Developer and curator setup guide

Introduction

This is a general guide to bootstrapping and maintaining a complete development environment for working as a curator or developer on the NIF-Ontology, protc, sparc-curation, scibot, etc. For a general introduction to the SPARC curation process see ./background.org The environment bootstrapped by running this file was originally developed on Gentoo, and is portable to other distributions with a few tweaks.

Please report any bugs you find in this file or during the execution of any of the workflows described in this file to the sparc-curation GitHub issue tracker.

Setup

Setup takes about 3 hours. OS level setup takes about and hour, and user setup takes about two hours.

If you do not have root or sudo access or do not administer the computer you are following this guide on you should start at user setup.

If you do have admin access then do the OS level setup first and then come back to the user setup once you are done.

User

If you are already on a system that has the prerequisites installed start here. If you are not you will find out fairly quickly when the following commands fail.

Git name and email

These workflows make extensive use of git. Git needs to know who you are (and so do we) so that it can stash files that you change (for example this file, which logs to itself). Use the email that you will use for curation or development for this. You should not use your primary email account for this because it will get a whole bunch of development related emails.

Run the following in a terminal replacing the examples with the fields that apply to you.

git config --global user.name "FIRST_NAME LAST_NAME"
git config --global user.email "MY_NAME@example.com"

Bootstrapping this `setup.org` file

You can run all the code in this setup.org file automatically using emacs org-mode. The easiest way to accomplish this is to install scimax which is an emacs starterkit for scientists and engineers that has everything we will need. The following steps will do this automatically for you.

All the code blocks in this Bootstrapping section need to be pasted into a terminal (shell) where you are logged in as your user. Run every code block in the order that they appear on this page. Do not skip any blocks. Read all the text between blocks. It will tell you what to do next.

When pasting blocks into the terminal (middles mouse, or C-V control-shift-v in the ubuntu terminal) if you do not copy the last newline of the blocks then you will have to hit enter to run the last command.

# TODO emacs auto setup to be able to run this file
mkdir -p ~/.local/bin
mkdir ~/bin
mkdir ~/opt
mkdir ~/git
mkdir ~/files
source .profile

Run the following block to clone this repository and the scimax repository.

pushd ~/git
git clone https://github.com/SciCrunch/sparc-curation.git
git clone https://github.com/jkitchin/scimax.git
popd

Run the following command to initialize texlive for your user. It is needed for scimax to install correctly.

tlmgr init-usertree

Run the following commands to create the scimax command (~/bin/scimax on linux and macos, ~/bin/scimax.ps1 on windows), and the config file user.el that is needed for the rest of the process.

echo '(defvar *path-to-setup.org* "~/git/sparc-curation/docs/setup.org")' > vars.el
emacs --batch --load vars.el --load org --load ob-shell --eval '(org-babel-tangle-file *path-to-setup.org*)' --load ~/opt/scimax/user/user.el --eval '(org-babel-tangle-file *path-to-setup.org*)'
rm vars.el

When running the next block scimax will launch emacs an install a number of packages (DON’T PANIC). It is normal to see errors during this step. When everything finishes installing you should find yourself staring at next section of this file Per user setup and can continue from there in scimax.

scimax --find-file ~/git/sparc-curation/docs/setup.org --eval "(add-hook 'window-setup-hook (lambda () (org-goto-section *section-per-user-setup*)))"

Per user setup

You should now have this file open in scimax and can run the code blocks directly by clicking on a block and typing C-c C-c (control c control c). In the default scimax setup code blocks will appear as yellow or green. Note that not all yellow blocks are source code, some may be examples, you can tell because examples won’t execute and the start with #+BEGIN_EXAMPLE instead of #+BEGIN_SRC.

All the following should be run as your user in scimax. If you run these blocks from the command line be sure to run nameref:remote-exports first.

When you run this block emacs will think for about 3 minutes as it retrieves everything. You can know that it is thinking because your mouse will be in thinking mode if you hover over emacs, and because in the minibuffer window at the bottom of the window there will be a message saying something to the effect of Wrote /tmp/babel-nonsense/ob-input-nonsense. If an error window appears when running this block just run it again.

You can also run this block to update an existing installation.

After running this block you can move on to the Configuration files section.

See Developer setup code in the appendix for the source for this block.

Configuration files

This section will create and populate ~/.config/pyontutils/config.yaml, ~/.config/sparcur/config.yaml, and ~/secrets.yaml. They are used to configure the various programs that are used by the SPARC curation workflow, and store the API keys and semi private information such as hypothes.is group names, and google doc ids.

