Install Fails when Directory name has a space in it

[digitaluniverse]

Description

Install Fails when Directory name has a space in it

Steps to Reproduce

Created a APFS Volume called 'Spine Data'
cd /Volumes/Spine\ Data/
Cloned the Repo to the main directory.
git clone https://github.com/neuropoly/spinalcordtoolbox
cd into spinalcordtoolbox folder
cd spinalcordtoolbox
Run Install
./install_sct
Install to current directory
Y

I just renamed the Volume to 'Spine' to get it working but adding handling for directory names with spaces might be a good idea

[jcohenadad]

Thank you for reporting this issue @digitaluniverse ! I am linking some related issues below to help the team get more context about how we have been treating this problem up to now:

• Check for space character " " in directory trees #2785
• System calls fail if the path contains a space #1095
• testing procedure should be run with folders that have spaces in them #259
• issue related to folder names with "space" #251

[joshuacwnewton]

Thank you for opening this issue!

I can reproduce this issue. Below, I've added the full log for ./install_sct -v:

Install log

❯ ./install_sct -v
 Full verbose!
+ getopts :iydbvh opt
+ trap detectKeyboardInterrupt INT
+ trap finish EXIT
+ print info '
*******************************
* Welcome to SCT installation *
*******************************
'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32m
*******************************
* Welcome to SCT installation *
*******************************
\033[0m\n'


*******************************
* Welcome to SCT installation *
*******************************


+ fetch_os_type
+ print info 'Checking OS type and version...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mChecking OS type and version...\033[0m\n'

Checking OS type and version...

+ OSver=unknown
++ uname -a
+ uname_output='Linux XPS-15-9560 5.8.0-50-generic #56~20.04.1-Ubuntu SMP Mon Apr 12 21:46:35 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'
+ echo 'Linux XPS-15-9560 5.8.0-50-generic #56~20.04.1-Ubuntu SMP Mon Apr 12 21:46:35 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'
Linux XPS-15-9560 5.8.0-50-generic #56~20.04.1-Ubuntu SMP Mon Apr 12 21:46:35 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
+ echo 'Linux XPS-15-9560 5.8.0-50-generic #56~20.04.1-Ubuntu SMP Mon Apr 12 21:46:35 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'
+ grep -i darwin
+ echo 'Linux XPS-15-9560 5.8.0-50-generic #56~20.04.1-Ubuntu SMP Mon Apr 12 21:46:35 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'
+ grep -i linux
+ OS=linux
+ check_requirements
+ print info 'Checking requirements...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mChecking requirements...\033[0m\n'

Checking requirements...

++ command -v curl
+ [[ -n /usr/bin/curl ]]
+ gcc --version
+ print info 'OK!'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mOK!\033[0m\n'

OK!

+ [[ -e spinalcordtoolbox/version.txt ]]
++ cat spinalcordtoolbox/version.txt
+ SCT_VERSION=dev
+ [[ -z '' ]]
+ [[ -d .git ]]
+ SCT_INSTALL_TYPE=in-place
+ get_shell_rc_path
+ [[ /usr/bin/zsh == *\b\a\s\h* ]]
+ [[ /usr/bin/zsh == *\/\s\h* ]]
+ [[ /usr/bin/zsh == *\z\s\h* ]]
+ THE_RC=bash
+ RC_FILE_PATH=/home/joshua/.zshrc
+ echo -e '\nSCT version ......... dev'

SCT version ......... dev
+ echo -e 'Installation type ... in-place'
Installation type ... in-place
+ echo -e 'Operating system .... linux (unknown)'
Operating system .... linux (unknown)
+ echo -e 'Shell config ........ /home/joshua/.zshrc'
Shell config ........ /home/joshua/.zshrc
+ REPORT_STATS=no
+ '[' -z '' ']'
+ print question 'To improve user experience and fix bugs, the SCT development team is using a
report system to automatically receive crash reports and errors from users.
These reports are anonymous.

Do you agree to help us improve SCT? [y]es/[n]o: '
+ type=question
+ shift
+ case "$type" in
+ echo -e -n '\n\033[0;92mTo improve user experience and fix bugs, the SCT development team is using a
report system to automatically receive crash reports and errors from users.
These reports are anonymous.

Do you agree to help us improve SCT? [y]es/[n]o: \033[0m'

To improve user experience and fix bugs, the SCT development team is using a
report system to automatically receive crash reports and errors from users.
These reports are anonymous.

Do you agree to help us improve SCT? [y]es/[n]o: + read -r REPORT_STATS
n
+ [[ n =~ [Yy](es)? ]]
+ print info '--> Crash reports will not be sent.'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32m--> Crash reports will not be sent.\033[0m\n'

--> Crash reports will not be sent.

