[med-svn] [Git][med-team/pixelmed][master] 8 commits: d/control: Add missing Depends on libbcprov-java
Mathieu Malaterre
gitlab at salsa.debian.org
Wed Aug 5 11:34:51 BST 2020
Mathieu Malaterre pushed to branch master at Debian Med / pixelmed
Commits:
b0ed0251 by Mathieu Malaterre at 2020-08-05T12:34:05+02:00
d/control: Add missing Depends on libbcprov-java
- - - - -
e13fa150 by Mathieu Malaterre at 2020-08-05T12:34:07+02:00
d/p/addmanifest.patch: Add missing ref to slf4j. Closes: #967936
- - - - -
81fe601c by Mathieu Malaterre at 2020-08-05T12:34:07+02:00
d/p/dicomimageviewer: Add missing pixelmed_imageio jar
- - - - -
581c5e6e by Mathieu Malaterre at 2020-08-05T12:34:07+02:00
d/p/jpegblock.patch: Remove template cruft
- - - - -
5ea200b0 by Mathieu Malaterre at 2020-08-05T12:34:07+02:00
d/p/add_usage.patch: Add missing help message for help2man
- - - - -
d742a861 by Mathieu Malaterre at 2020-08-05T12:34:07+02:00
d/rules: Simplify help2man generation for version number
- - - - -
5cf51703 by Mathieu Malaterre at 2020-08-05T12:34:07+02:00
d/*1.: Refresh man pages
- - - - -
c63749fa by Mathieu Malaterre at 2020-08-05T12:34:07+02:00
d/control Add missing pixelmed-imageio package
- - - - -
16 changed files:
- debian/DicomSRValidator.1
- debian/ImageToDicom.1
- debian/NIfTI1ToDicom.1
- debian/NRRDToDicom.1
- debian/PDFToDicomImage.1
- debian/StructuredReport.1
- debian/VerificationSOPClassSCU.1
- debian/control
- debian/patches/add_usage.patch
- debian/patches/addmanifest.patch
- debian/patches/dicomimageviewer.patch
- debian/patches/jpegblock.patch
- debian/patches/remove-build-date-file.patch
- debian/patches/removeicon.patch
- debian/patches/set_java_home.patch
- debian/rules
Changes:
=====================================
debian/DicomSRValidator.1
=====================================
@@ -1,22 +1,9 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10.
-.TH JAVA.IO.FILENOTFOUNDEXCEPTION: "1" "June 2014" "java.io.FileNotFoundException: --version (No such file or directory)" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH DICOMSRVALIDATOR "1" "August 2020" "DicomSRValidator 20200416" "User Commands"
.SH NAME
-java.io.FileNotFoundException: \- Works with DICOM files
+DicomSRValidator \- Works with DICOM files
+.SH SYNOPSIS
+.B DicomSRValidator
+\fI\,dicom_sr_filename\/\fR
.SH DESCRIPTION
-java.io.FileNotFoundException: \fB\-\-help\fR (No such file or directory)
-.IP
-at java.io.FileInputStream.open(Native Method)
-at java.io.FileInputStream.<init>(FileInputStream.java:137)
-at com.pixelmed.dicom.AttributeList.read(AttributeList.java:1355)
-at com.pixelmed.dicom.AttributeList.read(AttributeList.java:1331)
-at com.pixelmed.dicom.AttributeList.read(AttributeList.java:1484)
-at com.pixelmed.validate.DicomSRValidator.validate(DicomSRValidator.java:257)
-at com.pixelmed.validate.DicomSRValidator.main(DicomSRValidator.java:315)
-.IP
-at java.io.FileInputStream.open(Native Method)
-at java.io.FileInputStream.<init>(FileInputStream.java:137)
-at com.pixelmed.dicom.AttributeList.read(AttributeList.java:1355)
-at com.pixelmed.dicom.AttributeList.read(AttributeList.java:1331)
-at com.pixelmed.dicom.AttributeList.read(AttributeList.java:1484)
-at com.pixelmed.validate.DicomSRValidator.validate(DicomSRValidator.java:257)
-at com.pixelmed.validate.DicomSRValidator.main(DicomSRValidator.java:315)
+Error: Incorrect number of arguments
=====================================
debian/ImageToDicom.1
=====================================
@@ -1,11 +1,9 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10.
