Adventures & experiences in contemporary technology
While I continue to use Spyder as my preferred Python code editor, I also tried out Visual Studio Code. Handily, this Integrated Development Environment also has facilities for working with R and Julia code as well as MarkDown text editing and adding the required extensions is enough for these applications; it helps that there is an unofficial Grammarly extension for content creation.
My Python code development makes use of the Pylance extension and it works a little differently from Spyder when it comes to including files using import statements. Spyder will look into the folder where the base script is located but the default behaviour of Pylance is that it looks in the root path of your workspace. This meant that any code that ran successfully in Spyder failed in Visual Studio Code.
The way around this was to add the required location using the python.analysis.extraPaths setting for the workspace. That meant opening Settings by navigating to File > Preferences > Settings in the menu system and entering python.analysis.extraPaths into the search box. That took me to the section that I needed and I then clicked on Add Item before entering the required path and clicking on the OK button. That was enough to fix the problem and all worked as it should after that.
Recently, I had someone ask me how to create PNG files in SAS using ODS Graphics so I sought out the answer for them. Normally, the suggestion would have been to create RTF or PDF files instead but there was a specific need so a different approach was taken. Adding the something like following lines before an SGPLOT, SGPANEL or SGRENDER procedure does the needful:
ods listing gpath='E:\';
ods graphics / imagename="test" imagefmt=png;
Here, the ODS LISTING statement declares the destination for the desired graphics file while the ODS GRAPHICS statement defines the file name and type. In the above example, the file test.png would be created in the root of the E drive of a Windows machine. However, this also works with Linux or UNIX directory paths.
Over the weekend, I finally got to fixing a problem that has affected Ubuntu 18.04 virtual machine for quite a while. The usual checks on Guest Additions installation and vboxsf group access assignment were performed but were not causing the issue. Also, no other VM (Windows (7 & 10) and Linux Mint Debian Edition) on the same Linux Mint 19.2 machine was experiencing the same issue. The latter observation made the problem intrinsic to the Ubuntu VM itself.
Because I install the Guest Additions software from the included virtual CD, I executed the following command to open the relevant file for editing:
sudo systemctl edit --full vboxadd-service
If I had installed installed virtualbox-guest-dkms and virtualbox-guest-utils from the Ubuntu repositories instead, then this would have been the command that I needed to execute instead of the above.
sudo systemctl edit --full virtualbox-guest-utils
Whichever configuration gets opened, the line that needs attention is the one beginning with Conflicts (line 6 in the file on my system). The required edit removes systemd-timesync.service from the list following the equals sign. It is worth checking that file paths include the correct version number for the Guest Additions software that is installed in case this was not the case. The only change that was needed on my Ubuntu VM was to the Conflicts line and rebooting it got the Shared Folder automatically mounted under the /media directory as expected.
Because updating Piwik using its web interface has proved tempestuous, I have decided update the self-hosted analytics application an ssh session. The production web servers that I use are hosted on Linux systems so that is why any commands apply to the Linux or UNIX command line only. What is needed for Windows servers may differ.
The first step is to down the required ZIP file with this command:
wget https://builds.piwik.org/piwik.zip
Once the download is complete, the contents of the ZIP archive are extracted into a new subfolder. This is a process that I carry out in a separate folder to that where the website files are kept before copying everything from the extract folder in there. Here is the unzip command and the -o switch turns on overwriting of any previously existing files:
unzip -o piwik.zip
Without the requirement folder in web server area updated, the next step is to do the actual system update that includes any updates to the Piwik database that you are using. There are two commands that you can use once you have specified the location of your Piwik installation. The second is needed when the first option cannot find where the PHP executable is stored. My systems had something more specific than these because both PHP 5.6 and PHP 7.0 are installed. Looking in /usr/bin was enough to find what i needed to execute in place of php below. Otherwise, the command was the same.
./[path to piwik]/console core:update
php [path to piwik]/console core:update
While the upgrade is ongoing, it prompts you to permit it to continue before it goes and makes changes to the database. This did not take long on my systems but that depends on how much data there is. Once, the process has completed, you can delete any extraneous files using the rm command.