+ [[ in-place == \i\n\-\p\l\a\c\e ]]
+ SCT_DIR='/home/joshua/Desktop/Test Directory/spinalcordtoolbox'
+ true
+ keep_default_path=
+ [[ ! '' =~ ^([Yy](es)?|[Nn]o?)$ ]]
+ print info 'SCT will be installed here: [/home/joshua/Desktop/Test Directory/spinalcordtoolbox]'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mSCT will be installed here: [/home/joshua/Desktop/Test Directory/spinalcordtoolbox]\033[0m\n'

SCT will be installed here: [/home/joshua/Desktop/Test Directory/spinalcordtoolbox]

+ keep_default_path=yes
+ '[' -z '' ']'
+ print question '
Do you agree? [y]es/[n]o: '
+ type=question
+ shift
+ case "$type" in
+ echo -e -n '\n\033[0;92m
Do you agree? [y]es/[n]o: \033[0m'


Do you agree? [y]es/[n]o: + read -r keep_default_path
y
+ [[ ! y =~ ^([Yy](es)?|[Nn]o?)$ ]]
+ [[ y =~ ^[Yy] ]]
+ break
+ add_to_path=
+ [[ ! '' =~ ^([Yy](es)?|[Nn]o?)$ ]]
+ add_to_path=yes
+ '[' -z '' ']'
+ print question 'Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: '
+ type=question
+ shift
+ case "$type" in
+ echo -e -n '\n\033[0;92mDo you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: \033[0m'

Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: + read -r add_to_path
n
+ [[ ! n =~ ^([Yy](es)?|[Nn]o?)$ ]]
+ mkdir -p '/home/joshua/Desktop/Test Directory/spinalcordtoolbox'
+ [[ -d /home/joshua/Desktop/Test Directory/spinalcordtoolbox ]]
+ [[ ! -w /home/joshua/Desktop/Test Directory/spinalcordtoolbox ]]
+ [[ bash == \b\a\s\h ]]
+ DISPLAY_UPDATE_PATH='export PATH="/home/joshua/Desktop/Test Directory/spinalcordtoolbox/bin:$PATH"'
+ [[ -z '' ]]
+ export MPLBACKEND=Agg
+ MPLBACKEND=Agg
+ [[ /home/joshua/Desktop/Test Directory/spinalcordtoolbox != \/\h\o\m\e\/\j\o\s\h\u\a\/\D\e\s\k\t\o\p\/\T\e\s\t\ \D\i\r\e\c\t\o\r\y\/\s\p\i\n\a\l\c\o\r\d\t\o\o\l\b\o\x ]]
+ print info 'Skipping copy of source files (source and destination folders are the same)'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mSkipping copy of source files (source and destination folders are the same)\033[0m\n'

Skipping copy of source files (source and destination folders are the same)

+ [[ -x /home/joshua/Desktop/Test Directory/spinalcordtoolbox/bin ]]
+ cd '/home/joshua/Desktop/Test Directory/spinalcordtoolbox'
+ [[ ! -f spinalcordtoolbox/version.txt ]]
+ print info 'Installing conda...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mInstalling conda...\033[0m\n'

Installing conda...

+ run rm -rf '/home/joshua/Desktop/Test Directory/spinalcordtoolbox/python'
+ print code rm -rf '/home/joshua/Desktop/Test Directory/spinalcordtoolbox/python'
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mrm -rf /home/joshua/Desktop/Test Directory/spinalcordtoolbox/python\033[0m\n'

rm -rf /home/joshua/Desktop/Test Directory/spinalcordtoolbox/python

+ rm -rf '/home/joshua/Desktop/Test Directory/spinalcordtoolbox/python'
+ run mkdir -p '/home/joshua/Desktop/Test Directory/spinalcordtoolbox/python'
+ print code mkdir -p '/home/joshua/Desktop/Test Directory/spinalcordtoolbox/python'
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mmkdir -p /home/joshua/Desktop/Test Directory/spinalcordtoolbox/python\033[0m\n'

mkdir -p /home/joshua/Desktop/Test Directory/spinalcordtoolbox/python

+ mkdir -p '/home/joshua/Desktop/Test Directory/spinalcordtoolbox/python'
+ case $OS in
+ download /tmp/tmp.B02ywAbuYm/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+ command -v wget
+ run wget -O /tmp/tmp.B02ywAbuYm/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+ print code wget -O /tmp/tmp.B02ywAbuYm/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mwget -O /tmp/tmp.B02ywAbuYm/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\033[0m\n'

wget -O /tmp/tmp.B02ywAbuYm/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

+ wget -O /tmp/tmp.B02ywAbuYm/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
--2021-04-29 13:09:07--  https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.anaconda.com (repo.anaconda.com)... 104.16.130.3, 104.16.131.3, 2606:4700::6810:8203, ...
Connecting to repo.anaconda.com (repo.anaconda.com)|104.16.130.3|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 94235922 (90M) [application/x-sh]
Saving to: ‘/tmp/tmp.B02ywAbuYm/miniconda.sh’