-.TH ERROR: "1" "June 2014" "Error: Incorrect number of arguments" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH IMAGETODICOM "1" "August 2020" "ImageToDicom 20200416" "User Commands"
.SH NAME
-Error: \- Works with DICOM files
+ImageToDicom \- Works with DICOM files
.SH SYNOPSIS
.B ImageToDicom
-\fIinputFile outputFile patientName patientID studyID seriesNumber instanceNumber \fR[\fImodality \fR[\fISOPClass\fR]]
+\fI\,inputFile outputFile patientName patientID studyID seriesNumber instanceNumber \/\fR[\fI\,modality \/\fR[\fI\,SOPClass\/\fR]]
.SH DESCRIPTION
Error: Incorrect number of arguments
-.PP
-Usage: ImageToDicom inputFile outputFile patientName patientID studyID seriesNumber instanceNumber [modality [SOPClass]]
=====================================
debian/NIfTI1ToDicom.1
=====================================
@@ -1,11 +1,9 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10.
-.TH ERROR: "1" "June 2014" "Error: Incorrect number of arguments" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH NIFTI1TODICOM "1" "August 2020" "NIfTI1ToDicom 20200416" "User Commands"
.SH NAME
-Error: \- Works with DICOM files
+NIfTI1ToDicom \- Works with DICOM files
.SH SYNOPSIS
.B NIfTI1ToDicom
-\fIinputFile outputFile patientName patientID studyID seriesNumber instanceNumber \fR[\fImodality \fR[\fISOPClass\fR]]
+\fI\,inputFile outputFile patientName patientID studyID seriesNumber instanceNumber \/\fR[\fI\,modality \/\fR[\fI\,SOPClass\/\fR]]
.SH DESCRIPTION
Error: Incorrect number of arguments
-.PP
-Usage: NIfTI1ToDicom inputFile outputFile patientName patientID studyID seriesNumber instanceNumber [modality [SOPClass]]
=====================================
debian/NRRDToDicom.1
=====================================
@@ -1,11 +1,9 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10.
-.TH ERROR: "1" "June 2014" "Error: Incorrect number of arguments" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH NRRDTODICOM "1" "August 2020" "NRRDToDicom 20200416" "User Commands"
.SH NAME
-Error: \- Works with DICOM files
+NRRDToDicom \- Works with DICOM files
.SH SYNOPSIS
.B NRRDToDicom
-\fIinputFile outputFile patientName patientID studyID seriesNumber instanceNumber \fR[\fImodality \fR[\fISOPClass\fR]]
+\fI\,inputFile outputFile patientName patientID studyID seriesNumber instanceNumber \/\fR[\fI\,modality \/\fR[\fI\,SOPClass\/\fR]]
.SH DESCRIPTION
Error: Incorrect number of arguments
-.PP
-Usage: NRRDToDicom inputFile outputFile patientName patientID studyID seriesNumber instanceNumber [modality [SOPClass]]
=====================================
debian/PDFToDicomImage.1
=====================================
@@ -1,10 +1,9 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10.
-.TH JAVA.LANG.ARRAYINDEXOUTOFBOUNDSEXCEPTION: "1" "June 2014" "java.lang.ArrayIndexOutOfBoundsException: 1" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH PDFTODICOMIMAGE "1" "August 2020" "PDFToDicomImage 20200416" "User Commands"
.SH NAME
-java.lang.ArrayIndexOutOfBoundsException: \- Works with DICOM files
+PDFToDicomImage \- Works with DICOM files
+.SH SYNOPSIS
+.B PDFToDicomImage
+\fI\,inputFile outputFile patientName patientID studyID seriesNumber instanceNumber requestedDpi\/\fR
.SH DESCRIPTION
-java.lang.ArrayIndexOutOfBoundsException: 1
-.IP
-at com.pixelmed.dicom.PDFToDicomImage.main(PDFToDicomImage.java:193)
-.IP
-at com.pixelmed.dicom.PDFToDicomImage.main(PDFToDicomImage.java:193)
+Error: Incorrect number of arguments
=====================================
debian/StructuredReport.1
=====================================
@@ -1,20 +1,9 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10.