NOTE: If you are on macos =~/.config= is =~/Library/Application Support=
NOTE: If you are on windows =~/.config= is =~/AppData/Local= \

The templates below should have already been tangled to the correct locations when setup.org was tangled.

auth-stores:
  secrets:
    path: '{:user-config-path}/orthauth/secrets.yaml'
auth-variables:
  curies:
  git-local-base: ~/git
  git-remote-base:
  google-api-creds-file:
    path: google api creds-file
  google-api-store-file:
    path: google api store-file
  google-api-store-file-readonly:
    path: google api store-file-readonly
  nifstd-checkout-ok:
  ontology-local-repo:
  ontology-org:
  ontology-repo:
  patch-config:
  resources:
  scigraph-api: https://scigraph.olympiangods.org/scigraph
  scigraph-api-key:
  scigraph-graphload:
  scigraph-java:
  scigraph-services:
  scigraph-start:
  scigraph-stop:
  scigraph-systemd:
  zip-location:

auth-stores:
  secrets:
    path: '{:user-config-path}/orthauth/secrets.yaml'
auth-variables:
  blackfynn-organization:
  cache-path:
  export-path:
  hypothesis-api-key: hypothesis api *replace-me-with-:your-user-name*
  hypothesis-group: hypothesis group sparc-curation
  hypothesis-user:
  log-path:
  protocols-io-api-creds-file: protocols-io api creds-file
  protocols-io-api-store-file: protocols-io api store-file

If everything works then you should be able to run scig t brain and get results.

You can move your ~/.config/orthauth/secrets.yaml to live where ever you want, but you will need to update the auth-stores: secrets: path: entry in ~/.config/pyontutils/config.yaml and ~/.config/sparcur/config.yaml.

blackfynn:
  sparc:
    key: fake-api-key
    secret: fake-api-secret
google:
  api:
    creds-file: /path/to/creds-file.json
    store-file: google-api-token-rw.pickle
    store-file-readonly: google-api-token.pickle
  sheets:
    sparc-consistency: document-hash-id
    sparc-master: document-hash-id
hypothesis:
  api:
    *replace-me-with-:your-user-name*: fake-api-key
  group:
    sparc-curation: FakeId12
protocols-io:
  api:
    creds-file: /path/to/creds-file.json
    store-file: protocols-io-api-token-rw.pickle

At this point installation is complete. Congratulations!

You should log out and log back in to your window manager so that any new terminal you open will have access to all the programs you just installed. Logout on the default ubuntu window manager is located in the upper right.

When you you log back in run the following command to start at the next step.

scimax --find-file ~/git/sparc-curation/docs/setup.org --eval "(add-hook 'window-setup-hook (lambda () (org-goto-section *section-accounts-and-api-access*)))"

When you exit emacs it may ask you if you want to save, say yes so that the logs of the install are saved.

NOTE this will cause problems down the line when you try to pull updates for sparc-curation because git will complain.

The next section will walk you through the steps needed to get access to all the various systems holding different pieces of data that we need.

Accounts and API access

Create accounts, obtain various API keys. After you finish this section you can jump to getting data!.

The notation (-> key1 key2 key3) indicates a path in your secrets.yaml file. In a yaml file this looks like the block below. Replace the fake-value with the real value you obtain in the following sections.

key1:
  key2:
    key3: fake-value

You can open the secrets.yaml file in another buffer by clicking on the link to it here. When you edit the file and to add api keys you should save it after each one using the file menu or C-x C-x.

Ontology

SciGraph

For some use cases you will need access to the SciCrunch production SciGraph endpoint. Register for an account and get an api key. Edit config.yaml and update the scigraph-api-key: path: entry to point to scicrunch api name-of-user-or-name-for-the-key. Edit secrets.yaml and add the api key to (-> scicrunch api name-of-user-or-name-for-the-key).

Data

Blackfynn

Once you have a Blackfynn account on the sparc org go to your profile and create an API key. Put they key in (-> blackfynn sparc key) and the secret in (-> blackfynn sparc secret). ~~While you are there you should also connect your ORCiD.~~ Broken at the moment.

Human workflows

Google

Enable the google sheets API from the google api dashboard. If you need other APIs you can enable them via the library page.

If you do not do this then at the end of the client flow you will receive a =invalid_clientUnauthorized= error.

(-> google api creds-file) https://developers.google.com/identity/protocols/OAuth2 https://developers.google.com/api-client-library/python/guide/aaa_oauth

You will need to get API access for a OAuth client. https://console.developers.google.com/apis/credentials create credentials -> OAuth client ID Fill in the consent screen, you only need the Application name field. Download JSON Add the name of the downloaded JSON file to secrets.yaml (-> google api creds-file). Then run python ~/git/pyontutils/pyontutils/sheets.py auth sheets and python ~/git/pyontutils/pyontutils/sheets.py auth sheets --readonly. Those commands will run the auth workflow and create the file specified at (-> google api store-file) for you.

Get the document ids for the following.

(-> google sheets sparc-master)
(-> google sheets sparc-consistency)
(-> google sheets sparc-affiliations)
(-> google sheets sparc-field-alignment) Document id matches this pattern https://docs.google.com/spreadsheets/d/{document_id}/edit.

