diff --git a/ODM-to-i2b2.properties b/ODM-to-i2b2.properties index c9e4262..5f9fb98 100755 --- a/ODM-to-i2b2.properties +++ b/ODM-to-i2b2.properties @@ -2,7 +2,8 @@ # of the properties after the = signs according to your needs. # The path to the file with log4j properties for logging errors, warnings, info, etc. -log4j-properties-file=src/main/resources/log4j.xml +# log4j-properties-file=src/main/resources/log4j.xml +log4j-properties-file=log4j.xml # The property below specifies the maximum length that a clinical data entry may have. # Longer strings will be cut off in order to assure that the length of the string does diff --git a/releases/release-3.0/odm-to-i2b2-3.0.jar b/releases/release-3.0/odm-to-i2b2-3.0.jar deleted file mode 100755 index fb7629c..0000000 Binary files a/releases/release-3.0/odm-to-i2b2-3.0.jar and /dev/null differ diff --git a/src/documentation/DevelopersInformation.md b/src/documentation/DevelopersInformation.md index bd7dd3f..adb7537 100755 --- a/src/documentation/DevelopersInformation.md +++ b/src/documentation/DevelopersInformation.md @@ -127,8 +127,8 @@ Maven ----- We use [Maven](http://maven.apache.org/) as our build tool. This makes it easier to use certain tools (like Checkstyle -and FindBugs) and to manage the third-party libraries (dependencies) we use. The pom.xml file for the trait_odm_to_i2b2 -conversion tool is stored in the root directory. +and FindBugs) and to manage the third-party libraries (dependencies) we use. The pom.xml file that Maven needs +is stored in the root directory: trait_odm_to_i2b2. All the maven commands need to be executed in this root directory. Some commonly used Maven commands are (see [Introduction to the Build Lifecycle](http://maven.apache.org/guides/introduction/introduction-to-the-lifecycle.html) @@ -167,6 +167,28 @@ for an explanation of the build lifecycle and the build phases): \# Check for CPD issues (report in target\cpd.xml):
**`mvn compile pmd:cpd-check`** +\# Create the jar file in the trait_odm_to_i2b2\target directory +**`mvn clean compile assembly:single`** + +Auto-generating the java files from the ODM-specification +--------------------------------------------------------- +Java classes are generated for handling ODM files using the JAXB (Java Architecture for XML Binding) related xjc binding +compiler. The source code of these ODM reader classes are created by the xjc tool with xsd files that describe the ODM +standard as input. See for example https://jaxb.java.net/2.2.11/docs/ch04.html#tools-xjc or +https://en.wikipedia.org/wiki/Java_Architecture_for_XML_Binding for more information on xjc and JAXB. + +The main schema file (ODM1-3-1.xsd) depends on several other schema files: ODM1-3-1-foundation.xsd, xml.xsd, and +xmldsig-core-schema.xsd. The bindings file (bindings.xml) modifies the default package names that are used. The Java +classes are put in two packages: org.cdisk.odm.jaxb (ODM1-3-1.xsd) and org.w3.xmldsig.jaxb (xmldsig-core-schema.xsd). + +The call to xjc looks something like this:
+**`xjc [schema file] -b [bindings file] -d [destination directory]`** + +For example, on the Windows platform (with xjc.bat in the jaxb-ri\bin directory at your install location) using ODM 1.3.1, +you could generate the ODM reader classes like this:
+**`mkdir java-generated`**
+**`xjc.bat xsd\cdisc-odm-1.3.1\ODM1-3-1.xsd -b xsd\cdisc-odm-1.3.1\bindings.xml -d java-generated`** + Checkstyle ---------- diff --git a/src/documentation/UsersInformation.md b/src/documentation/UsersInformation.md index 766384b..e5e9e9b 100755 --- a/src/documentation/UsersInformation.md +++ b/src/documentation/UsersInformation.md @@ -3,19 +3,14 @@ Users information This page is meant for users who want to install and use ODM-to-i2b2 in order to convert an ODM file to three tabular files. -Windows: ```sh -$ cd C:\path\to\workspace -$ mkdir ODM-to-i2b2 -$ cd ODM-to-i2b2 -$ mkdir input-ODMs -$ mkdir output-tabular-files -$ git clone https://github.com/CTMM-TraIT/trait_odm_to_i2b2.git -$ cd trait_odm_to_i2b2 -$ git checkout tags/v3.0 -$ copy odm\examples\odm130.XML ..\input-ODMs\test.xml -$ mvn test -$ mvn exec:java -Dexec.mainClass="com.recomdata.i2b2.I2B2ODMStudyHandlerCMLClient" -Dexec.args="C:\path\to\workspace\ODM-to-i2b2\input-ODMs\test.xml C:\path\to\workspace\ODM-to-i2b2\output-tabular-files" -$ cd ..\output-tabular-files -$ dir +Download odm-to-i2b2-3.0.zip from the [release directory](https://github.com/CTMM-TraIT/trait_odm_to_i2b2/blob/master/releases/release-3.0) and unzip it. +Save your ODM file in odm-to-i2b2-3.0\input-ODMs (e.g. odm130.XML) +Start the command line terminal (e.g. cmd.exe) +$ cd C:\path\to\odm-to-i2b2-3.0 +$ java -jar odm-to-i2b2-3.0.jar input-ODMs\odm130.XML output-tabular-files +$ cd output-tabular-files +$ ls -l ``` + +![Image cmd execution](https://github.com/CTMM-TraIT/trait_odm_to_i2b2/blob/master/src/documentation/cmd_execution.png) diff --git a/src/documentation/cmd_execution.png b/src/documentation/cmd_execution.png new file mode 100755 index 0000000..a6c28fb Binary files /dev/null and b/src/documentation/cmd_execution.png differ diff --git a/src/examples/split_odm_aa.xml b/src/examples/split_odm_aa.xml deleted file mode 100644 index 548c189..0000000 --- a/src/examples/split_odm_aa.xml +++ /dev/null @@ -1,9488 +0,0 @@ - - - - PCMM 2 - - The Prostate Cancer Molecular Medicine (PCMM) project. - - PCMM 2 - - - - - % - - - - - cc - - - - - cm - - - - - cM - - - - - cm3 - - - - - cN - - - - - cT - - - - - days - - - - - glasses/day - - - - - kg - - - - - min - - - - - ml - - - - - mm - - - - - ng/ml - - - - - pM - - - - - pN - - - - - pT - - - - - - - - - - - - - Max. 8 weeks before surgery - - - - - - 6-8 weeks after surgery - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Prostatectomy v1.7 - Tim Hulsen, 2010-12-20 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Prostatectomy v1.8 - Tim Hulsen, 2011-05-24 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - General 1 - - - - - - - - - - General 2 - - - - - - - - - - - - - - General 3 - - - - - - - - - - - - - - - Comorbidity 1 - - - - - - - - - - - - - - - Comorbidity 2 - - - - - - - - - - - - cTNM 1 - - - - - - - - - - - cTNM 2 - - - - - - - - - - - cTNM 3 - - - - - - - - - - - - pTNM 1 - - - - - - - - - - - pTNM 2 - - - - - - - - - - - - pTNM 3 - - - - - - - - - - - - - Treatment 1 - - - - - - - - - - - - - Treatment 2 - - - - - - - - - - - Postoperative RT (fossa) - - - - - - - - - - - - - Nervesparing - - - - - - - - - - - - - OR data - - - - - - - - - Comment - - - - - - - - - - - Complications - - - - - - - - - - - CEUS - - - - - - - - - - - - MRI - - - - - - - - - - - Transrectal echo - - - - - - - - - - - Bone scan - - - - - - - - - - - PET scan - - - - - - - - - - Pathology review - - - - - - - - - - - Urine sample - - - - - - - - - - - - Blood sample - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - General 1 - - - - - - - - - - General 2 - - - - - - - - - - - - - - General 3 - - - - - - - - - - - - - - - Comorbidity 1 - - - - - - - - - - - - - - - Comorbidity 2 - - - - - - - - - - - - cTNM 1 - - - - - - - - - - - cTNM 2 - - - - - - - - - - - cTNM 3 - - - - - - - - - - - - pTNM 1 - - - - - - - - - - - pTNM 2 - - - - - - - - - - - - pTNM 3 - - - - - - - - - - - - - Treatment 1 - - - - - - - - - - - - - Treatment 2 - - - - - - - - - - - Postoperative RT (fossa) - - - - - - - - - - - - - Nervesparing - - - - - - - - - - - - - OR data - - - - - - - - - Comment - - - - - - - - - - - Complications - - - - - - - - - - - CEUS - - - - - - - - - - - - MRI - - - - - - - - - - - Transrectal echo - - - - - - - - - - - Bone scan - - - - - - - - - - - PET scan - - - - - - - - - - Pathology review - - - - - - - - - - - Urine sample - - - - - - - - - - - - Blood sample - - - - - - - 1. Do you have trouble doing strenuous activities like carrying a heavy shopping bag or a suitcase? - - - - - - 1. Do you have trouble doing strenuous activities like carrying a heavy shopping bag or a suitcase? - Questionnaire - - - - - - - - 2. Do you have difficulty making a long walk? - - - - - - 2. Do you have difficulty making a long walk? - Questionnaire - - - - - - - - 3. Do you have difficulty making a short walk outdoors? - - - - - - 3. Do you have difficulty making a short walk outdoors? - Questionnaire - - - - - - - - 4. Do you have to stay in bed or a chair during daytime? - - - - - - 4. Do you have to stay in bed or a chair during daytime? - Questionnaire - - - - - - - - 5. Do you need help with eating, dressing, washing yourself or going to the toilet? - - - - - - 5. Do you need help with eating, dressing, washing yourself or going to the toilet? - Questionnaire - - - - - - - - 6. Were you limited in doing your work or other daily activities? - - - - - - 6. Were you limited in doing your work or other daily activities? - Questionnaire - - - - - - - - 7. Were you restricted in exercising your hobby `s or whatever else you do in your spare time? - - - - - - 7. Were you restricted in exercising your hobby `s or whatever else you do in your spare time? - Questionnaire - - - - - - - - 8. Were you short of breath? - - - - - - 8. Were you short of breath? - Questionnaire - - - - - - - - 9. Have you had pain? - - - - - - 9. Have you had pain? - Questionnaire - - - - - - - - 10. Did you need to rest? - - - - - - 10. Did you need to rest? - Questionnaire - - - - - - - - 11. Have you had trouble sleeping? - - - - - - 11. Have you had trouble sleeping? - Questionnaire - - - - - - - - 12. Have you felt weak? - - - - - - 12. Have you felt weak? - Questionnaire - - - - - - - - 13. Did you have a loss of appetite? - - - - - - 13. Did you have a loss of appetite? - Questionnaire - - - - - - - - 14. Have you felt nauseated? - - - - - - 14. Have you felt nauseated? - Questionnaire - - - - - - - - 15. Did you vomit? - - - - - - 15. Did you vomit? - Questionnaire - - - - - - - - 16. Did you suffer from constipation? - - - - - - 16. Did you suffer from constipation? - Questionnaire - - - - - - - - 17. Did you have diarrhea? - - - - - - 17. Did you have diarrhea? - Questionnaire - - - - - - - - 18. Were you tired? - - - - - - 18. Were you tired? - Questionnaire - - - - - - - - 19. Did pain interfere with your daily activities? - - - - - - 19. Did pain interfere with your daily activities? - Questionnaire - - - - - - - - 20. Have you had difficulty concentrating on things such as reading newspapers or watching television? - - - - - - 20. Have you had difficulty concentrating on things such as reading newspapers or watching television? - Questionnaire - - - - - - - - 21. Did you feel tense? - - - - - - 21. Did you feel tense? - Questionnaire - - - - - - - - 22. Did you worry? - - - - - - 22. Did you worry? - Questionnaire - - - - - - - - 23. Did you feel irritable? - - - - - - 23. Did you feel irritable? - Questionnaire - - - - - - - - 24. Did you feel sad? - - - - - - 24. Did you feel sad? - Questionnaire - - - - - - - - 25. Have you had difficulty remembering things? - - - - - - 25. Have you had difficulty remembering things? - Questionnaire - - - - - - - - 26. Has your physical condition or medical treatment bothered your family life? - - - - - - 26. Has your physical condition or medical treatment bothered your family life? - Questionnaire - - - - - - - - 27. Has your physical condition or medical treatment hampered you in your social activities? - - - - - - 27. Has your physical condition or medical treatment hampered you in your social activities? - Questionnaire - - - - - - - - 28. Has your physical condition or medical treatment entailed financial difficulties? - - - - - - 28. Has your physical condition or medical treatment entailed financial difficulties? - Questionnaire - - - - - - - - 29. How would you rate your overall "quality of life" during the past week? - - - - - - 29. How would you rate your overall "quality of life" during the past week? - Questionnaire - - - - - - - - 30. Did you have to urinate frequently during the day? - - - - - - 30. Did you have to urinate frequently during the day? - Questionnaire - - - - - - - - 31. Did you have to urinate frequently during the night? - - - - - - 31. Did you have to urinate frequently during the night? - Questionnaire - - - - - - - - 32. Did you have to rush to the toilet when you felt the urge to pee? - - - - - - 32. Did you have to rush to the toilet when you felt the urge to pee? - Questionnaire - - - - - - - - 33. Did you find it hard to get enough sleep, because you often had to pee at night? - - - - - - 33. Did you find it hard to get enough sleep, because you often had to pee at night? - Questionnaire - - - - - - - - 34. Did you have problems doing things outdoors, because you had to stay near a toilet? - - - - - - 34. Did you have problems doing things outdoors, because you had to stay near a toilet? - Questionnaire - - - - - - - - 35. Have you unintentionally lost urine? - - - - - - 35. Have you unintentionally lost urine? - Questionnaire - - - - - - - - 36. Did you have pain when urinating? - - - - - - 36. Did you have pain when urinating? - Questionnaire - - - - - - - - 37. Was it a problem for you to wear incontinence pads? - - - - - - 37. Was it a problem for you to wear incontinence pads? - Questionnaire - - - - - - - - 38. Were you limited in your daily activities by urination problems? - - - - - - 38. Were you limited in your daily activities by urination problems? - Questionnaire - - - - - - - - 39. Were you limited in your daily activities by stool problems? - - - - - - 39. Were you limited in your daily activities by stool problems? - Questionnaire - - - - - - - - 40. Have you inadvertently lost stools? - - - - - - 40. Have you inadvertently lost stools? - Questionnaire - - - - - - - - 41. Did you have blood in your stools? - - - - - - 41. Did you have blood in your stools? - Questionnaire - - - - - - - - 42. Did you have a bloated feeling in your stomach? - - - - - - 42. Did you have a bloated feeling in your stomach? - Questionnaire - - - - - - - - 43. Have you had hot flashes? - - - - - - 43. Have you had hot flashes? - Questionnaire - - - - - - - - 44. Did you have sore or swollen breasts or nipples? - - - - - - 44. Did you have sore or swollen breasts or nipples? - Questionnaire - - - - - - - - 45. Have you had swollen legs or ankles? - - - - - - 45. Have you had swollen legs or ankles? - Questionnaire - - - - - - - - 46. Was your weight loss a problem for you? - - - - - - 46. Was your weight loss a problem for you? - Questionnaire - - - - - - - - 47. Was your weight gain a problem for you? - - - - - - 47. Was your weight gain a problem for you? - Questionnaire - - - - - - - - 48. Did you feel less masculin because of your illness or treatment? - - - - - - 48. Did you feel less masculin because of your illness or treatment? - Questionnaire - - - - - - - - 49. To what extent did you want to have sex? - - - - - - 49. To what extent did you want to have sex? - Questionnaire - - - - - - - - 50. To what extent were you sexually active (with or without intercourse)? - - - - - - 50. To what extent were you sexually active (with or without intercourse)? - Questionnaire - - - - - - - - 51. To what extent was sex enjoyable for you? - - - - - - 51. To what extent was sex enjoyable for you? - Questionnaire - - - - - - - - 52. Did you have trouble getting or maintaining an erection? - - - - - - 52. Did you have trouble getting or maintaining an erection? - Questionnaire - - - - - - - - 53. Did you have problems with getting an ejaculation (eg a so-called "dry" ejaculation)? - - - - - - 53. Did you have problems with getting an ejaculation (eg a so-called "dry" ejaculation)? - Questionnaire - - - - - - - - 54. Did you dread to have sexual contact, or did you feel uncomfortable regarding sexually intimacy? - - - - - - 54. Did you dread to have sexual contact, or did you feel uncomfortable regarding sexually intimacy? - Questionnaire - - - - - - - - 55. Did you use any erectile pills (like Viagra, Cialis, Levitra) in recent months? - - - - - - 55. Did you use any erectile pills (like Viagra, Cialis, Levitra) in recent months? - Questionnaire - - - - - - - - 56. How often were you able to get an erection when sexually active, during the past 4 weeks? - - - - - - 56. How often were you able to get an erection when sexually active, during the past 4 weeks? - Questionnaire - - - - - - - - 57. How often did it occur that, after getting an erection from sexual stimulation, your penis was hard enough to penetrate, during the past 4 weeks? - - - - - - 57. How often did it occur that, after getting an erection from sexual stimulation, your penis was hard enough to penetrate, during the past 4 weeks? - Questionnaire - - - - - - - - 58. How often were you able to penetrate your partner when you tried to have sexual intercourse, during the past 4 weeks? - - - - - - 58. How often were you able to penetrate your partner when you tried to have sexual intercourse, during the past 4 weeks? - Questionnaire - - - - - - - - 59. How often were you able to maintain your erection during sexual intercourse after you had penetrated your partner, during the past 4 weeks? - - - - - - 59. How often were you able to maintain your erection during sexual intercourse after you had penetrated your partner, during