My usual method for copying a directory tree without any of the files in there involves the use of the Windows commands line XCOPY and the command takes the following form:
xcopy /t /e <source> <destination>
The /t switch tells XCOPY to copy only the directory structure while the /e one tells it to include empty directories too. Substituting /s for /e would ensure that only non-empty directories are copied. <source> and <destination> are the directory paths that you want to use and need to be enclosed in quotes if you have a space in a directory name.
There is one drawback to this approach that I have discovered. When you have long directory paths, messages about there being insufficient memory are issued and the command fails. The limitation has nothing to do with the machine that you are using but is a limitation of XCOPY itself.
After discovering that, I got to checking if ROBOCOPY can do the same thing without the same file path length limitation because I did not have the liberty of shortening folder names to get the whole path within the length expected by XCOPY. The following is the form of the command that I found did what I needed:
robocopy <source> <destination> /e /xf *.* /r:0 /w:0 /fft
Again, <source> and <destination> are the directory paths that you want to use and need to be enclosed in quotes if you have a space in a directory name. The /e switch copies all subdirectories and not just non-empty ones. Then, the xf *.* portion excludes all files from the copying process. The remaining options are added to help with getting around access issues and to try copy only those directories that do not exist in the destination location. The /ftt switch was added to address the latter by causing ROBOCOPY to assume FAT file times. To get around the folder permission delays, the /r:0 switch was added to stop any operation being retried with /w:0 setting wait times to 0 seconds. All this was enough to achieve what I wanted and I am keeping it on file for my future reference as well as sharing it with you.
At the time of writing, Google Drive is unable to accept DNG files, the Adobe file type for RAW images from digital cameras. The uploads themselves work fine but the additional processing at the end that I believe is needed for Google Photos appears to be failing. Because of this, I thought of other possibilities like uploading them to Dropbox or enclosing them in ZIP archives instead; of these, it is the first that I have been doing and with nothing but success so far. Another idea is to convert the files into an image format that Google Drive can handle and TIFF came to mind because it keeps all the detail from the original image. In contrast, JPEG files lose some information because of the nature of the compression.
Handily, a one line command does the conversion for all files in a directory once you have all the required software installed:
find -type f | grep -i “DNG” | parallel mogrify -format tiff {}
The find and grep commands are standard with the first getting you a list of all the files in the current directory and sending (piping) these to the grep command so the list only retains the names of all DNG files. The last part uses two commands for which I found installation was needed on my Linux Mint machine. The parallel package is the first of these and distributes the heavy workload across all the cores in your processor and this command will add it to your system:
sudo apt-get install parallel
The mogrify command is part of the ImageMagick suite along with others like convert and this is how you add that to your system:
sudo apt-get install imagemagick
In the command at the top, the parallel command works through all the files in the list provided to it and feeds them to mogrify for conversion. Without the use of parallel, the basic command is like this:
mogrify -format tiff *.DNG
In both cases, the -format switch specifies the output file type with tiff triggering the creation of TIFF files. The *.DNG portion itself captures all DNG files in a directory but {} does this in the main command at the top of this post. If you wanted JPEG ones, you would replace tiff with jpg. Shoudl you ever need them, a full list of what file types are supported is produced using the identify command (also part of ImageMagick) as follows:
identify -list format
In the world of UNIX and Linux, symbolic links are shortcuts but they do not work like normal Windows shortcuts because you do not jump from one location to another with the file manager’s address bar changing what it shows. Instead, it is as if you see the contents of the directory at another quicker to access location in the file system and the same sort of thinking applies to files too. In some ways, it is like giving files and directories alternative aliases. There are soft links that point to the name of a given directory or file and hard links that point to actual files or directories.
For a long time, I was under the mistaken impression that such things did not exist in Windows until I came across the mklink command, which came with the launch of Windows Vista at the start of 2007. While the then new feature may not be an obvious to most of us, it does does that Windows did incorporate a feature from UNIX and Linux well before the advent of virtual desktops on Windows 10.
By default, the aforementioned command sets up symbolic links to files and the /D switch allows the same to be done for directories too. The /H switch makes a hard link instead of a soft link so we get much of the functionality of the ln command in UNIX and Linux. Here is an example that creates a soft symbolic link for a directory:
mklink /D shortcut target_directory
Above, shortcut is the name of the symbolic link file and target_directory is the destination to which it links. In my experience, it works best for destinations beyond your home folder and, from what I have read, hard links may not be possible across different disks either.
