DFpdfpkg — Generate multiple bookmarked PDF files for specified subject IDs or sites
DFpdfpkg
[-S server]
[-U username]
[-C password]
[-A]
[-n]
[-color]
[-hd]
[-b blind_spec]
[-f filemap]
[-v visitmap]
[-g pagemap]
[-s sortmap]
[-t title]
[-j header]
[-k footer]
[
[-P pdfpasswd]
]
[-history
[-bookmark label]
]
{
[-data data,missed]
[-image primary|all]
}
{-output out_dir_name
}
[-prefix file_prefix]
{
[-subject pid_list]
[-site site_list]
}
[-visit visnum_list]
[-plate pltnum_list]
[-e errlog]
{study#}
DFpdfpkg generates a set of optionally password-protected PDF documents (one per subject) containing one or more pages representing data records (EDC, fax, email, DFsend), and images and audit trail information. The resulting PDF documents follow the Adobe PDF specification, version 1.4, and as a result can be read by Acrobat Reader versions 5.X and greater.
If a password is provided, files are encrypted and stored in binary format. Otherwise, the file is stored in plain text format.
DFpdfpkg requires a study number argument and an output folder name.
Records are output ascending numeric order
by visit and plate. If the -s
option is specified, sort order
will follow the rules specified by the DFsortmap file.
Bookmarks are created at the document root, ID, visit, and plate levels. The
label for the document root bookmark is ID, Visit, Plate
but can be
over-ridden through the use of -t.
A visit bookmark is created for each new visit number
within the current ID. The label is created from
field 3 of the study visit map
if the visit is defined in the visit map; otherwise,
it has the form Visit .
A plate bookmark is created for each CRF in the visit.
The label is created from the matching page map entry, if it is defined;
from field 2 of the study DFfilemap if the plate is defined
(which it should always be); or, it has the form
#####Plate .
For secondary records, an asterisk
(#####*) is appended to the end of the page bookmark label. Hence it is easy to
scan the list of expanded bookmarks and identify those records that are
secondaries.
Using the -j and -k options, custom page
header and footer labels, respectively, can be created for each CRF page
in the output document.
If no labels are specified, the default header label is
ID %DFID : %DFPMLBL and there is no footer label.
The desired label is specified in a string
[12]
and may contain any combination
of fixed text and zero or more of the following keywords, which are
replaced at output creation time with the matching database value:
%DFSTATUS - record status (the status label is returned, rather
than the status number)
%DFVALID - record validation level
%DFRASTER - image ID
%DFSTUDY - DFdiscover study number
%DFPLATE - plate number
%DFSEQ - visit or sequence number
%DFID - subject ID
%DFCREATE - record creation time stamp
%DFMODIFY - record modification time stamp
%DFPMLBL - page map label for the current keys as defined in
DFpage_map
%DFVLBL - visit label for the current keys as defined in
DFvisit_map
%DFPLBL - plate label for the current keys as defined
in DFschema
It is possible to override the default labeling for study visits and plates
by providing alternative visit map, file map, and page map files with the
-v, -f, and -g
options respectively.
-S server | DFdiscover server name |
-U username | DFdiscover login username |
-C password | login password. Refer to Section 3.2, “User Credentials” for recommended/better solutions for safe password handling. |
-A | output PDF in A4 size |
-n | nest visits within plates |
-color | apply field color to completed pages |
-hd | output the PDF file with images in higher definition (HD), which is 300dpi while the default standard definition (SD) is 100dpi. |
-b string | allows the specification of fields to be blinded (blanked out)
in the output PDF file.
The plate:field,field,field;plate:field,field
where Field numbers that are not valid for the plate are skipped. Where multiple plates are required, plate specifications are separated by semi-colons.
To implement the blindlist, DFpdf must read the study setup file.
The study
setup file may be provided with
|
-f filemap | alternate study filemap |
-v visitmap | alternate study visitmap |
-g pagemap | alternate study pagemap |
-s string | allows the specification of sort order by an external file. The file is expected to be in query sort order format. Without this option, no sorting of the input file is performed and images appear in the PDF document in the order that records appear in the input file. With this option, consecutive records for the same ID are sorted to follow the rules stated by the sortmap file. Note that no sorting is performed across IDs, only within IDs, and only when the IDs appear consecutively in the input file. |
-t string | the title to appear at the top of the
bookmark list. If a title is supplied, in addition to setting the text of
the bookmark title object, the title is also set in the document information
(which is accessed from the Reader's "Document Info-General-Title"
attribute. If the title contains any characters that are meaningful to the
shell, including spaces, the title must be enclosed in double quotes.
If no title is supplied, the default title of
|
-j string | customize the page header label using a combination of fixed
text and references to key and meta information. The default header is
|
-k string | customize the page footer label using a combination of fixed text and references to key and meta information. The default footer is blank. |
-P password |
If |
-history | data and metadata change history. This outputs the audit trail for each record. |
-bookmark label | bookmark label for history |
-data data,missed | data record options. Data records are included for the record types listed - data for records that include EDC and image-based, or missed which includes any records marked as missed. |
-image primary|all | image options. Include only primary images or include all images attached to a record. |
-output dirname | output folder for PDFs (required). This must be the full path to an existing directory or folder that is writable by the user. |
-prefix file_prefix | PDF file prefix. Each file written to the output directory with a filename comprised of the prefix and the subject ID. |
-subject pid_list | subject ID list. Output packages for the subject IDs in this comma-delimited list. |
-site site_list | site number list. Output packages for the subject IDs that belong to sites in this comma-delimited list. |
-visit visnum_list | visit number list. Include pages with the specified visit numbers. |
-plate pltnum_list | plate number list. Include pages with the specified plate numbers. |
-e errlog | error log file. Write any error or warning message to this filename. The default is to write any error or warning messages to stderr. |
| the DFdiscover study number (required) |
DFpdfpkg exits with one of the following statuses:
0 | The command was successful, one or more PDF output files were created. |
1 | The command was not successful. |
Example 3.62. Use DFpdfpkg without the use of the DFexplore option
The following example creates subject packages for subject ID 2035 and 2049 from Site 2.
% DFpdfpkg -S example.server.com -U example_user -C passwd \
-t "Site 2 Subject Packages" -color -data data -image primary \
-output /opt/studies/demo253/work -prefix "Site2_" \
-subject 2035,2049 253
[12] If the string contains characters that are meaningful to the shell, such as space, quote, percent, etc., then the entire string must be enclosed in double quotes. The string can always be enclosed in double quotes, to ensure that no characters are interpreted by the shell.