the past 4 weeks? - Questionnaire - - - - - - - - 60. How difficult was it to maintain your erection until the intercourse was completed, during the past 4 weeks? - - - - - - 60. How difficult was it to maintain your erection until the intercourse was completed, during the past 4 weeks? - Questionnaire - - - - - - - - 61. How often have you tried to have intercourse, during the past 4 weeks? - - - - - - 61. How often have you tried to have intercourse, during the past 4 weeks? - Questionnaire - - - - - - - - 62. How often was it satisfactory for you when you tried to have sexual intercourse, during the past 4 weeks? - - - - - - 62. How often was it satisfactory for you when you tried to have sexual intercourse, during the past 4 weeks? - Questionnaire - - - - - - - - 63. To what extent did you enjoy having sexual intercourse, during the past 4 weeks? - - - - - - 63. To what extent did you enjoy having sexual intercourse, during the past 4 weeks? - Questionnaire - - - - - - - - 64. How often have you had an ejaculation when you were sexually stimulated or had sexual intercourse, during the past 4 weeks? - - - - - - 64. How often have you had an ejaculation when you were sexually stimulated or had sexual intercourse, during the past 4 weeks? - Questionnaire - - - - - - - - 65. How often did you have the feeling of an orgasm, with or without ejaculation, while you were sexually stimulated or had sexual intercourse, during the past 4 weeks? - - - - - - 65. How often did you have the feeling of an orgasm, with or without ejaculation, while you were sexually stimulated or had sexual intercourse, during the past 4 weeks? - Questionnaire - - - - - - - - 66. How often did you have sexual desires during the past 4 weeks? - - - - - - 66. How often did you have sexual desires during the past 4 weeks? - Questionnaire - - - - - - - - 67. How strong did you think your sexual desires were, during the past 4 weeks? - - - - - - 67. How strong did you think your sexual desires were, during the past 4 weeks? - Questionnaire - - - - - - - - 68. How satisfied were you with your sex life in general, during the past 4 weeks? - - - - - - 68. How satisfied were you with your sex life in general, during the past 4 weeks? - Questionnaire - - - - - - - - 69. How satisfied were you about the sexual relationship with your partner, during the past 4 weeks? - - - - - - 69. How satisfied were you about the sexual relationship with your partner, during the past 4 weeks? - Questionnaire - - - - - - - - 70. How strong would you say your confidence was about getting and maintaining an erection, during the past 4 weeks? - - - - - - 70. How strong would you say your confidence was about getting and maintaining an erection, during the past 4 weeks? - Questionnaire - - - - - - - - 71. Number of times urine loss - - - - - - 71. Number of times urine loss - Questionnaire - - - - - - - - 72. Amount of urine loss - - - - - - 72. Amount of urine loss - Questionnaire - - - - - - - - 73. When urine loss? Never - - - - - - 73. When urine loss? Never - Questionnaire - - - - - - - - 74. When urine loss? Before urination - - - - - - 74. When urine loss? Before urination - Questionnaire - - - - - - - - 75. When urine loss? When sneezing - - - - - - 75. When urine loss? When sneezing - Questionnaire - - - - - - - - 76. When urine loss? During sleep - - - - - - 76. When urine loss? During sleep - Questionnaire - - - - - - - - 77. When urine loss? During physical exertion - - - - - - 77. When urine loss? During physical exertion - Questionnaire - - - - - - - - 78. When urine loss? During urination - - - - - - 78. When urine loss? During urination - Questionnaire - - - - - - - - 79. When urine loss? No apparent reason - - - - - - 79. When urine loss? No apparent reason - Questionnaire - - - - - - - - 80. When urine loss? Continuous - - - - - - 80. When urine loss? Continuous - Questionnaire - - - - - - - - Year of birth - - - - 1900 - Not within the allowed range (1900-2010) - - - 2010 - Not within the allowed range (1900-2010) - - - - Year of birth - Patient information - - - - - - - - Allergy / hypersensitivity - - - - - - Allergy / hypersensitivity - Patient information - - - - - - - - Smoker - - - - - - Smoker - Patient information - - - - - - - - Ex-smoker - Only if 'Smoker' = 'Yes - - - - - - Ex-smoker - Only if 'Smoker' = 'Yes - Patient information - - - - - - - - Do you drink alcoholic beverages? - - - - - - Do you drink alcoholic beverages? - Patient information - - - - - - - - How many glasses per day? - - - - - 0 - - Not within the allowed range (0-99) - - - 99 - - Not within the allowed range (0-99) - - - - How many glasses per day? - Patient information - - - - - - - - WHO score at diagnosis - - - - - - WHO score at diagnosis - Patient information - - - - - - - - Medication - - - - - - Medication - Patient information - - - - - - - - Which medication - Only if 'Medication' = 'Yes - - - - - Which medication - Only if 'Medication' = 'Yes - Patient information - - - - - - - - Previously treated - - - - - - Previously treated - Patient information - - - - - - - - Treated by urologist - - - - - - Treated by urologist - Patient information - - - - - - - - Biopsies of prostate - - - - - - Biopsies of prostate - Patient information - - - - - - - - PSA determined - - - - - - PSA determined - Patient information - - - - - - - - Cancer in family - - - - - - Cancer in family - Patient information - - - - - - - - Which type of cancer - Only if 'Cancer in family' = 'Yes - - - - - Which type of cancer - Only if 'Cancer in family' = 'Yes - Patient information - - - - - - - - Comorbidity - - - - - - Comorbidity - Patient information - - - - - - - - Cardiac - - - - - - Cardiac - Patient information - - - - - - - - Vascular - - - - - - Vascular - Patient information - - - - - - - - Diabetes - - - - - - Diabetes - Patient information - - - - - - - - Pulmonary - - - - - - Pulmonary - Patient information - - - - - - - - Neurological - - - - - - Neurological - Patient information - - - - - - - - Gastrointestinal - - - - - - Gastrointestinal - Patient information - - - - - - - - Urogenital - - - - - - Urogenital - Patient information - - - - - - - - Thrombotic - - - - - - Thrombotic - Patient information - - - - - - - - Muscles and joints - - - - - - Muscles and joints - Patient information - - - - - - - - Endocrine disorders - - - - - - Endocrine disorders - Patient information - - - - - - - - Infectious diseases - - - - - - Infectious diseases - Patient information - - - - - - - - Malignity - - - - - - Malignity - Patient information - - - - - - - - Other comorbidity - - - - - - Other comorbidity - Patient information - - - - - - - - cTNM date - - - - - cTNM date - TNM - - - - - - - - cT - - - - - - - cT - TNM - - - - - - - - cN - - - - - - - cN - TNM - - - - - - - - cM - - - - - - - cM - TNM - - - - - - - - Biopsy Gleason 1 - - - - - - Biopsy Gleason 1 - TNM - - - - - - - - Biopsy Gleason 2 - - - - - - Biopsy Gleason 2 - TNM - - - - - - - - Biopsy Gleason Sum - - - - - Biopsy Gleason Sum - TNM - - - - - - - - PSA before treatment - - - - - 0 - - Not within the allowed range (0-99) - - - 99 - - Not within the allowed range (0-99) - - - - PSA before treatment - TNM - - - - - - - - Side - - - - - - Side - TNM - - - - - - - - Prostate size - - - - - 0 - - Not within the allowed range (0-150) - - - 150 - - Not within the allowed range (0-150) - - - - Prostate size - TNM - - - - - - - - Prostatectomy date - - - - - Prostatectomy date - TNM - - - - - - - - pT - - - - - - - pT - TNM - - - - - - - - pN - - - - - - - pN - TNM - - - - - - - - pM - - - - - - - pM - TNM - - - - - - - - Prostatectomy Gleason 1 - - - - - - Prostatectomy Gleason 1 - TNM - - - - - - - - Prostatectomy Gleason 2 - - - - - - Prostatectomy Gleason 2 - TNM - - - - - - - - Prostatectomy Gleason Sum - - - - - Prostatectomy Gleason Sum - TNM - - - - - - - - Side - - - - - - Side - TNM - - - - - - - - Prostate size - - - - - 0 - - Not within the allowed range (0-150) - - - 150 - - Not within the allowed range (0-150) - - - - Prostate size - TNM - - - - - - - - Margin status - - - - - - Margin status - TNM - - - - - - - - Location of positive margin - - - - - - Location of positive margin - TNM - - - - - - - - MDO - - - - - - MDO - TNM - - - - - - - - Treatment - - - - - - Treatment - TNM - - - - - - - - Treatment scroll out - - - - - - Treatment scroll out - TNM - - - - - - - - Neoadj. horm. - - - - - - Neoadj. horm. - TNM - - - - - - - - Adj. horm. - - - - - - Adj. horm. - TNM - - - - - - - - Vesiculectomie - - - - - - Vesiculectomie - TNM - - - - - - - - LND - - - - - - LND - TNM - - - - - - - - Number of removed lymph nodes - - - - 0 - Not within the allowed range (0-30) - - - 30 - Not within the allowed range (0-30) - - - - Number of removed lymph nodes - TNM - - - - - - - - Number positive - Must be <= 'Number of removed lymph nodes - - - - - Number positive - Must be <= 'Number of removed lymph nodes - TNM - - - - - - - - PA-number - - - - - PA-number - TNM - - - - - - - - Postoperative RT (fossa) date - - - - - Postoperative RT (fossa) date - TNM - - - - - - - - Postoperative RT (fossa) gray - - - - 0 - Not within the allowed range (0-99) - - - 99 - Not within the allowed range (0-99) - - - - Postoperative RT (fossa) gray - TNM - - - - - - - - Postoperative RT - - - - - - Postoperative RT - TNM - - - - - - - - FP-score - - - - 0 - Not within the allowed range (0-12) - - - 12 - Not within the allowed range (0-12) - - - - FP-score - TNM - - - - - - - - Nerve sparing Left - - - - - - Nerve sparing Left - TNM - - - - - - - - Nerve sparing type Left - - - - - - Nerve sparing type Left - TNM - - - - - - - - Nerve sparing Right - - - - - - Nerve sparing Right - TNM - - - - - - - - Nerve sparing type Right - - - - - - Nerve sparing type Right - TNM - - - - - - - - OR time - - - - - 0 - - Not within the allowed range (0-600) - - - 600 - - Not within the allowed range (0-600) - - - - OR time - TNM - - - - - - - - Peroperative blood loss - - - - - 0 - - Not within the allowed range (0-9999) - - - 9999 - - Not within the allowed range (0-9999) - - - - Peroperative blood loss - TNM - - - - - - - - Admission time - - - - - 0 - - Not within the allowed range (0-30) - - - 30 - - Not within the allowed range (0-30) - - - - Admission time - TNM - - - - - - - - TUC(d) - - - - 0 - Not within the allowed range (0-30) - - - 30 - Not within the allowed range (0-30) - - - - TUC(d) - TNM - - - - - - - - Surgeon - - - - - Surgeon - TNM - - - - - - - - Comment - - - - - Comment - TNM - - - - - - - - Complication - - - - - Complication - Complications - - - - - - - - Date - - - - - Date - Complications - - - - - - - - Clavien grade - - - - - - Clavien grade - Complications - - - - - - - - CEUS done? - - - - - - CEUS done? - Other - - - - - - - - CEUS date - Only if 'CEUS done?' = 'Yes - - - - - CEUS date - Only if 'CEUS done?' = 'Yes - Other - - - - - - - - CEUS location - Only if 'CEUS done?' = 'Yes - - - - - - CEUS location - Only if 'CEUS done?' = 'Yes - Other - - - - - - - - MRI done? - - - - - - MRI done? - Other - - - - - - - - MRI date - Only if 'MRI done?' = 'Yes - - - - - MRI date - Only if 'MRI done?' = 'Yes - Other - - - - - - - - MRI location - Only if 'MRI done?' = 'Yes - - - - - - MRI location - Only if 'MRI done?' = 'Yes - Other - - - - - - - - MRI type - Only if 'MRI done?' = 'Yes - - - - - - MRI type - Only if 'MRI done?' = 'Yes - Other - - - - - - - - Transrectal echo done? - - - - - - Transrectal echo done? - Other - - - - - - - - Transrectal echo date - Only if 'Transrectal echo done?' = 'Yes - - - - - Transrectal echo date - Only if 'Transrectal echo done?' = 'Yes - Other - - - - - - - - Transrectal echo location - Only if 'Transrectal echo done?' = 'Yes - - - - - - Transrectal echo location - Only if 'Transrectal echo done?' = 'Yes - Other - - - - - - - - Bone scan done? - - - - - - Bone scan done? - Other - - - - - - - - Bone scan date - Only if 'Bone scan done?' = 'Yes - - - - - Bone scan date - Only if 'Bone scan done?' = 'Yes - Other - - - - - - - - Bone scan location - Only if 'Bone scan done?' = 'Yes - - - - - - Bone scan location - Only if 'Bone scan done?' = 'Yes - Other - - - - - - - - PET scan done? - - - - - - PET scan done? - Other - - - - - - - - PET scan date - Only if 'PET scan done?' = 'Yes - - - - - PET scan date - Only if 'PET scan done?' = 'Yes - Other - - - - - - - - PET scan location - Only if 'PET scan done?' = 'Yes - - - - - - PET scan location - Only if 'PET scan done?' = 'Yes - Other - - - - - - - - Pathology review done? - - - - - - Pathology review done? - Other - - - - - - - - Pathology reviewer - Only if 'Pathology review done?' = 'Yes - - - - - Pathology reviewer - Only if 'Pathology review done?' = 'Yes - Other - - - - - - - - Urine sample done? - - - - - - Urine sample done? - Other - - - - - - - - Urine sample date - Only if 'Urine sample done?' = 'Yes - - - - - Urine sample date - Only if 'Urine sample done?' = 'Yes - Other - - - - - - - - Urine sample location - Only if 'Urine sample done?' = 'Yes - - - - - - Urine sample location - Only if 'Urine sample done?' = 'Yes - Other - - - - - - - - Blood sample done? - - - - - - Blood sample done? - Other - - - - - - - - Blood sample date - Only if 'Blood sample done?' = 'Yes - - - - - Blood sample date - Only if 'Blood sample done?' = 'Yes - Other - - - - - - - - Blood sample location - Only if 'Blood sample done?' = 'Yes - - - - - - Blood sample location - Only if 'Blood sample done?' = 'Yes - Other - - - - - - - - Blood sample type - Only if 'Blood sample done?' = 'Yes - - - - - - Blood sample type - Only if 'Blood sample done?' = 'Yes - Other - - - - - - - - 1. Do you have trouble doing strenuous activities like carrying a heavy shopping bag or a suitcase? - - - - - - 1. Do you have trouble doing strenuous activities like carrying a heavy shopping bag or a suitcase? - Questionnaire - - - - - - - - 2. Do you have difficulty making a long walk? - - - - - - 2. Do you have difficulty making a long walk? - Questionnaire - - - - - - - - 3. Do you have difficulty making a short walk outdoors? - - - - - - 3. Do you have difficulty making a short walk outdoors? - Questionnaire - - - - - - - - 4. Do you have to stay in bed or a chair during daytime? - - - - - - 4. Do you have to stay in bed or a chair during daytime? - Questionnaire - - - - - - - - 5. Do you need help with eating, dressing, washing yourself or going to the toilet? - - - - - - 5. Do you need help with eating, dressing, washing yourself or going to the toilet? - Questionnaire - - - - - - - - 6. Were you limited in doing your work or other daily activities? - - - - - - 6. Were you limited in doing your work or other daily activities? - Questionnaire - - - - - - - - 7. Were you restricted in exercising your hobby `s or whatever else you do in your spare time? - - - - - - 7. Were you restricted in exercising your hobby `s or whatever else you do in your spare time? - Questionnaire - - - - - - - - 8. Were you short of breath? - - - - - - 8. Were you short of breath? - Questionnaire - - - - - - - - 9. Have you had pain? - - - - - - 9. Have you had pain? - Questionnaire - - - - - - - - 10. Did you need to rest? - - - - - - 10. Did you need to rest? - Questionnaire - - - - - - - - 11. Have you had trouble sleeping? - - - - - - 11. Have you had trouble sleeping? - Questionnaire - - - - - - - - 12. Have you felt weak? - - - - - - 12. Have you felt weak? - Questionnaire - - - - - - - - 13. Did you have a loss of appetite? - - - - - - 13. Did you have a loss of appetite? - Questionnaire - - - - - - - - 14. Have you felt nauseated? - - - - - - 14. Have you felt nauseated? - Questionnaire - - - - - - - - 15. Did you vomit? - - - - - - 15. Did you vomit? - Questionnaire - - - - - - - - 16. Did you suffer from constipation? - - - - - - 16. Did you suffer from constipation? - Questionnaire - - - - - - - - 17. Did you have diarrhea? - - - - - - 17. Did you have diarrhea? - Questionnaire - - - - - - - - 18. Were you tired? - - - - - - 18. Were you tired? - Questionnaire - - - - - - - - 19. Did pain interfere with your daily activities? - - - - - - 19. Did pain interfere with your daily activities? - Questionnaire - - - - - - - - 20. Have you had difficulty concentrating on things such as reading newspapers or watching television? - - - - - - 20. Have you had difficulty concentrating on things such as reading newspapers or watching television? - Questionnaire - - - - - - - - 21. Did you feel tense? - - - - - - 21. Did you feel tense? - Questionnaire - - - - - - - - 22. Did you worry? - - - - - - 22. Did you worry? - Questionnaire - - - - - - - - 23. Did you feel irritable? - - - - - - 23. Did you feel irritable? - Questionnaire - - - - - - - - 24. Did you feel sad? - - - - - - 24. Did you feel sad? - Questionnaire - - - - - - - - 25. Have you had difficulty remembering things? - - - - - - 25. Have you had difficulty remembering things? - Questionnaire - - - - - - - - 26. Has your physical condition or medical treatment bothered your family life? - - - - - - 26. Has your physical condition or medical treatment bothered your family life? - Questionnaire - - - - - - - - 27. Has your physical condition or medical treatment hampered you in your social