The progress of Windows 10 is something that I have been watching. Early signs have been promising and the most recent live event certainly contained its share of excitement. The subsequent build that was released was another step in the journey though the new Start Menu appears more of a work in progress than it did in previous builds. Keeping up with these advances sometimes steps ahead of VirtualBox support for them and I discovered that again in the last few days. VMware Player seems unaffected so I thought that I’d try a migration of the VirtualBox VM with Windows 10 onto there. In the past, I did something similar with a 32-bit instance of Windows 7 that subsequently got upgraded all the the way up to 8.1 but that may not have been as slick as the latest effort so I thought that I would share it here.
The first step was to export the virtual machine as an OVF appliance and I used File > Export Appliance… only to make a foolish choice regarding the version of OVF. The one that I picked was 2.0 and I subsequently discovered that 1.0 was the better option. The equivalent command line would look like the following (there are two dashes before the ovf10 option below):
VboxManage export [name of VM] -o [name of file].ova --ovf10
VMware have a tool for extracting virtual machines from OVF files that will generate a set of files that will work with Player and other similar products of theirs. It goes under the unsurprising name of OVF Tool and it usefully works from a command line session. When I first tried it with an OVF 2.0 files, I got the following error and it stopped doing anything as a result:
Line 2: Incorrect namespace http://schemas.dmtf.org/ovf/envelope/2 found.
The only solution was to create a version 1.0 file and use a command like the following (it’s a single line though it wraps over two here and there are two dashes before the lax switch):
ovftool --lax [name of file].ova [directory location of VM files]/[name of file].vmx
The --lax option is needed to ensure successful execution even with an OVF 1.0 file as the input. Once I had done this on my Ubuntu GNOME system, the virtual machine could be opened up on VMware Player and I could use the latest build of Windows 10 at full screen, something that was not possible with VirtualBox. This may be how I survey the various builds of the operating that appear before its final edition is launched later this year.
It seems that the Rename-Item commandlet in Powershell is a very useful tool when it comes to smarter renaming of files. Even text substitution is a possibility and what follows is an example that takes the output of the Dir command for listing the files in a directory and replaces hyphens with underscores in each one.
Dir | Rename-Item –NewName { $_.name –replace “-“,”_” }
The result is that something like the-file.txt becomes the_file.txt. This behaviour is reminiscent of the rename command found on Linux and UNIX systems, where regular expressions can be used like in the following example that has the same result as the above:
rename ‘s/-/_/g’ *
In both cases, you do need to be careful as to what files are in a directory for this though the wildcard syntax on Linux or UNIX will be more familiar who has worked with files via almost any command line. Another thing to watch in the UNIX world is that ** parses the whole directory structure and that could be something that is not wanted for much of the time.
All of this is a far cry from the capabilities of the ren or rename command used in the days of MS-DOS and what has become the legacy Windows command line. Apart from simple renaming, any attempt at tweaking a filename through substitution ended up with the extra string getting appended to filenames when I tried it. Thus, the Powershell option looks better in comparison.
It appears that PROC SGPLOT and other statistical graphics procedures create image files even if you are creating RTF or PDF files. By default, these are PNG files but there are other possibilities. When working with PC SAS , I have seen them written to the current working directory and that could clutter up your folder structure, especially if they are unwanted.
Being unable to track down a setting that controls this behaviour, I resolved to find a way around it by sending the files to the SAS work directory so they are removed when a SAS session is ended. One option is to set the session’s working directory to be the SAS work one and that can be done in SAS code without needing to use the user interface. As a result, you get some automation.
The method is implicit though in that you need to use an X statement to tell the operating system to change folder for you. Here is the line of code that I have used:
x "cd %sysfunc(pathname(work))";
The X statement passes commands to an operating system’s command line and they are enclosed in quotes. %sysfunc then is a macro command that allows certain data step functions or call routines as well as some SCL functions to be executed. An example of the latter is pathname and this resolves library or file references and it is interrogating the location of the SAS work library here so it can be passed to the operating systems cd (change directory) command for processing. This method works on Windows and UNIX so Linux should be covered too, offering a certain amount of automation since you don’t have to specify the location of the SAS work library in every session due to the folder name changing all the while.
Of course, if someone were to tell me of another way to declare the location of the generated PNG files that works with RTF and PDF ODS destinations, then I would be all ears. Even direct output without image file creation would be even better. Until then though, the above will do nicely.