-.TH JAVA.IO.FILENOTFOUNDEXCEPTION: "1" "June 2014" "java.io.FileNotFoundException: --version (No such file or directory)" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH STRUCTUREDREPORT "1" "August 2020" "StructuredReport 20200416" "User Commands"
.SH NAME
-java.io.FileNotFoundException: \- Works with DICOM files
+StructuredReport \- Works with DICOM files
+.SH SYNOPSIS
+.B Structured
+\fI\,dicom_sr_filename\/\fR
.SH DESCRIPTION
-java.io.FileNotFoundException: \fB\-\-help\fR (No such file or directory)
-.IP
-at java.io.FileInputStream.open(Native Method)
-at java.io.FileInputStream.<init>(FileInputStream.java:137)
-at com.pixelmed.dicom.AttributeList.read(AttributeList.java:1355)
-at com.pixelmed.dicom.AttributeList.read(AttributeList.java:1331)
-at com.pixelmed.dicom.AttributeList.read(AttributeList.java:1484)
-at com.pixelmed.dicom.StructuredReport.main(StructuredReport.java:371)
-.IP
-at java.io.FileInputStream.open(Native Method)
-at java.io.FileInputStream.<init>(FileInputStream.java:137)
-at com.pixelmed.dicom.AttributeList.read(AttributeList.java:1355)
-at com.pixelmed.dicom.AttributeList.read(AttributeList.java:1331)
-at com.pixelmed.dicom.AttributeList.read(AttributeList.java:1484)
-at com.pixelmed.dicom.StructuredReport.main(StructuredReport.java:371)
+Error: Incorrect number of arguments
=====================================
debian/VerificationSOPClassSCU.1
=====================================
@@ -1,11 +1,9 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10.
-.TH ERROR: "1" "June 2014" "Error: Incorrect number of arguments" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH VERIFICATIONSOPCLASSSCU "1" "August 2020" "VerificationSOPClassSCU 20200416" "User Commands"
.SH NAME
-Error: \- Works with DICOM files
+VerificationSOPClassSCU \- Works with DICOM files
.SH SYNOPSIS
.B VerificationSOPClassSCU
-\fIhostname port ae_title called_ae_title \fR[\fISECURE|NONSECURE\fR] [\fIusername\fR] [\fIpassword\fR]
+\fI\,hostname port ae_title called_ae_title \/\fR[\fI\,SECURE|NONSECURE\/\fR] [\fI\,username\/\fR] [\fI\,password\/\fR]
.SH DESCRIPTION
Error: Incorrect number of arguments
-.PP
-Usage: VerificationSOPClassSCU hostname port ae_title called_ae_title [SECURE|NONSECURE] [username] [password]
=====================================
debian/control
=====================================
@@ -15,6 +15,7 @@ Build-Depends-Indep: default-jdk,
libjmdns-java,
libjsonp-java,
libpixelmed-codec-java,
+ libpixelmed-imageio-java,
libvecmath-java
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/pixelmed
@@ -67,7 +68,9 @@ Description: DICOM implementation containing Image Viewer and a ECG Viewer - cli
Package: pixelmed-webstart-apps
Architecture: all
Section: utils
-Depends: libpixelmed-java (= ${binary:Version}), ${misc:Depends}
+Depends: libbcprov-java,
+ libpixelmed-java (= ${binary:Version}),
+ ${misc:Depends}
Description: DICOM implementation containing Image Viewer and a ECG Viewer - jnlp
This is a stand-alone DICOM toolkit that implements code for reading