activities? - - - - - - 27. Has your physical condition or medical treatment hampered you in your social activities? - Questionnaire - - - - - - - - 28. Has your physical condition or medical treatment entailed financial difficulties? - - - - - - 28. Has your physical condition or medical treatment entailed financial difficulties? - Questionnaire - - - - - - - - 29. How would you rate your overall health during the past week? - - - - - - 29. How would you rate your overall health during the past week? - Questionnaire - - - - - - - - 30. How would you rate your overall "quality of life" during the past week? - - - - - - 30. How would you rate your overall "quality of life" during the past week? - Questionnaire - - - - - - - - 31. Did you have to urinate frequently during the day? - - - - - - 31. Did you have to urinate frequently during the day? - Questionnaire - - - - - - - - 32. Did you have to urinate frequently during the night? - - - - - - 32. Did you have to urinate frequently during the night? - Questionnaire - - - - - - - - 33. Did you have to rush to the toilet when you felt the urge to pee? - - - - - - 33. Did you have to rush to the toilet when you felt the urge to pee? - Questionnaire - - - - - - - - 34. Did you find it hard to get enough sleep, because you often had to pee at night? - - - - - - 34. Did you find it hard to get enough sleep, because you often had to pee at night? - Questionnaire - - - - - - - - 35. Did you have problems doing things outdoors, because you had to stay near a toilet? - - - - - - 35. Did you have problems doing things outdoors, because you had to stay near a toilet? - Questionnaire - - - - - - - - 36. Have you unintentionally lost urine? - - - - - - 36. Have you unintentionally lost urine? - Questionnaire - - - - - - - - 37. Did you have pain when urinating? - - - - - - 37. Did you have pain when urinating? - Questionnaire - - - - - - - - 38. Was it a problem for you to wear incontinence pads? - - - - - - 38. Was it a problem for you to wear incontinence pads? - Questionnaire - - - - - - - - 39. Were you limited in your daily activities by urination problems? - - - - - - 39. Were you limited in your daily activities by urination problems? - Questionnaire - - - - - - - - 40. Were you limited in your daily activities by stool problems? - - - - - - 40. Were you limited in your daily activities by stool problems? - Questionnaire - - - - - - - - 41. Have you inadvertently lost stools? - - - - - - 41. Have you inadvertently lost stools? - Questionnaire - - - - - - - - 42. Did you have blood in your stools? - - - - - - 42. Did you have blood in your stools? - Questionnaire - - - - - - - - 43. Did you have a bloated feeling in your stomach? - - - - - - 43. Did you have a bloated feeling in your stomach? - Questionnaire - - - - - - - - 44. Have you had hot flashes? - - - - - - 44. Have you had hot flashes? - Questionnaire - - - - - - - - 45. Did you have sore or swollen breasts or nipples? - - - - - - 45. Did you have sore or swollen breasts or nipples? - Questionnaire - - - - - - - - 46. Have you had swollen legs or ankles? - - - - - - 46. Have you had swollen legs or ankles? - Questionnaire - - - - - - - - 47. Was your weight loss a problem for you? - - - - - - 47. Was your weight loss a problem for you? - Questionnaire - - - - - - - - 48. Was your weight gain a problem for you? - - - - - - 48. Was your weight gain a problem for you? - Questionnaire - - - - - - - - 49. Did you feel less masculin because of your illness or treatment? - - - - - - 49. Did you feel less masculin because of your illness or treatment? - Questionnaire - - - - - - - - 50. To what extent did you want to have sex? - - - - - - 50. To what extent did you want to have sex? - Questionnaire - - - - - - - - 51. To what extent were you sexually active (with or without intercourse)? - - - - - - 51. To what extent were you sexually active (with or without intercourse)? - Questionnaire - - - - - - - - 52. To what extent was sex enjoyable for you? - - - - - - 52. To what extent was sex enjoyable for you? - Questionnaire - - - - - - - - 53. Did you have trouble getting or maintaining an erection? - - - - - - 53. Did you have trouble getting or maintaining an erection? - Questionnaire - - - - - - - - 54. Did you have problems with getting an ejaculation (eg a so-called "dry" ejaculation)? - - - - - - 54. Did you have problems with getting an ejaculation (eg a so-called "dry" ejaculation)? - Questionnaire - - - - - - - - 55. Did you dread to have sexual contact, or did you feel uncomfortable regarding sexually intimacy? - - - - - - 55. Did you dread to have sexual contact, or did you feel uncomfortable regarding sexually intimacy? - Questionnaire - - - - - - - - 56. Did you use any erectile pills (like Viagra, Cialis, Levitra) in recent months? - - - - - - 56. Did you use any erectile pills (like Viagra, Cialis, Levitra) in recent months? - Questionnaire - - - - - - - - 57. How often were you able to get an erection when sexually active, during the past 4 weeks? - - - - - - 57. How often were you able to get an erection when sexually active, during the past 4 weeks? - Questionnaire - - - - - - - - 58. How often did it occur that, after getting an erection from sexual stimulation, your penis was hard enough to penetrate, during the past 4 weeks? - - - - - - 58. How often did it occur that, after getting an erection from sexual stimulation, your penis was hard enough to penetrate, during the past 4 weeks? - Questionnaire - - - - - - - - 59. How often were you able to penetrate your partner when you tried to have sexual intercourse, during the past 4 weeks? - - - - - - 59. How often were you able to penetrate your partner when you tried to have sexual intercourse, during the past 4 weeks? - Questionnaire - - - - - - - - 60. How often were you able to maintain your erection during sexual intercourse after you had penetrated your partner, during the past 4 weeks? - - - - - - 60. How often were you able to maintain your erection during sexual intercourse after you had penetrated your partner, during the past 4 weeks? - Questionnaire - - - - - - - - 61. How difficult was it to maintain your erection until the intercourse was completed, during the past 4 weeks? - - - - - - 61. How difficult was it to maintain your erection until the intercourse was completed, during the past 4 weeks? - Questionnaire - - - - - - - - 62. How often have you tried to have intercourse, during the past 4 weeks? - - - - - - 62. How often have you tried to have intercourse, during the past 4 weeks? - Questionnaire - - - - - - - - 63. How often was it satisfactory for you when you tried to have sexual intercourse, during the past 4 weeks? - - - - - - 63. How often was it satisfactory for you when you tried to have sexual intercourse, during the past 4 weeks? - Questionnaire - - - - - - - - 64. To what extent did you enjoy having sexual intercourse, during the past 4 weeks? - - - - - - 64. To what extent did you enjoy having sexual intercourse, during the past 4 weeks? - Questionnaire - - - - - - - - 65. How often have you had an ejaculation when you were sexually stimulated or had sexual intercourse, during the past 4 weeks? - - - - - - 65. How often have you had an ejaculation when you were sexually stimulated or had sexual intercourse, during the past 4 weeks? - Questionnaire - - - - - - - - 66. How often did you have the feeling of an orgasm, with or without ejaculation, while you were sexually stimulated or had sexual intercourse, during the past 4 weeks? - - - - - - 66. How often did you have the feeling of an orgasm, with or without ejaculation, while you were sexually stimulated or had sexual intercourse, during the past 4 weeks? - Questionnaire - - - - - - - - 67. How often did you have sexual desires during the past 4 weeks? - - - - - - 67. How often did you have sexual desires during the past 4 weeks? - Questionnaire - - - - - - - - 68. How strong did you think your sexual desires were, during the past 4 weeks? - - - - - - 68. How strong did you think your sexual desires were, during the past 4 weeks? - Questionnaire - - - - - - - - 69. How satisfied were you with your sex life in general, during the past 4 weeks? - - - - - - 69. How satisfied were you with your sex life in general, during the past 4 weeks? - Questionnaire - - - - - - - - 70. How satisfied were you about the sexual relationship with your partner, during the past 4 weeks? - - - - - - 70. How satisfied were you about the sexual relationship with your partner, during the past 4 weeks? - Questionnaire - - - - - - - - 71. How strong would you say