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caTissue Suite Creating Dynamic Extensions using XMI Import

caTissue Suite Creating Dynamic Extensions using XMI Import. Session Overview. Training Topic Statement This section of the training provides an overview of local Extensions using XMI Import. Target Audience This training program is designed for Administrators Training Prerequisites

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caTissue Suite Creating Dynamic Extensions using XMI Import

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  1. caTissue Suite Creating Dynamic Extensions using XMI Import

  2. Session Overview • Training Topic Statement This section of the training provides an overview of local Extensions using XMI Import. • Target Audience This training program is designed for Administrators • Training Prerequisites • The user should be familiar with basic cancer related terminology and tissue bank related activities • The user should have basic computer literacy

  3. Session Goals By the end of this training, you will: Gain introduction to the local extensions XMI Import feature Be able to create local extensions using XMI Import

  4. Contents Chapter 1: Introduction Chapter 2: Creating Annotations using XMI Import Chapter 3: Annotation Data Entry Chapter 4: Summary Chapter 5: Quiz

  5. Chapter1:Introduction In this topic, you will be introduced to: • The basic overview of dynamic extensions or local extensions using XMI Import

  6. Chapter 1: IntroductionOverview • We have seen how annotations can be created dynamically through the UI for participants, specimen collection groups, and specimens using the Local Extensions feature of caTissue Suite • To create annotations through the UI, the Administrator needs to create forms one at a time, add attributes to each form, and save each form individually • Now imagine a situation where the user needs to create; for example, 50 forms, each having around 10 to 15 attributes. To do this task manually using the Local Extensions would be a time consuming task • To overcome the difficulty, caTissue Suite has an additional functionality to create Dynamic Annotations using XMI Import

  7. Chapter2:CreatingAnnotations using XMI Import In this topic, you will be introduced to: • A scenario on creating annotations • The outline to create an annotation • The detailed steps involved in creating an annotation using the XMI Import feature

  8. Chapter2:CreatingAnnotations Using XMI ImportScenario Scenario: Dr. Hughes, a Supervisor has requested Jack, the Administrator to create pathology annotations for specimen. • Annotations for Pathological State of the specimen are to be created • These will include the data regarding the pathological state, procedure, histological type, and pathological findings about the available specimens • When these annotations are created by the Administrator, they will be available for data entry • Here the annotations will be associated with (hooked with) specimens • Jack will create these annotations through the Import XMI feature of caTissue Suite

  9. Chapter2:CreatingAnnotations Using XMI ImportOutline to Create an Annotation Jack performs the following steps to create the Pathological Annotations: • Create an UML model for the Pathological Annotations using Enterprise Architect (v6.1 currently supported) UML modeling tool. • Export the XMI format of the UML model created in Step1 using Enterprise Architect to a file. • Create a list of main containers in the UML model and condition file to specify the collection protocols to which these annotations will be limited. • Go to the command prompt and run the ant task to import this xmi. • Restart the jboss server. The annotations are ready for data entry.

  10. Chapter2:CreatingAnnotations Using XMI ImportSteps to Create an Annotation Step 1: Create an UML model for Pathological Annotations using the Enterprise Architecture tool as outlined in the following image: Figure 1

  11. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation • Open the template.eap file provided in Enterprise Architecture (EA). This file • contains all the classes required to specify data-types for attributes supported in DE.

  12. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation 1 2 3 4 5 • Add a Package named PathologyAnnotations in the Project View by performing the following steps: • Right-click Logical View. • Select Add. • Click New Package. • Specify the name of the package in the New Package box as PathologyAnnotations. • Click the OK button.

  13. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation • Add a class named Base Pathology Annotation to the package by performing the following steps. Here, each class corresponds to an entity in caTissue Suite. • Right-click Logical View. • Select Add. • Click New Element. • Specify the name of the package in the Insert New Element box as BasePathologyAnnotation. • Click the OK button.

  14. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation • Add a class named Base Pathology Annotation to the package by performing the following steps (continued):

  15. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation • Add attributes to the Base Pathology Annotation class by performing the following steps: • Double-click the BasePathologyAnnotation class. • Select the Detail tab. • Click Attributes. • In the attributes window, enter the attribute name as Comments. • Specify the Type as String. • Click the Save button. • Click the New button to add another attribute. • All the attributes are listed in the Attributes frame in the lower pane.

  16. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation 2 1 3 4 5 7 6 8 • Add attributes to the Base Pathology Annotation class by performing the following steps (continued):

  17. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation • Similarly, add all the classes and attributes to the respective classes as per the model specified in Figure 1. • The model will appear like the adjoining figure.