and creating DICOM data, DICOM network and file support, a database of
=====================================
debian/patches/add_usage.patch
=====================================
@@ -27,7 +27,7 @@ Index: pixelmed/com/pixelmed/validate/DicomSRValidator.java
* @param arg optionally -describe, -donotmatchcase, -checkambiguoustemplate, -checkcontentitemorder, -checktemplateid, then the name of the file containing the DICOM SR instance to be validated
*/
public static void main(String arg[]) {
-+ if (arg.length < 1) {
++ if (arg.length < 1 || arg[0].equals("--help")) {
+ System.err.println("Error: Incorrect number of arguments");
+ System.err.println("Usage: DicomSRValidator dicom_sr_filename");
+ System.exit(1);
@@ -35,3 +35,36 @@ Index: pixelmed/com/pixelmed/validate/DicomSRValidator.java
try {
DicomSRValidator validator = new DicomSRValidator();
boolean describe = false;
+Index: pixelmed/com/pixelmed/dicom/PDFToDicomImage.java
+===================================================================
+--- pixelmed.orig/com/pixelmed/dicom/PDFToDicomImage.java
++++ pixelmed/com/pixelmed/dicom/PDFToDicomImage.java
+@@ -194,6 +194,11 @@ public class PDFToDicomImage {
+ */
+ public static void main(String arg[]) {
+ try {
++ if (arg.length <= 4) {
++ System.err.println("Error: Incorrect number of arguments");
++ System.err.println("Usage: PDFToDicomImage inputFile outputFile patientName patientID studyID seriesNumber instanceNumber requestedDpi");
++ System.exit(1);
++ }
+ new PDFToDicomImage(arg[0],arg[1],arg[2],arg[3],arg[4],arg[5],arg[6],Integer.parseInt(arg[7]));
+ }
+ catch (Exception e) {
+Index: pixelmed/com/pixelmed/dicom/StructuredReport.java
+===================================================================
+--- pixelmed.orig/com/pixelmed/dicom/StructuredReport.java
++++ pixelmed/com/pixelmed/dicom/StructuredReport.java
+@@ -386,6 +386,12 @@ public class StructuredReport implements
+ */
+ public static void main(String arg[]) {
+ try {
++ if (arg.length < 1 || arg[0].equals("--help")) {
++ System.err.println("Error: Incorrect number of arguments");
++ System.err.println("Usage: Structured dicom_sr_filename");
++ System.exit(1);
++ }
++
+ AttributeList list = new AttributeList();
+ list.read(arg[0]);
+ StructuredReport sr = new StructuredReport(list);
=====================================
debian/patches/addmanifest.patch
=====================================
@@ -12,7 +12,7 @@ Index: pixelmed/Makefile
(cd com/pixelmed/test; make all)
date >BUILDDATE
- jar -cvf $@ BUILDDATE COPYRIGHT \
-+ echo "Class-Path: jmdns.jar hsqldb.jar vecmath.jar commons-codec.jar bcprov.jar commons-net2.jar" > manifest.txt
++ echo "Class-Path: jmdns.jar hsqldb.jar vecmath.jar commons-codec.jar bcprov.jar commons-net.jar slf4j-api.jar slf4j-jdk14.jar" > manifest.txt
+ jar -cvfm $@ manifest.txt BUILDDATE COPYRIGHT \
com/pixelmed/display/*.class \
com/pixelmed/display/*.properties \
=====================================
debian/patches/dicomimageviewer.patch
=====================================
@@ -12,4 +12,4 @@ Index: pixelmed/DicomImageViewer.sh
PIXELMEDDIR=.
