Issue 553: add --skip-group-datablock option (#554)

* add --skip-group-datablock option

* check if odfile is not empty

* apply pep8

ChangeLog

@@ -1,6 +1,7 @@
 2023-12-19 Jan Kotanski <jankotan@gmail.com>
 	* fix convention for entry names in multi-scan NeXus files (#552)
-	* tagged as v3.55.1
+	* add --skip-group-datablock option (#554)
+	* tagged as v3.56.0
 
 2023-12-15 Jan Kotanski <jankotan@gmail.com>
 	* add support for fetching metadata from multi-scan Nexus files (#542)

doc/nxsfileinfo.rst

@@ -384,8 +384,11 @@ Options:
   -p PID, --pid PID     dataset pid
   --raw                 raw dataset type
   -i BEAMTIMEID, --beamtimeid  BEAMTIMEID beamtime id
+  -s, --skip-group-datablock
+                        skip group datablock
   -w, --allow-duplication
                         allow to merge metadata with duplicated pid
+  -q, --raw             raw dataset type
   -f, --write-files     write output to files
   -k SCICATVERSION, --scicat-version SCICATVERSION
                         major scicat version metadata

man/nxscollect.1

@@ -1,5 +1,8 @@
 .\" Man page generated from reStructuredText.
 .
+.TH "NXSCOLLECT" "1" "Dec 20, 2023" "3.56" "NXSTools"
+.SH NAME
+nxscollect \- upload external images into NeXus/HDF5 file
 .
 .nr rst2man-indent-level 0
 .
@@ -27,9 +30,6 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
 .\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
 .in \\n[rst2man-indent\\n[rst2man-indent-level]]u
 ..
-.TH "NXSCOLLECT" "1" "Dec 17, 2023" "3.55" "NXSTools"
-.SH NAME
-nxscollect \- upload external images into NeXus/HDF5 file
 .SH DESCRIPTION
 .sp
 The nxscollect is  a command\-line tool dedicated to collect detector images.
@@ -61,7 +61,7 @@ nexus_file            nexus files to be collected
 .B Options:
 .INDENT 7.0
 .TP
-.B  \-h\fP,\fB  \-\-help
+.B \-h\fP,\fB  \-\-help
 show this help message and exit
 .TP
 .BI \-c \ COMPRESSION\fR,\fB \ \-\-compression \ COMPRESSION
@@ -88,20 +88,20 @@ datatype of input data \- only for raw data, e.g.
 shape of input data \- only for raw data, e.g.
 ‘[4096,2048]’
 .TP
-.B  \-s\fP,\fB  \-\-skip_missing
+.B \-s\fP,\fB  \-\-skip_missing
 skip missing files
 .TP
-.B  \-r\fP,\fB  \-\-replace_nexus_file
+.B \-r\fP,\fB  \-\-replace_nexus_file
 if it is set the old file is not copied into a file
 with .__nxscollect__old__* extension
 .TP
-.B  \-\-test
+.B \-\-test
 execute in the test mode
 .TP
-.B  \-\-h5py
+.B \-\-h5py
 use h5py module as a nexus reader/writer
 .TP
-.B  \-\-h5cpp
+.B \-\-h5cpp
 use h5cpp module as a nexus reader/writer
 .UNINDENT
 .UNINDENT
@@ -142,7 +142,7 @@ nexus_file_path       nexus files with the nexus directory to place the link
 .B Options:
 .INDENT 7.0
 .TP
-.B  \-h\fP,\fB  \-\-help
+.B \-h\fP,\fB  \-\-help
 show this help message and exit
 .TP
 .BI \-n \ NAME\fR,\fB \ \-\-name \ NAME
@@ -151,17 +151,17 @@ link name
 .BI \-t \ TARGET\fR,\fB \ \-\-target \ TARGET
 link target with the file name if external
 .TP
-.B  \-r\fP,\fB  \-\-replace_nexus_file
+.B \-r\fP,\fB  \-\-replace_nexus_file
 if it is set the old file is not copied into a file
 with .__nxscollect__old__* extension
 .TP
-.B  \-\-test
+.B \-\-test
 execute in the test mode
 .TP
-.B  \-\-h5py
+.B \-\-h5py
 use h5py module as a nexus reader/writer
 .TP
-.B  \-\-h5cpp
+.B \-\-h5cpp
 use h5cpp module as a nexus reader
 .UNINDENT
 .UNINDENT
@@ -205,7 +205,7 @@ Options:
 .INDENT 3.5
 .INDENT 0.0
 .TP
-.B  \-h\fP,\fB  \-\-help
+.B \-h\fP,\fB  \-\-help
 show this help message and exit
 .TP
 .BI \-t \ DTYPE\fR,\fB \ \-\-dtype \ DTYPE
@@ -304,17 +304,17 @@ sepatated by ‘,’ and different fields separated by ‘;’
 or spaces e.g. ‘:,0:50,: :,0:50,:’ where U means span
 along the layout
 .TP
-.B  \-r\fP,\fB  \-\-replace\-nexus\-file
+.B \-r\fP,\fB  \-\-replace\-nexus\-file
 if it is set the old file is not copied into a file
 with .__nxscollect__old__* extension
 .TP
-.B  \-\-test
+.B \-\-test
 execute in the test mode
 .TP
-.B  \-\-h5cpp
+.B \-\-h5cpp
 use h5cpp module as a nexus reader
 .TP
-.B  \-\-h5py
+.B \-\-h5py
 use h5py module as a nexus reader/writer
 .UNINDENT
 .UNINDENT

man/nxsconfig.1

@@ -1,5 +1,8 @@
 .\" Man page generated from reStructuredText.
 .
+.TH "NXSCONFIG" "1" "Dec 20, 2023" "3.56" "NXSTools"
+.SH NAME
+nxsconfig \- read NeXus Configuration Server settings
 .
 .nr rst2man-indent-level 0
 .
@@ -27,9 +30,6 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
 .\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
 .in \\n[rst2man-indent\\n[rst2man-indent-level]]u
 ..
-.TH "NXSCONFIG" "1" "Dec 17, 2023" "3.55" "NXSTools"
-.SH NAME
-nxsconfig \- read NeXus Configuration Server settings
 .SH DESCRIPTION
 .sp
 The nxsconfig program
@@ -132,25 +132,25 @@ show transformation parameters of given components
 .B Options:
 .INDENT 7.0
 .TP
-.B  \-h\fP,\fB  \-\-help
+.B \-h\fP,\fB  \-\-help
 show this help message and exit
 .TP
 .BI \-s \ SERVER\fR,\fB \ \-\-server\fB= SERVER
 configuration server device name
 .TP
-.B  \-d\fP,\fB  \-\-datasources
+.B \-d\fP,\fB  \-\-datasources
 perform operation on datasources
 .TP
-.B  \-m\fP,\fB  \-\-mandatory
+.B \-m\fP,\fB  \-\-mandatory
 make use mandatory components as well
 .TP
-.B  \-p\fP,\fB  \-\-private
+.B \-p\fP,\fB  \-\-private
 make use private components, i.e. starting with ‘__’
 .TP
-.B  \-n\fP,\fB  \-\-no\-newlines
+.B \-n\fP,\fB  \-\-no\-newlines
 split result with space characters
 .TP
-.B  \-f\fP,\fB  \-\-force
+.B \-f\fP,\fB  \-\-force
 do not ask
 .UNINDENT
 .UNINDENT