Oracle® Life Sciences Data Hub User's Guide Release 2.2 Part Number E22747-02 |
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This section contains information on the following topics:
See also:
An output is a file generated by the system when a user submits a Program, Report Set, Load Set, Data Mart, or Workflow for execution. Most of the outputs you see are either Report Sets or individual reports generated by Programs.
Depending on your security privileges and the way your company has set up classifications, you may see other types of outputs including log files, error files, Data Marts that contain Oracle LSH data ready for export to a different system (for submission or for sharing with a partner institution, for example), and copies of data loaded into Oracle LSH in file format (SAS or text).
The Outputs subtab of the Oracle LSH Reports tab displays all types of outputs as well as Execution Setups for generating new outputs on fresh data; see Chapter 5, "Generating Reports and Running Other Jobs."
You can see only those outputs and Execution Setups to which you have security access.
Oracle LSH displays outputs according to the way they are classified in your company. Classifications are based on hierarchies. You can select the hierarchy, or classification system, through which you want to browse for outputs. To find an output, do the following:
Click the Reports tab. The Outputs subtab is displayed by default.
From the Select Hierarchy drop-down list, select the classification system you want to use and click Go. The system displays the most general classifications as folders.
You can tell they are folders because they have a + icon next to their name and in the Type column it says Folder.
Click the + icon for the folder that is most likely to contain the output you are looking for. The system displays folders for the more specific classifications that are related to the general classification you clicked, as well as any outputs that are classified directly to the general classification.
Continue to click + icons until you reach the specific classification you need.
When you find the output you want, click the Report-with-Glasses icon in the Action column The system displays information about the output.
Click the View File button to see the output.
The same output may be classified in several ways; if so, it appears in several folders, possibly in different hierarchies.
If you have many folders or many outputs in a folder, you may want to sort the folders or outputs to change the display order and make it easier to find the one you are looking for. See "Sorting to Change the Display Order" for further information.
Example You are looking for a demography report on patients participating in Study 12345 at Boston Hospital. Study 12345 is part of Project ABC.
Your company uses a Project/Study hierarchy to classify all reports by the name of their study or project. When you select Project/Study from the Select Hierarchy drop-down list, you see a folder for each Project, including Project ABC. When you click the + icon next to the folder for Project ABC, you see a folder for each of the studies included in that project, including Study 12345, plus any reports that are classified to Project ABC as a whole. If you click the + icon next to the folder for Study 12345, you see all the reports that are classified to Study 12345, including the Boston Hospital demography report.
Your company also classifies reports by the geographical location of the site that collected the report data. Therefore you can find the same report using the hierarchy Continent/Country/Site. The system displays a folder for each continent that has at least one study site, including North America. You click the + icon for the North America folder. The system displays two folders labeled U.S. and Canada. You click the + icon for the U.S. folder. The system displays a folder for every site in the U.S. that is participating in any study for your company. You click the + icon for the Boston Hospital folder. The system displays all reports classified to Boston Hospital, including Study 12345 Demography.
Note:
Oracle LSH displays the most recent report that was submitted with its Parameters set the same way. If the same Execution Setup was submitted multiple times, each with different Parameter settings, Oracle LSH displays all the outputs. But if it ran multiple times with the same Parameter and other settings, Oracle LSH displays the outputs of only the most recent job.To see older outputs, use Advanced Search with Show Identical Outputs set to Yes.
Information Displayed For each output and Execution Setup, the Outputs subtab displays the following information:
Name. For outputs, this is the title. For Execution Setups, this is the name of the Execution Setup.
Action. Click the icon in the Action column to submit an Execution Setup or to view an output's properties and the output itself.
Submit Execution Setup icon:
View output icon:
Type. The type of object displayed: Hierarchy, Folder, Execution Setup, or Output.
Description. The description defined for the hierarchy, folder, Execution Setup, or output.
Version.
Validation Status. The validation status of the Execution Setup or output; it can be either Development, Quality Control, Production, or Retired.
Date and Time. For outputs, this is the date and time the output was executed. For Execution Setups, this is the date and time of the most recent execution.
To change the display order and make folders and outputs easier to find, use the Sort function. You can sort on any combination of Name, Date, Type, and Validation Status, in any combination of ascending or descending order.
To sort, do the following:
In the Select column, click the radio button for the folder whose contents you want to sort.
Click Sort. The system displays the Sort screen.
In the First Row, from the Column drop-down list, select the name of the column you want to use as the primary sort criteria. The choices are:
Name. The name of the folder, output, or execution setup. Folders are always listed above outputs and execution setups, but you can sort them relative to each other.
Type. The type of object displayed: Hierarchy, Folder, Execution Setup, or Output.
Validation Status. There are four validation statuses: Development, Quality Control, Production, and Retired. Unless you are a programmer you probably have access only to Production items.
Date and Time. The date and time the folder or execution setup was created, or that the output was generated.
In the First Sort row, from the Order drop-down list, select the type of order you want the system to use: Ascending or Descending.
For the Name, Type, and Validation Status columns, ascending means in alphabetical order from A to Z, while descending means reverse alphabetical order (from Z to A). For the Date column, ascending means chronological order, while descending means reverse chronological order (most recent on top).
(Optional) In the Second Sort row, from the Column drop-down list, select the secondary sort criteria you want to use. From the Order drop-down list, select the type of order you want the system to use: Ascending or Descending. The system uses this column to sort items that have the same value for the primary criteria.
For example, if you use Type for the First Sort criteria in descending order, you see all the outputs just below the folders. If you use Date and Time as the Second Sort criteria, the system displays the outputs in the order in which they were generated.