-java -Xmx512m -Xms512m -cp "${PIXELMEDDIR}/pixelmed.jar:${PIXELMEDDIR}/lib/additional/pixelmed_imageio.jar:${PIXELMEDDIR}/lib/additional/hsqldb.jar:${PIXELMEDDIR}/lib/additional/commons-compress-1.12.jar:${PIXELMEDDIR}/lib/additional/vecmath1.2-1.14.jar:${PIXELMEDDIR}/lib/additional/jmdns.jar:${PIXELMEDDIR}/lib/additional/commons-codec-1.3.jar:${PIXELMEDDIR}/lib/additional/jai_imageio.jar" com.pixelmed.display.DicomImageViewer "${dicomfile}"
-+java -Xmx512m -Xms512m -cp "${PIXELMEDDIR}/pixelmed.jar:${PIXELMEDDIR}/hsqldb.jar:${PIXELMEDDIR}/commons-compress.jar:${PIXELMEDDIR}/vecmath.jar:${PIXELMEDDIR}/jmdns.jar:${PIXELMEDDIR}/commons-codec.jar:${PIXELMEDDIR}/jai_imageio.jar" com.pixelmed.display.DicomImageViewer "${dicomfile}"
++java -Xmx512m -Xms512m -cp "${PIXELMEDDIR}/pixelmed.jar:${PIXELMEDDIR}/pixelmed_imageio.jar:${PIXELMEDDIR}/hsqldb.jar:${PIXELMEDDIR}/commons-compress.jar:${PIXELMEDDIR}/vecmath.jar:${PIXELMEDDIR}/jmdns.jar:${PIXELMEDDIR}/commons-codec.jar:${PIXELMEDDIR}/jai_imageio.jar" com.pixelmed.display.DicomImageViewer "${dicomfile}"
=====================================
debian/patches/jpegblock.patch
=====================================
@@ -1,27 +1,5 @@
-Description: <short summary of the patch>
- TODO: Put a short summary on the line above and replace this paragraph
- with a longer explanation of this change. Complete the meta-information
- with other relevant fields (see below for details). To make it easier, the
- information below has been extracted from the changelog. Adjust it or drop
- it.
- .
- pixelmed (20200416-1) UNRELEASED; urgency=medium
- .
- * Non-maintainer upload.
- *
+Description: Add missing jpeg block redaction jar
Author: Mathieu Malaterre <malat at debian.org>
-
----
-The information above should follow the Patch Tagging Guidelines, please
-checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
-are templates for supplementary fields that you might want to add:
-
-Origin: <vendor|upstream|other>, <url of original patch>
-Bug: <url in upstream bugtracker>
-Bug-Debian: https://bugs.debian.org/<bugnumber>
-Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
-Forwarded: <no|not-needed|url proving that it has been forwarded>
-Reviewed-By: <name and email of someone who approved the patch>
Last-Update: 2020-07-31
--- pixelmed-20200416.orig/com/pixelmed/display/Makefile
=====================================
debian/patches/remove-build-date-file.patch
=====================================
@@ -8,7 +8,7 @@ Index: pixelmed/Makefile
@@ -392,7 +392,7 @@ pixelmed.jar: generateicons
(cd com/pixelmed/test; make all)
date >BUILDDATE
- echo "Class-Path: jmdns.jar hsqldb.jar vecmath.jar commons-codec.jar bcprov.jar commons-net2.jar" > manifest.txt
+ echo "Class-Path: jmdns.jar hsqldb.jar vecmath.jar commons-codec.jar bcprov.jar commons-net.jar slf4j-api.jar slf4j-jdk14.jar" > manifest.txt
- jar -cvfm $@ manifest.txt BUILDDATE COPYRIGHT \
+ jar -cvfm $@ manifest.txt COPYRIGHT \
com/pixelmed/display/*.class \
=====================================
debian/patches/removeicon.patch
=====================================
@@ -11,7 +11,7 @@ Index: pixelmed/icons/Makefile
WatchFolderAndSend.png
-all: ${DERIVEDPNG1024FILES} ${PNG256FILES} ${ICOFILES} ${ICONFILES}
-+all: #${DERIVEDPNG1024FILES} ${PNG256FILES} #${ICOFILES} ${ICONFILES}
++all: #${DERIVEDPNG1024FILES} ${PNG256FILES} ${ICOFILES} ${ICONFILES}
PATHTOROOT = ..