/tmp/tmp.B02ywAbuYm 100%[===================>]  89.87M  8.78MB/s    in 11s     

2021-04-29 13:09:18 (8.53 MB/s) - ‘/tmp/tmp.B02ywAbuYm/miniconda.sh’ saved [94235922/94235922]

+ run bash /tmp/tmp.B02ywAbuYm/miniconda.sh -p '/home/joshua/Desktop/Test Directory/spinalcordtoolbox/python' -b -f
+ print code bash /tmp/tmp.B02ywAbuYm/miniconda.sh -p '/home/joshua/Desktop/Test Directory/spinalcordtoolbox/python' -b -f
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mbash /tmp/tmp.B02ywAbuYm/miniconda.sh -p /home/joshua/Desktop/Test Directory/spinalcordtoolbox/python -b -f\033[0m\n'

bash /tmp/tmp.B02ywAbuYm/miniconda.sh -p /home/joshua/Desktop/Test Directory/spinalcordtoolbox/python -b -f

+ bash /tmp/tmp.B02ywAbuYm/miniconda.sh -p '/home/joshua/Desktop/Test Directory/spinalcordtoolbox/python' -b -f
ERROR: did not recognize option 'Directory/spinalcordtoolbox/python', please try -h
+ die 'ERROR: Command failed.'
+ print error 'ERROR: Command failed.'
+ type=error
+ shift
+ case "$type" in
+ echo -e '\n\033[0;31mERROR: Command failed.\033[0m\n'

ERROR: Command failed.

+ exit 1
+ finish
+ value=1
+ cd '/home/joshua/Desktop/Test Directory/spinalcordtoolbox'
+ [[ 1 -eq 0 ]]
+ [[ 1 -eq 99 ]]
+ print error 'Installation failed!\n
Please copy the output of this Terminal (starting with the command install_sct) and upload it as a .txt attachment in a new topic on SCT'\''s forum:\n
--> http://forum.spinalcordmri.org/c/sct'
+ type=error
+ shift
+ case "$type" in
+ echo -e '\n\033[0;31mInstallation failed!\n
Please copy the output of this Terminal (starting with the command install_sct) and upload it as a .txt attachment in a new topic on SCT'\''s forum:\n
--> http://forum.spinalcordmri.org/c/sct\033[0m\n'

Installation failed!

Please copy the output of this Terminal (starting with the command install_sct) and upload it as a .txt attachment in a new topic on SCT's forum:

--> http://forum.spinalcordmri.org/c/sct

+ rm -rf /tmp/tmp.B02ywAbuYm
+ exit 1

The culprit is this line:

https://github.com/neuropoly/spinalcordtoolbox/blob/35e914cd99f6f8750e648a109f63318520cf91c0/install_sct#L587-L588

Which results in:

> bash /tmp/tmp.B02ywAbuYm/miniconda.sh -p '/home/joshua/Desktop/Test Directory/spinalcordtoolbox/python' -b -f
ERROR: did not recognize option 'Directory/spinalcordtoolbox/python', please try -h

The environment variable appears to be properly enclosed in double-quotes, but because the value is being used as an argument, I believe we need to add a second set of quotes.

> echo "$TEST_DIRECTORY"
/home/joshua/Desktop/Test Directory
> echo ""$TEST_DIRECTORY""  # Note: Nesting double-quotes doesn't work
/home/joshua/Desktop/Test Directory
> echo '"$TEST_DIRECTORY"'  # Note: Nesting ' and " this way doesn't substitute the env variable
"$TEST_DIRECTORY"
> echo "'$TEST_DIRECTORY'"
'/home/joshua/Desktop/Test Directory'

However, when I try this, I get the following new error:

> bash Miniconda3-latest-Linux-x86_64.sh -p "'$TEST_DIRECTORY'" -b -f
ERROR: Cannot install into directories with spaces

So, even if we fix the quotes, we won't be able to get around this on Anaconda's end. From the -h of the miniconda script:

> bash Miniconda3-latest-Linux-x86_64.sh -h

usage: Miniconda3-latest-Linux-x86_64.sh [options]

Installs Miniconda3 py38_4.9.2

-b           run install in batch mode (without manual intervention),
             it is expected the license terms are agreed upon
-f           no error if install prefix already exists
-h           print this help message and exit
-p PREFIX    install prefix, defaults to /home/joshua/miniconda3, must not contain spaces.
-s           skip running pre/post-link/install scripts
-u           update an existing installation
-t           run package tests after installation (may install conda-build)

There is an open issue on Anaconda's end for this here: ContinuumIO/anaconda-issues#716

[jcohenadad]

thank you for doing all the digging @joshuacwnewton 🙏

[joshuacwnewton]

I like the idea proposed in #2785.

Checking $SCT_DIR for spaces earlier on would let us catch the issue before spending time downloading the Miniconda script, and would allow us to give a clearer explanation for why spaces are not permitted (e.g. by linking to the Anaconda issue).

I can open up a PR for this to close both issues.