your confidence was about getting and maintaining an erection, during the past 4 weeks? - - - - - - 71. How strong would you say your confidence was about getting and maintaining an erection, during the past 4 weeks? - Questionnaire - - - - - - - - 72. Number of times urine loss - - - - - - 72. Number of times urine loss - Questionnaire - - - - - - - - 73. Amount of urine loss - - - - - - 73. Amount of urine loss - Questionnaire - - - - - - - - 74. When urine loss? Never - - - - - - 74. When urine loss? Never - Questionnaire - - - - - - - - 75. When urine loss? Before urination - - - - - - 75. When urine loss? Before urination - Questionnaire - - - - - - - - 76. When urine loss? When sneezing - - - - - - 76. When urine loss? When sneezing - Questionnaire - - - - - - - - 77. When urine loss? During sleep - - - - - - 77. When urine loss? During sleep - Questionnaire - - - - - - - - 78. When urine loss? During physical exertion - - - - - - 78. When urine loss? During physical exertion - Questionnaire - - - - - - - - 79. When urine loss? During urination - - - - - - 79. When urine loss? During urination - Questionnaire - - - - - - - - 80. When urine loss? No apparent reason - - - - - - 80. When urine loss? No apparent reason - Questionnaire - - - - - - - - 81. When urine loss? Continuous - - - - - - 81. When urine loss? Continuous - Questionnaire - - - - - - - - Year of birth - - - - 1900 - Not within the allowed range (1900-2010) - - - 2010 - Not within the allowed range (1900-2010) - - - - Year of birth - Patient information - - - - - - - - Allergy / hypersensitivity - - - - - - Allergy / hypersensitivity - Patient information - - - - - - - - Smoker - - - - - - Smoker - Patient information - - - - - - - - Ex-smoker - Only if 'Smoker' = 'Yes - - - - - - Ex-smoker - Only if 'Smoker' = 'Yes - Patient information - - - - - - - - Do you drink alcoholic beverages? - - - - - - Do you drink alcoholic beverages? - Patient information - - - - - - - - How many glasses per day? - - - - - 0 - - Not within the allowed range (0-99) - - - 99 - - Not within the allowed range (0-99) - - - - How many glasses per day? - Patient information - - - - - - - - WHO score at diagnosis - - - - - - WHO score at diagnosis - Patient information - - - - - - - - Medication - - - - - - Medication - Patient information - - - - - - - - Which medication - Only if 'Medication' = 'Yes - - - - - Which medication - Only if 'Medication' = 'Yes - Patient information - - - - - - - - Previously treated - - - - - - Previously treated - Patient information - - - - - - - - Treated by urologist - - - - - - Treated by urologist - Patient information - - - - - - - - Biopsies of prostate - - - - - - Biopsies of prostate - Patient information - - - - - - - - PSA determined - - - - - - PSA determined - Patient information - - - - - - - - Cancer in family - - - - - - Cancer in family - Patient information - - - - - - - - Which type of cancer - Only if 'Cancer in family' = 'Yes - - - - - Which type of cancer - Only if 'Cancer in family' = 'Yes - Patient information - - - - - - - - Comorbidity - - - - - - Comorbidity - Patient information - - - - - - - - Cardiac - - - - - - Cardiac - Patient information - - - - - - - - Vascular - - - - - - Vascular - Patient information - - - - - - - - Diabetes - - - - - - Diabetes - Patient information - - - - - - - - Pulmonary - - - - - - Pulmonary - Patient information - - - - - - - - Neurological - - - - - - Neurological - Patient information - - - - - - - - Gastrointestinal - - - - - - Gastrointestinal - Patient information - - - - - - - - Urogenital - - - - - - Urogenital - Patient information - - - - - - - - Thrombotic - - - - - - Thrombotic - Patient information - - - - - - - - Muscles and joints - - - - - - Muscles and joints - Patient information - - - - - - - - Endocrine disorders - - - - - - Endocrine disorders - Patient information - - - - - - - - Infectious diseases - - - - - - Infectious diseases - Patient information - - - - - - - - Malignity - - - - - - Malignity - Patient information - - - - - - - - Other comorbidity - - - - - - Other comorbidity - Patient information - - - - - - - - cTNM date - - - - - cTNM date - TNM - - - - - - - - cT - - - - - - - cT - TNM - - - - - - - - cN - - - - - - - cN - TNM - - - - - - - - cM - - - - - - - cM - TNM - - - - - - - - Biopsy Gleason 1 - - - - - - Biopsy Gleason 1 - TNM - - - - - - - - Biopsy Gleason 2 - - - - - - Biopsy Gleason 2 - TNM - - - - - - - - Biopsy Gleason Sum - - - - - Biopsy Gleason Sum - TNM - - - - - - - - PSA before treatment - - - - - 0 - - Not within the allowed range (0-99) - - - 99 - - Not within the allowed range (0-99) - - - - PSA before treatment - TNM - - - - - - - - Side - - - - - - Side - TNM - - - - - - - - Prostate size - - - - - 0 - - Not within the allowed range (0-150) - - - 150 - - Not within the allowed range (0-150) - - - - Prostate size - TNM - - - - - - - - Prostatectomy date - - - - - Prostatectomy date - TNM - - - - - - - - pT - - - - - - - pT - TNM - - - - - - - - pN - - - - - - - pN - TNM - - - - - - - - pM - - - - - - - pM - TNM - - - - - - - - Prostatectomy Gleason 1 - - - - - - Prostatectomy Gleason 1 - TNM - - - - - - - - Prostatectomy Gleason 2 - - - - - - Prostatectomy Gleason 2 - TNM - - - - - - - - Prostatectomy Gleason Sum - - - - - Prostatectomy Gleason Sum - TNM - - - - - - - - Side - - - - - - Side - TNM - - - - - - - - Prostate size - - - - - 0 - - Not within the allowed range (0-150) - - - 150 - - Not within the allowed range (0-150) - - - - Prostate size - TNM - - - - - - - - Margin status - - - - - - Margin status - TNM - - - - - - - - Location of positive margin - - - - - - Location of positive margin - TNM - - - - - - - - MDO - - - - - - MDO - TNM - - - - - - - - Treatment - - - - - - Treatment - TNM - - - - - - - - Treatment scroll out - - - - - - Treatment scroll out - TNM - - - - - - - - Neoadj. horm. - - - - - - Neoadj. horm. - TNM - - - - - - - - Adj. horm. - - - - - - Adj. horm. - TNM - - - - - - - - Vesiculectomie - - - - - - Vesiculectomie - TNM - - - - - - - - LND - - - - - - LND - TNM - - - - - - - - Number of removed lymph nodes - - - - 0 - Not within the allowed range (0-30) - - - 30 - Not within the allowed range (0-30) - - - - Number of removed lymph nodes - TNM - - - - - - - - Number positive - Must be <= 'Number of removed lymph nodes - - - - - Number positive - Must be <= 'Number of removed lymph nodes - TNM - - - - - - - - PA-number - - - - - PA-number - TNM - - - - - - - - Postoperative RT (fossa) date - - - - - Postoperative RT (fossa) date - TNM - - - - - - - - Postoperative RT (fossa) gray - - - - 0 - Not within the allowed range (0-99) - - - 99 - Not within the allowed range (0-99) - - - - Postoperative RT (fossa) gray - TNM - - - - - - - - Postoperative RT - - - - - - Postoperative RT - TNM - - - - - - - - FP-score - - - - 0 - Not within the allowed range (0-12) - - - 12 - Not within the allowed range (0-12) - - - - FP-score - TNM - - - - - - - - Nerve sparing Left - - - - - - Nerve sparing Left - TNM - - - - - - - - Nerve sparing type Left - - - - - - Nerve sparing type Left - TNM - - - - - - - - Nerve sparing Right - - - - - - Nerve sparing Right - TNM - - - - - - - - Nerve sparing type Right - - - - - - Nerve sparing type Right - TNM - - - - - - - - OR time - - - - - 0 - - Not within the allowed range (0-600) - - - 600 - - Not within the allowed range (0-600) - - - - OR time - TNM - - - - - - - - Peroperative blood loss - - - - - 0 - - Not within the allowed range (0-9999) - - - 9999 - - Not within the allowed range (0-9999) - - - - Peroperative blood loss - TNM - - - - - - - - Admission time - - - - - 0 - - Not within the allowed range (0-30) - - - 30 - - Not within the allowed range (0-30) - - - - Admission time - TNM - - - - - - - - TUC(d) - - - - 0 - Not within the allowed range (0-30) - - - 30 - Not within the allowed range (0-30) - - - - TUC(d) - TNM - - - - - - - - Surgeon - - - - - Surgeon - TNM - - - - - - - - Comment - - - - - Comment - TNM - - - - - - - - Complication - - - - - Complication - Complications - - - - - - - - Date - - - - - Date - Complications - - - - - - - - Clavien grade - - - - - - Clavien grade - Complications - - - - - - - - CEUS done? - - - - - - CEUS done? - Other - - - - - - - - CEUS date - Only if 'CEUS done?' = 'Yes - - - - - CEUS date - Only if 'CEUS done?' = 'Yes - Other - - - - - - - - CEUS location - Only if 'CEUS done?' = 'Yes - - - - - - CEUS location - Only if 'CEUS done?' = 'Yes - Other - - - - - - - - MRI done? - - - - - - MRI done? - Other - - - - - - - - MRI date - Only if 'MRI done?' = 'Yes - - - - - MRI date - Only if 