=====================================
debian/patches/set_java_home.patch
=====================================
@@ -54,3 +54,28 @@ Index: pixelmed/com/pixelmed/utils/Makefile
-classpath ${PATHTOROOT}:${JPEGBLOCKREDACTIONJAR} \
-sourcepath ${PATHTOROOT} $<
+Index: pixelmed/com/pixelmed/convert/Makefile
+===================================================================
+--- pixelmed.orig/com/pixelmed/convert/Makefile
++++ pixelmed/com/pixelmed/convert/Makefile
+@@ -37,7 +37,7 @@ include ${PATHTOROOT}/Makefile.common.mk
+
+ # override javac command in Makefile.common.mk to add javax.json-api-1.0.jar to classpath for RawImageDescription
+ .java.class:
+- export JAVAVERSIONTARGETJARFILE=`/usr/libexec/java_home -v ${JAVAVERSIONTARGET} | tail -1`/jre/lib/rt.jar; javac ${JAVACOPTIONS} \
++ export JAVAVERSIONTARGETJARFILE=${JAVA_HOME}/jre/lib/rt.jar; javac ${JAVACOPTIONS} \
+ -classpath ${PATHTOROOT}:${SLF4JCOMPILEADDITIONALJAR}:${DICOMADDITIONALJARS}:${VIEWERADDITIONALJARS}:${FTPADDITIONALJARS}:${JUNITJAR}:${PATHTOADDITIONAL}/javax.json-api-1.0.jar \
+ -sourcepath ${PATHTOROOT} $<
+
+Index: pixelmed/com/pixelmed/slf4j/Makefile
+===================================================================
+--- pixelmed.orig/com/pixelmed/slf4j/Makefile
++++ pixelmed/com/pixelmed/slf4j/Makefile
+@@ -10,6 +10,6 @@ include ${PATHTOROOT}/Makefile.common.mk
+
+ # override javac command in Makefile.common.mk to add slf4j to classpath
+ .java.class:
+- export JAVAVERSIONTARGETJARFILE=`/usr/libexec/java_home -v ${JAVAVERSIONTARGET} | tail -1`/jre/lib/rt.jar; javac ${JAVACOPTIONS} -Xlint:unchecked \
++ export JAVAVERSIONTARGETJARFILE=${JAVA_HOME}/jre/lib/rt.jar; javac ${JAVACOPTIONS} -Xlint:unchecked \
+ -classpath ${PATHTOROOT}:${SLF4JCOMPILEADDITIONALJAR} \
+ -sourcepath ${PATHTOROOT}:${SLF4JCOMPILEADDITIONALJAR} $<
=====================================
debian/rules
=====================================
@@ -33,8 +33,10 @@ override_dh_clean:
# doc package:
rm -rf docs
+VER_FULL = $(shell dpkg-parsechangelog | grep '^Version' | cut -d' ' -f2 | cut -f1 -d-)
+
debian/%.1:
- help2man --name="Works with DICOM files" --no-discard-stderr --output=$@ --no-info `basename $@ .1`
+ help2man --name="Works with DICOM files" --no-discard-stderr --output=$@ --version-string=$(VER_FULL) --no-info `basename $@ .1`
pixelmed_manpages: debian/DicomSRValidator.1 debian/ImageToDicom.1 debian/NIfTI1ToDicom.1 debian/NRRDToDicom.1 debian/PDFToDicomImage.1 debian/StructuredReport.1 debian/VerificationSOPClassSCU.1
echo "all manpages done"
View it on GitLab: https://salsa.debian.org/med-team/pixelmed/-/compare/c78d44f262719d4df56a33bc5edddf5162354afb...c63749fa1f9dcc80c495fbf1bc642f456b1a49a8
--
View it on GitLab: https://salsa.debian.org/med-team/pixelmed/-/compare/c78d44f262719d4df56a33bc5edddf5162354afb...c63749fa1f9dcc80c495fbf1bc642f456b1a49a8
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