns so that they are.
Note:
You cannot sort records in a frozen column. If you want to sort records in either ascending or descending order, unfreeze the column first.To freeze or unfreeze a column:
Select the column heading.
Click the Freeze or Unfreeze icon or
click Freeze or Unfreeze in the View menu.
In many pages that are laid out like tables with columns and rows you can filter the rows displayed:
If empty fields above each column are not already displayed, click the Query By Example, or Filter, icon: 
The system displays an empty field above each column heading.
Enter a value in one or more fields above a column heading. Use the wildcard % before and after a string to return all values containing the string in that column. Values are case-sensitive.
Press Enter. The system displays only rows that have the specified value or values.
To show all rows again, delete all values in the Query By Example fields and press Enter.
You can hide the empty fields by clicking the Query By Example icon again.
Click the help icon (?) to see online help. Help icons that appear next to a specific field display help just for that field. Help icons that appear at the top of a tab, page, or pop-up window display help for that tab, page, or window that usually includes a description of each field.
The first time you open a help window in a session may take a long time. However, if you leave the window open, the next time you click a help icon, the display will be much faster.
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