  18. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation • Add containment association between Base Pathology Annotation and Histologic Type classes by performing the followings steps: • Click the Link drop-down arrow and select Association. • Select BasePathologyAnnotation and drag mouse to the target class, that is HistologicType. • Double-click the association you just added.

  19. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation 4 • Add containment association between Base Pathology Annotation and Histologic Type classes by performing the followings steps (continued): • In the General tab in Association Properties, type the link name and select Direction as Source-->Destination.

  20. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation 5 6 7 • Add containment association between Base Pathology Annotation and Histologic Type classes by performing the followings steps (continued): • On the Source Role tab, select Containment as Reference. • On the Target Role tab, select Containment as Value. • Click the OK button.

  21. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation • Similarly, add containment associations and specify appropriate multiplicity for all the required classes as shown in the adjoining diagram. • The multiplicity can be of two types: • One-to-One: A normal sub-form is created • One-to-many: A spreadsheet type sub-form with Add More button is created

  22. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation • Now add an Inheritance association between • BaseHematologyPathologyAnnotation and BasePathologyAnnotation by • performing the following steps: • Click the Link drop-down arrow and select Generalization. • Select child class, that is BaseHematologyPathologyAnnotation and drag the pointer up to the parent class, namely BasePathologyAnnotation. • An inheritance association will be added as shown in the figure on the following slide. • Thus, the model is ready to be imported in caTissue Suite application.

  23. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation • Now add an Inheritance • association between • BaseHematology • PathologyAnnotation • and • BasePathology • Annotation • by performing the • following • steps (continued):

  24. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation • Step 2: Export the data to XMI format. • Open the Export Package window by performing the following steps: • Click Model in Project View. • Select Export Model to XMI.

  25. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation Step 2: Export the data to XMI format (continued).

  26. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation • Step 2: Export the data to XMI • format (continued): • Export the data to an XMI file by performing the following steps: • Specify the name and path of the XMI file to which you need to export the data. • Clear the Enable full EA Roundtrip check-box. • Select UML 1.4(XMI 1.2) option from the XMI Type drop- down list. • Clear the Export Diagrams and Write Log File check boxes under General Options. • Click the Export button. • The XMI file is saved at the specified location.

  27. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation Step 3: Create the main container list and condition file. • To create the main container list and condition file, perform the following steps: • Main containers are all the classes that will be associated (hooked) to the hook entity; that is, participant, specimen, or SCG (specimen in this instance). • These include all the entities except the sub-classes; that is, classes contained within some main class. • In this model, BasePathologyAnnotation and BaseHematologyPathology Annotation are the two main containers. All the other classes are contained by these two classes. • Write the names of these two classes, separated by comma in a csv file named PathologyMainContainer.csv. • Create another file named ‘onditions.csv and write comma separated names of all the collection protocols in caTissue Suite application to which you wish to limit these annotations.

  28. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation Step 3: Create the main container list and condition file (continued). Figure 1

  29. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation Step 4: Import the XMI into caTissue Suite application by performing the following steps: • Go to the command prompt and change the directory to the one where caTissue Suite installable is unzipped. • Go to the command prompt and enter the following command: • ant -f deploy.xml import_xmi -Dfilename="E:\catissue\Annotation.xmi" • -Dhookentity=edu.wustl.catissuecore.domain.Specimen • -DmainContainerList="E:\catissue\PathologyMainContainer.csv" • -Dpackage=PathologyAnnotations -Dconditions="E:\catissue\Conditions.csv" • Press [Enter]. • The arguments used in the import command are as follows: • -Dfilename: The path and name of the xmi file created from the UML model. • -Dhookentity: The hook entity to which this package is to be associated. • -DmainContainerList: The path and name of the file in which the names of all the main • container classes have been added comma separated. • -Dpackage: The name of the package in the UML model that we need to import in the • caTissue Suite application. • -Dcondition: The name and path of the file in which the conditions on collection protocols are • specified.

  30. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation Step 4: Import the XMI into caTissue Suite application by performing the following steps (continued):

  31. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation Step 5: Restart the jboss server by performing the following steps: • Shut down the running jboss server that was started after deploying the caTissue Suite application. • Re-start the jboss server now so that the entities that we imported through XMI will be available for data entry in the application.

  32. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation A • Log on to the application as an Administrator. Enter the Email address and Password, and then click Login. By default, you will navigate to the Administrative Data tab after logging in as the Administrator.