(Optional) In the Third Sort row, from the Column drop-down list, select the tertiary sort criteria you want to use. From the Order drop-down list, select the type of order you want the system to use: Ascending or Descending. The system uses this column to sort items that have the same value for the secondary criteria.
For example, if you use Type for the First Sort criteria and Date and Time for the Second Sort, if you use Name for the Third Sort criteria, the system displays outputs that were created at the same time in alphabetical order.
(Optional) Do the same in the Fourth Sort row.
Click Apply. The system returns you to the Outputs screen with the items displayed in the order you specified.
You can use the Focus, Expand All and Collapse All functions to control the way items are displayed on screen.
Focus You can click the icon in the Focus column for any high-level folder to see only that folder, so that you can see more of the contents of that folder on screen at a time.
When you click Focus for a folder, the system adds a Focus icon with the name of the hierarchy as a hyperlink just below the Expand All and Collapse All links. To go back to the full display of all folders in the hierarchy, click this link.
Expand All Clicking Expand All is equivalent to clicking the + icon for all folders and all levels of subfolders, so that you can see all folders and all outputs and execution setups, except that no more than 10 items are displayed in any particular node. (You can click another link to see the next 10 items, and so on.) After clicking Expand All you can click the - icon for any folders whose contents you do not want to view.
Collapse All Clicking Collapse All is equivalent to clicking the - icon for all folders and all levels of subfolders, so that you can see only the top-level folders. After clicking Collapse All you can click the + icon for any folders whose contents you want to view.
To view an output in the Reports tab/Outputs subtab, do the following:
Find the output in the appropriate hierarchy; see "Browsing in the Outputs Screen" or Chapter 3, "Searching."
Click its icon in the Actions column:
Description of the illustration output_icon.gif
The main screen for the output opens, displaying submission information (see "Viewing Output Submission Information").
Click View File. The system opens a dialog box.
Click Open. The system opens the output file.
Or click Save to save the file to your PC.
Note:
If you submitted the job that generated the output you want to see, you can also view it from the Job Executions section of your My Home screen. See Chapter 7, "Tracking Job Execution."You can print the file if your company has set up global printing:
Find the output in the appropriate hierarchy; see "Browsing in the Outputs Screen" or Chapter 3, "Searching."
Click its icon in the Actions column:
Description of the illustration output_icon.gif
The main screen for the output opens, displaying submission information (see "Viewing Output Submission Information").
Click Print. The system opens a dialog box.
From the Printer drop-down list, select the printer you want to use.
From the Coversheet drop-down list, select Summary Coversheet, Detailed Coversheet, or blank (no coversheet). See "Generating a Coversheet with Validation and Data Currency Information".
Click Print. The system sends the job to the printer you specified and displays a confirmation message with a print job ID.
When you click on an output's View icon in the Action column, the system opens the Output Properties screen, which displays information about how the output was generated, as follows:
Title. The title of the actual report or other output.
File Name. The name of the actual file; it may or may not be the same as the title, plus an appropriate file type extension such as .pdf.
Job ID. The Job ID is a system-generated unique ID for the job—a single execution of the Program, Report Set, or other object—that produced the output.
You can click on the Job ID hyperlink to see additional information about the job; see "Viewing a Job's Details and Monitoring Its Progress".
Execution Status. The execution status displayed represents the stage of execution the job reached before it ended. See "Execution Statuses" for details.
Description. The description of the Program, Report Set, or other object that generated the output.
Validation Status. The validation status of the Program, Report Set, or other object that generated the output; the statuses are: Development, Quality Control, Production, and Retired. You may have access only to Production-status outputs.
Execution Setup. The name of the Execution Setup that a user submitted to generate the output.
Execution User. The username of the person who submitted the Program, Report Set, or other object to generate the output.
Job Start Time. The date and time at which the execution began.
Blinding Status. The blinding status of the output. If set to No, the output does not contain blinded data. If Yes, the output does contain blinded data and only users with special privileges can view the output.
Primary Output. If set to Yes, the output is the primary reason for executing a Program, Report Set, Data Mart, or Load Set input file. If set to No, the file is a log or error file.
Submission Parameters. Click the Submission Parameters subtab to see the values of all the user-defined Parameters that were used in the execution of the output.
System Parameters. Click the System Parameters subtab to see the values of all the system Parameters that were used in the execution of the output.
You can generate a summary or detailed coversheet for any job. The Summary Coversheet gives information on when the job ran, its parameter values and data currency, and the validation status of its outputs and source and target tables. The Detailed Coversheet provides the same information for every job that processed the data fed into the current job, beginning with the job or jobs that loaded data into Oracle LSH.
To help ensure that the data manipulation performed in Oracle LSH does not corrupt data, Oracle LSH provides tools to help your company test and validate the defined objects—such as Programs, Load Sets, and Tables—that affect data in Oracle LSH. As your developers create and test these objects, they change their validation status from Development to Quality Control to Production according to your company's standards.
To create a coversheet, do the following:
From the Job Details screen, select Generate Summary Coversheet or Generate Detailed Coversheet from the Actions drop-down list.
Click Go.
Click Refresh. The system displays a link to the coversheet in a new row in the Outputs subtab of the Job Details screen.
To view the coversheet, click its View icon.
Note:
When you print an output, you have the option to print either the summary or detailed coversheet; see "Printing Outputs".Note:
If the name of an executable has a tilde (~) preceding it, it has been removed. You cannot submit it for re-execution.To print an output, do the following:
In the Output properties screen (which you reach by clicking the Job ID from the Outputs or My Home screen) click Print.
From the Printer drop-down list, select the printer you want to use.
From the Coversheet drop-down list, select the coversheet you want to print, if any.
Click Print. The system sends the output to the printer.