'MRI done?' = 'Yes - Other - - - - - - - - MRI location - Only if 'MRI done?' = 'Yes - - - - - - MRI location - Only if 'MRI done?' = 'Yes - Other - - - - - - - - MRI type - Only if 'MRI done?' = 'Yes - - - - - - MRI type - Only if 'MRI done?' = 'Yes - Other - - - - - - - - Transrectal echo done? - - - - - - Transrectal echo done? - Other - - - - - - - - Transrectal echo date - Only if 'Transrectal echo done?' = 'Yes - - - - - Transrectal echo date - Only if 'Transrectal echo done?' = 'Yes - Other - - - - - - - - Transrectal echo location - Only if 'Transrectal echo done?' = 'Yes - - - - - - Transrectal echo location - Only if 'Transrectal echo done?' = 'Yes - Other - - - - - - - - Bone scan done? - - - - - - Bone scan done? - Other - - - - - - - - Bone scan date - Only if 'Bone scan done?' = 'Yes - - - - - Bone scan date - Only if 'Bone scan done?' = 'Yes - Other - - - - - - - - Bone scan location - Only if 'Bone scan done?' = 'Yes - - - - - - Bone scan location - Only if 'Bone scan done?' = 'Yes - Other - - - - - - - - PET scan done? - - - - - - PET scan done? - Other - - - - - - - - PET scan date - Only if 'PET scan done?' = 'Yes - - - - - PET scan date - Only if 'PET scan done?' = 'Yes - Other - - - - - - - - PET scan location - Only if 'PET scan done?' = 'Yes - - - - - - PET scan location - Only if 'PET scan done?' = 'Yes - Other - - - - - - - - Pathology review done? - - - - - - Pathology review done? - Other - - - - - - - - Pathology reviewer - Only if 'Pathology review done?' = 'Yes - - - - - Pathology reviewer - Only if 'Pathology review done?' = 'Yes - Other - - - - - - - - Urine sample done? - - - - - - Urine sample done? - Other - - - - - - - - Urine sample date - Only if 'Urine sample done?' = 'Yes - - - - - Urine sample date - Only if 'Urine sample done?' = 'Yes - Other - - - - - - - - Urine sample location - Only if 'Urine sample done?' = 'Yes - - - - - - Urine sample location - Only if 'Urine sample done?' = 'Yes - Other - - - - - - - - Blood sample done? - - - - - - Blood sample done? - Other - - - - - - - - Blood sample date - Only if 'Blood sample done?' = 'Yes - - - - - Blood sample date - Only if 'Blood sample done?' = 'Yes - Other - - - - - - - - Blood sample location - Only if 'Blood sample done?' = 'Yes - - - - - - Blood sample location - Only if 'Blood sample done?' = 'Yes - Other - - - - - - - - Blood sample type - Only if 'Blood sample done?' = 'Yes - - - - - - Blood sample type - Only if 'Blood sample done?' = 'Yes - Other - - - - - - - - Not - - - - - A little - - - - - Quite - - - - - A lot - - - - - - - Very bad - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Very well - - - - - - - Niet - - - - - 1x per mnd - - - - - 1x per wk - - - - - >1x/wk - - - - - - - Did not try to have intercourse - - - - - Almost never or never - - - - - A few times (much less than half of the time) - - - - - Sometimes (about half of the time) - - - - - Mostly (much more than half of the time) - - - - - Almost always or always - - - - - - - Did not try to have sexual intercourse - - - - - Almost never or never - - - - - A few times (much less than half the time) - - - - - Sometimes (about half the time) - - - - - Usually (more than half the time) - - - - - Almost always or always - - - - - - - Did not try - - - - - Extremely difficult - - - - - Very difficult - - - - - Difficult - - - - - A little difficult - - - - - Not difficult - - - - - - - Did not try - - - - - 1-2 times - - - - - 3-4 times - - - - - 5-6 times - - - - - 7-10 times - - - - - 11 times or more - - - - - - - Did not have intercourse - - - - - Did not enjoy - - - - - Did not enjoy much - - - - - Did enjoy fairly - - - - - Did enjoy much - - - - - Did enjoy very much - - - - - - - Very weak or totally absent - - - - - Poor - - - - - Moderate - - - - - Strong - - - - - Very strong - - - - - - - Very dissatisfied - - - - - Fairly satisfied - - - - - About equally satisfied and dissatisfied - - - - - Quite satisfied - - - - - Very satisfied - - - - - - - Never - - - - - Once a week or less - - - - - 2-3 times a week - - - - - Once a day - - - - - Several times a day - - - - - Continuous - - - - - - - Nothing - - - - - A little - - - - - Fairly much - - - - - Much - - - - - - - Yes - - - - - No - - - - - - - Yes - - - - - No - - - - - - - Asymptomatic - normal activity - - - - - Symptomatic - ambulant - - - - - Symptomatic - in bed <50% per day - - - - - Symptomatic - in bed >50% per day - - - - - 100% in bed - - - - - - - No - - - - - Yes - - - - - Unknown - - - - - - - cTx - - - - - cT0 - - - - - cT1a - - - - - cT1b - - - - - cT1c - - - - - cT2a - - - - - cT2b - - - - - cT2c - - - - - cT3a - - - - - cT3b - - - - - cT4a - - - - - cT4b - - - - - - - cNx - - - - - cN0 - - - - - cN1 - - - - - - - cMx - - - - - cM0 - - - - - cM1a - - - - - cM1b - - - - - cM1c - - - - - - - 1 - - - - - 2 - - - - - 3 - - - - - 4 - - - - - 5 - - - - - - - L - - - - - R - - - - - L+R - - - - - - - pTx - - - - - pT0 - - - - - pT2a - - - - - pT2b - - - - - pT2c - - - - - pT3a - - - - - pT3b - - - - - pT4a - - - - - pT4b - - - - - - - pNx - - - - - pN0 - - - - - pN1 - - - - - - - pMx - - - - - pM0 - - - - - pM1a - - - - - pM1b - - - - - pM1c - - - - - - - Negative - - - - - Positive - - - - - - - Apical - - - - - Basal - - - - - Peripheral - - - - - Multiple locations - - - - - - - Robot-assisted laparoscopic prostatectomy (RALP) - - - - - Laparoscopic prostatectomy - - - - - Open retropubic prostatectomy - - - - - Perineal prostatectomy - - - - - - - Extraperitoneal - - - - - Transperitoneal - - - - - - - Unknown - - - - - None - - - - - Bicalutamide - - - - - LHRH agonist - - - - - LHRH antagonist - - - - - 5-alpha reductase inhibitor - - - - - - - Unknown - - - - - None - - - - - L - - - - - R - - - - - L+R - - - - - - - Unknown - - - - - None - - - - - L limited - - - - - R limited - - - - - L+R limited - - - - - L extensive - - - - - R extensive - - - - - L+R extensive - - - - - - - Adjuvant radiotherapy - - - - - Salvage radiotherapy - - - - - - - No - - - - - Yes - - - - - - - Interfascial - - - - - Intrafascial - - - - - - - I - - - - - II - - - - - IIIa - - - - - IIIb - - - - - IVa - - - - - IVb - - - - - V - - - - - - - No - - - - - Yes - - - - - - - Erasmus MC - - - - - NKI - - - - - UMC St. Radboud - - - - - UMC Groningen - - - - - - - DCE - - - - - DWI - - - - - T2 - - - - - - - Serum - - - - - Plamsa heparin - - - - - Plasma EDTA - - - - - Plasma sodium citrate - - - - - Whole blood (DNA) - - - - - RNA - - - - - Urine PROGENSA kit - - - - - Urine supernatant - - - - - Urine sediment - - - - - - - Not - - - - - A little - - - - - Quite - - - - - A lot - - - - - - - 1 Very bad - - - - - 2 - - - - - 3 - - - - - 4 - - - - - 5 - - - - - 6 - - - - - 7 Very well - - - - - - - Niet - - - - - 1x per mnd - - - - - 1x per wk - - - - - >1x/wk - - - - - - - Did not try to have intercourse - - - - - Almost never or never - - - - - A few times (much less than half of the time) - - - - - Sometimes (about half of the time) - - - - - Mostly (much more than half of the time) - - - - - Almost always or always - - - - - - - Did not try to have sexual intercourse - - - - - Almost never or never - - - - - A few times (much less than half the time) - - - - - Sometimes (about half the time) - - - - - Usually (more than half the time) - - - - - Almost always or always - - - - - - - Did not try - - - - - Extremely difficult - - - - - Very difficult - - - - - Difficult - - - - - A little difficult - - - - - Not difficult - - - - - - - Did not try - - - - - 1-2 times - - - - - 3-4 times - - - - - 5-6 times - - - - - 7-10 times - - - - - 11 times or more - - - - - - - Did not have intercourse - - - - - Did not enjoy - - - - - Did not enjoy much - - - - - Did enjoy fairly - - - - - Did enjoy much - - - - - Did enjoy very much - - - - - - - Almost never or never - - - - - A few times (much less than half the time) - - - - - Sometimes (about half the time) - - - - - Usually (more than half the time) - - - - - Almost always or always - - - - - - - Very weak or totally absent - - - - - Poor - - - - - Moderate - - - - - Strong - - - - - Very strong - - - - - - - Very dissatisfied - - - - - Fairly satisfied - - - - - About equally satisfied and dissatisfied - - - - - Quite satisfied - - - - - Very satisfied - - - - - - - Never - - - - - Once a week or less - - - - - 2-3 times a week - - - - - Once a day - - - - - Several times a day - - - - - Continuous - - - - - - - Nothing - - - - - A little - - - - - Fairly much - - - - - Much - - - - - - - Yes - - - - - No - - - - - - - Yes - - - - - No - - - - - - - Asymptomatic - normal activity - - - - - Symptomatic - ambulant - - - - - Symptomatic - in bed <50% per day - - - - - Symptomatic - in bed >50% per day - - - - - 100% in bed - - - - - - - No - - - - - Yes - - - - - Unknown - - - - - - - cTx - - - - - cT0 - - - - - cT1a - - - - - cT1b - - - - - cT1c - - - - - cT2a - - - - - cT2b - - - - - cT2c - - - - - cT3a - - - - - cT3b - - - - - cT4a - - - - - cT4b - - - - - - - cNx - - - - - cN0 - - - - - cN1 - - - - - - - cMx - - - - - cM0 - - - - - cM1a - - - - - cM1b - - - - - cM1c - - - - - - - 1 - - - - - 2 - - - - - 3 - - - - - 4 - - - - - 5 - - - - - - - L - - - - - R - - - - - L+R - - - - - - - pTx - - - - - pT0 - - - - - pT2a - - - - - pT2b - - - - - pT2c - - - - - pT3a - - - - - pT3b - - - - - pT4a - - - - - pT4b - - - - - - - pNx - - - - - pN0 - - - - - pN1 - - - - - - - pMx - - - - - pM0 - - - - - pM1a - - - - - pM1b - - - - - pM1c - - - - - - - Negative - - - - - Positive - - - - - - - Apical - - - - - Basal - - - - - Peripheral - - - - - Multiple locations - - - - - - - Robot-assisted laparoscopic prostatectomy (RALP) - - - - - Laparoscopic prostatectomy - - - - - Open retropubic prostatectomy - - - - - Perineal prostatectomy - - - - - - - Extraperitoneal - - - - - Transperitoneal - - - - - - - Unknown - - - - - None - - - - - Bicalutamide - - - - - LHRH agonist - - - - - LHRH antagonist - - - - - 5-alpha reductase inhibitor - - - - - - - Unknown - - - - - None - - - - - L - - - - - R - - - - - L+R - - - - - - - Unknown - - - - - None - - - - - L limited - - - - - R limited - - - - - L+R limited - - - - - L extensive - - - - - R extensive - - - - - L+R extensive - - - - - - - Adjuvant radiotherapy - - - - - Salvage radiotherapy - - - - - - - No - - - - - Yes - - - - - - - Interfascial - - - - - Intrafascial - - - - - - - I - - - - - II - - - - - IIIa - - - - - IIIb - - - - - IVa - - - - - IVb - - - - - V - - - - - - - No - - - - - Yes - - - - - - - Erasmus MC - - - - - NKI - - - - - UMC St. Radboud - - - - - UMC Groningen - - - - - - - DCE - - - - - DWI - - - - - T2 - - - - - - - Serum - - - - - Plamsa heparin - - - - - Plasma EDTA - - - - - Plasma sodium citrate - - - - - Whole blood (DNA) - - - - - RNA - - - - - Urine PROGENSA kit - - - - - Urine supernatant - - - - - Urine sediment - - - - - - - - - - available - Prof. Dr. Chris Bangma - n_a - N/A - Interventional - Diagnosis - - - Male - No - 200 - - - No - - - - - - - - - - - - - - - - - - - - - Yes - - - - - Only Year of Birth - - - - - Not Used - - - - - - - Yes - - - - - No - - - - - - - Required - - - - - Optional - - - - - Not Used - - - - - - - Yes - - - - - No - - - - - - - Manual Entry - - - - - Auto-generated and Editable - - - - - Auto-generated and Non-editable - - - - - - - Yes - - - - - No - - - - - Not Used - - - - - - - Blank - - - - - Pre-Populated from active user - - - - - - - Yes - - - - - No - - - - - - - Yes - - - - - No - - - - - Not Used - - - - - - - Blank - - - - - Pre-Populated from Study Event - - - - - - - Yes - - - - - No - - - - - - - Yes - - - - - No - - - - - - - Yes - - - - - No - - - - - - - Yes - - - - - No - - - - - - - Required - - - - - Optional - - - - - Not Used - - - - - - - - - - PCMM 2 - Erasmus MC - - The Prostate Cancer Molecular Medicine (PCMM) project. - - - PCMM 2 - Erasmus MC - - - - - % - - - - - cc - - - - - cm - - - - - cM - - - - - cm3 - - - - - cN - - - - - cT - - - - - days - - - - - glasses/day - - - - - kg - - - - - min - - - - - ml - - - - - mm - - - - - ng/ml - - - - - pM - - - - - pN - - - - - pT - - - - - - - - - - - - - - PCMM 2 - NKI - - The Prostate Cancer Molecular Medicine (PCMM) project. - - - PCMM 2 - NKI - - - - - % - - - - - cc - - - - - cm - - - - - cM - - - - - cm3 - - - - - cN - - - - - cT - - - - - days - - - - - glasses/day - - - - - kg - - - - - min - - - - - ml - - - - - mm - - - - - ng/ml - - - - - pM - - - - - pN - - - - - pT - - - - - - - - - - - - - - PCMM 2 - UMC St. Radboud - - The Prostate Cancer Molecular Medicine (PCMM) project. - - - PCMM 2 - UMC St. Radboud - - - - - % - - - - - cc - - - - - cm - - - - - cM - - - - - cm3 - - - - - cN - - - - - cT - - - - - days - - - - - glasses/day - - - - - kg - - - - - min - - - - - ml - - - - - mm - - - - - ng/ml - - - - - pM - - - - - pN - - - - - pT - - - - - - - - - - - - - - PCMM 2 - UMC Groningen - - The Prostate Cancer Molecular Medicine (PCMM) project. - - - PCMM 2 - UMC Groningen - - - - - % - - - - - cc - - - - - cm - - - - - cM - - - - - cm3 - - - - - cN - - - - - cT - - - - - days - - - - - glasses/day - - - - - kg - - - - - min - - - - - ml - - - - - mm - - - - - ng/ml - - - - - pM - - - - - pN - - - - - pT - - - - - - - - - - - - - - Root User - Root - User - Philips Research - - - Tim Hulsen - Tim - Hulsen - Philips Research - - - Henk Obbink - Henk - Obbink - Philips Research - - - Test Test - Test - Test - NKI - - - Cees de Jonge - Cees - de Jonge - Philips Research - - - Marc van Driel - Marc - van Driel - Philips Research - - - - - Mark Wildhagen - Mark - Wildhagen - Erasmus MC - - - Chris Bangma - Chris - Bangma - Erasmus MC - - - - - Henk van der Poel - Henk - van der Poel - NKI - - - - - Inge van Oort - Inge - van Oort - UMC St. Radboud - - - Jelle Barentsz - Jelle - Barentsz - UMC St. Radboud - - - Petra Frenken - Petra - Frenken - UMC St. Radboud - - - Margot Polfliet - Margot - Polfliet - UMC St. Radboud - - - Hilde Witjes-van Os - Hilde - Witjes-van Os - UMC St. Radboud - - - - - Saskia Dijkstra - Saskia - Dijkstra - UMC Groningen - - - Igle Jan de Jong - Igle Jan - de Jong - UMC Groningen - - - Hilde Hoving - Hilde - Hoving - UMC Groningen - - - diff --git a/src/main/java/com/recomdata/i2b2/I2B2ODMStudyHandlerCMLClient.java b/src/main/java/com/recomdata/i2b2/I2B2ODMStudyHandlerCMLClient.java index 971b676..97f678e 100755 --- a/src/main/java/com/recomdata/i2b2/I2B2ODMStudyHandlerCMLClient.java +++ b/src/main/java/com/recomdata/i2b2/I2B2ODMStudyHandlerCMLClient.java @@ -91,9 +91,9 @@ public static void main(String[] args) { try { logger.info("ODM-to-i2b2 version v3.0 (2015-05-28) started running."); if (args.length >= 1) { - String propertiesFilePath = "ODM-to-i2b2.properties"; + final String propertiesFilePath = "ODM-to-i2b2.properties"; final Configuration configuration = new Configuration(propertiesFilePath); - DOMConfigurator.configure(configuration.getLog4jPath()); + DOMConfigurator.configure(I2B2ODMStudyHandlerCMLClient.class.getResource(configuration.getLog4jPath())); if (EXPORT_TO_DATABASE) { logger.info("Initializing database connection..."); diff --git a/src/main/resources/log4j.xml b/src/main/resources/com/recomdata/i2b2/log4j.xml similarity index 100% rename from src/main/resources/log4j.xml rename to src/main/resources/com/recomdata/i2b2/log4j.xml diff --git a/src/examples/CDISC_ODM_example_maxim.xml b/src/main/resources/examples/CDISC_ODM_example_maxim.xml similarity index 100% rename from src/examples/CDISC_ODM_example_maxim.xml rename to src/main/resources/examples/CDISC_ODM_example_maxim.xml diff --git a/src/examples/CDISC_ODM_example_minim.xml b/src/main/resources/examples/CDISC_ODM_example_minim.xml similarity index 100% rename from src/examples/CDISC_ODM_example_minim.xml rename to src/main/resources/examples/CDISC_ODM_example_minim.xml diff --git a/src/examples/CDISC_ODM_example_web1.xml b/src/main/resources/examples/CDISC_ODM_example_web1.xml similarity index 100% rename from src/examples/CDISC_ODM_example_web1.xml rename to src/main/resources/examples/CDISC_ODM_example_web1.xml diff --git a/src/examples/CHB_REDCap_2.xml b/src/main/resources/examples/CHB_REDCap_2.xml similarity index 100% rename from src/examples/CHB_REDCap_2.xml rename to src/main/resources/examples/CHB_REDCap_2.xml diff --git a/src/examples/odm121.XML b/src/main/resources/examples/odm121.XML similarity index 100% rename from src/examples/odm121.XML rename to src/main/resources/examples/odm121.XML diff --git a/src/examples/odm130.XML b/src/main/resources/examples/odm130.XML similarity index 100% rename from src/examples/odm130.XML rename to src/main/resources/examples/odm130.XML diff --git a/src/examples/odm130data.XML b/src/main/resources/examples/odm130data.XML similarity index 100% rename from src/examples/odm130data.XML rename to src/main/resources/examples/odm130data.XML diff --git a/src/examples/odm130valueErrors.xml b/src/main/resources/examples/odm130valueErrors.xml similarity index 100% rename from src/examples/odm130valueErrors.xml rename to src/main/resources/examples/odm130valueErrors.xml diff --git a/src/releases/odm-to-i2b2-3.0.zip b/src/releases/odm-to-i2b2-3.0.zip new file mode 100755 index 0000000..e6f719f Binary files /dev/null and b/src/releases/odm-to-i2b2-3.0.zip differ