  33. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation • Click Define under LOCAL EXTENSIONS. • Read the warning carefully and click the Next button. C 2 B

  34. Chapter2:CreatingAnnotations Using XMI Import Steps to Create an Annotation D • Select the PathologyAnnotations group and verify that it contains the following two forms: • BasePathologyAnnotation • BaseHematologyPathologyAnnotation

  35. Chapter 3: Annotation Data Entry In this topic, you will be introduced to: • A scenario on annotation data entry • The outline to annotation data entry • The detailed steps involved in annotation data entry

  36. Chapter3:Annotation Data EntryScenario Scenario 2: Dr. Hughes, a Supervisor logs on to the caTissue Suite application and enters data for the Pathology Annotations created by Jack, the Administrator using XMI Import. • Now that Jack has created the Dynamic Extensions (DE) for Pathology Annotations using XMI Import, any Supervisor can use these dynamic forms for annotating the specimens of collection protocols to which these forms were associated with • These forms can be edited through the UI as well as through XMI • To edit the forms through XMI, necessary changes are made in the UML model itself and the entire XMI Import process is repeated to the updated UML model. The main container list is also updated as per the changes made

  37. Chapter3:Annotation Data EntryOutline to Annotation Data Entry Dr. Hughes performs the following steps to enter data for the created DE annotations: • Logs on to the system as a Supervisor. • Navigates to the Biospecimen Data tab. • Selects an available collection protocol; for example, B n B study. • Selects a participant, Robin S registered under the B n B Study CP. • Selects the SCG named T1.0. • Selects specimen 18. • Clicks the View Annotation tab in the right pane for the specimen. • Selects a form from the Annotation Forms drop-down list and clicks GO. • Enters data for the Pathology Annotations.

  38. Chapter3:Annotation Data EntrySteps to Perform Annotation Data Entry • Log on to the application as a Supervisor by entering valid Email address and Password.

  39. Chapter3:Annotation Data EntrySteps to Perform Annotation Data Entry • In the CP based view: • Select a collection protocol. • Select the participant registered under the CP. • Select the SCG. • Select the required specimen. • Click the View Annotations tab. The image on the following slide outlines the above enumerated steps.

  40. Chapter3:Annotation Data EntrySteps to Perform Annotation Data Entry e a b c d • In the CP based view (continued):

  41. Chapter3:Annotation Data EntrySteps to Perform Annotation Data Entry 3 • Select an annotation form for data entry and click the GO button. The • BaseHematologyPathologyAnnotation form will be displayed for data entry.

  42. Chapter3:Annotation Data EntrySteps to Perform Annotation Data Entry 4 • Enter valid data in the annotation form as outlined in the following figure and click the Submit button. You can use the “Add More” button to add more rows for the “Smoking Health Annotations” Sub-form

  43. Chapter3:Annotation Data EntrySteps to Perform Annotation Data Entry • A record is saved for the DE annotation form Base Hematology Pathology Annotation. • The same record can be edited by clicking the record link. • Another record for another DE form can be added by repeating the same procedure in step 3 and step 4. • Another record for the same form can also be entered by following the same procedure. • These saved annotations can be queried through the Advanced Search module of caTissue Suite.

  44. Summary In this lesson, you have learned to create annotation forms using the XMI Import functionality of caTissue Suite and enter data for the same: • In caTissue Suite, annotations can be created dynamically for participants, specimen, or SCGs using XMI Import • An Administrator can create Dynamic Annotations in UML model and import them into caTissue Suite through XMI Import • Once the Administrator creates Dynamic Extension forms using the import XMI functionality, a Supervisor can annotate the specific entities (participants, specimen, or SCGs) by entering data for these forms in the same manner as for annotations created using Local Extensions UI • This data is saved and can be later queried by Scientists.

  45. Quiz • Annotations are created for import using: a) UML model b) XML model c) HTML model d) All of these • A main container list contains: a) Hook Entities b) Main Classes to be associated to hook entities c) Attributes of all classes d) Collection Protocols • In caTissue Suite, dynamic extensions can be created through: a) Local Extensions UI b) Import XMI c) Both (a) and (b) d) None of these

  46. Quiz • Annotations are created for import using: a) UML model (correct answer) b) XML model c) HTML model d) All of these • A main container list contains: a) Hook Entities b) Main Classes to be associated to hook entities (correct answer) c) Attributes of all classes d) Collection Protocols • In caTissue Suite, dynamic extensions can be created through: a) Local Extensions UI b) Import XMI c) Both (a) and (b) (correct answer) d) None of these

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