Protocol annotation set up

Hypothes.is

google-chrome-stable https://chrome.google.com/webstore/detail/hypothesis-web-pdf-annota/bjfhmglciegochdpefhhlphglcehbmek

To get Hypothes.is API keys create an account, login, and go to your developer page.

Temporary additions to .bashrc until this can be sourced from secrets directly

HYP_USER=your-hypothesis-user-name
HYP_GROUP=$(cat ~/secrets.yaml | grep sparc-curation: | awk '{ print $2 }')
HYP_API_TOKEN=$(cat ~/secrets.yaml | grep "${HYP_USER}:" | awk '{ print $2 }')

protocols.io

To get protocols.io API keys create an account, login, and go to your developer page. You will need to set the redirect uri on that page to match the redirect uri in the json below.

Use the information from that page to fill in a json file with the structure below. Add the full path to that json file to (-> protocols-io api creds-file) in secrets.yaml like you did for the google json file.

{
    "installed": {
        "client_id": "pr_live_id_fake-client-id<<<",
        "client_secret": "pr_live_sc_fake-client-secret<<<",
        "auth_uri": "https://www.protocols.io/api/v3/oauth/authorize",
        "token_uri": "https://www.protocols.io/api/v3/oauth/token",
        "redirect_uris": [
            "https://sparc.olympiangods.org/curation/"
        ]
    }
}

You will be prompted for your protocols.io email and password the first time you run.

Developer extras

If you can use python3.7 (>=ubuntu-19.04) you can set the embedded debugger as follows.

pip install --user pudb

export PYTHONBREAKPOINT=pudb.set_trace

~/.vimrc settings to prevent klobbering of xattrs

augroup HasXattrs
 autocmd BufRead,BufNewFile * let x=system('getfattr ' . bufname('%')) | if len(x) | call HasXattrs() | endif
augroup END

function HasXattrs()
 " don't create new inodes
 setlocal backupcopy=yes
endfunction

One shot

These bits are os specific setup instructions that need to be run as root. They only need to be run once.

Gentoo

app-editors/emacs
app-editors/gvim
app-text/texlive
dev-vcs/git
dev-scheme/racket
dev-lisp/sbcl
www-client/google-chrome-stable

Ubuntu

18.10 cosmic cuttlefish (and presumably other debian derivatives)

The following need to be run in a shell where you have root (e.g. via sudo su -).

apt install openssh-server net-tools

Add your ssh public key to ~/.ssh/authorized_keys if you want to run this remotely.

wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -
echo 'deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main' \
>> /etc/apt/sources.list.d/google-chrome.list
add-apt-repository ppa:plt/racket
add-apt-repository ppa:kelleyk/emacs
add-apt-repository ppa:pypy/ppa
apt update
apt install build-essential lib64readline-dev rxvt-unicode htop attr tree sqlite curl git
apt install emacs26 vim-gtk3 texlive-full pandoc hunspell
apt install librdf0-dev python3-dev python3-pip pypy3 jupyter racket sbcl r-base r-base-dev maven
apt install inkscape gimp krita graphviz firefox google-chrome-stable xfce4
apt install nginx
update-alternatives --install /usr/bin/python python /usr/bin/python3 10
update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10

Ubuntu struggles to set user specific PATHs correctly via ~/.profile This code works when the user logs in. It does not work correctly if you su to the user. Not entirely sure why. Doesn’t work on xfce either apparently. The absolute madness.

{ cat <<EOL
# set PATH so it includes user's private bin if it exists
if [ -d "$HOME/bin" ] ; then
    PATH="$HOME/bin:$PATH"
fi

# set PATH so it includes user's private bin if it exists
if [ -d "$HOME/.local/bin" ] ; then
    PATH="$HOME/.local/bin:$PATH"
fi
EOL
} > /etc/profile.d/user-home-paths.sh

Other software that you will probably need at some point but that is not packaged on ubuntu.

Fiji/ImageJ

Windows

Symlinks

augpathlib makes extensive use of symlinks to store metadata for remote files that have not been downloaded. By default normal users cannot create symlinks on windows. The best way to fix this is by granting the user that will run sparcur permission to create symlinks (NOT to run the process as Administrator).

Three relevant links: stackoverflow superuser powershell script source.

You will need to log out and log back in for the setting to take effect.

You can use gpedit.msc to grant these permissions by adding the user by navigating the menu tree below. You can run gpedit.msc directly with Win-r or often Win gpedit enter.

Computer configuration
└── Windows Settings
    └── Security Settings
        └── Local Policies
            └── User Rights Assignment
                Create symbolic links

Alternately you can define and run the function below as Administrator. Run it as addSymLinkPermissions("user-to-add").

function addSymLinkPermissions($accountToAdd){
    Write-Host "Checking SymLink permissions.."
    $sidstr = $null
    try {
        $ntprincipal = new-object System.Security.Principal.NTAccount "$accountToAdd"
        $sid = $ntprincipal.Translate([System.Security.Principal.SecurityIdentifier])
        $sidstr = $sid.Value.ToString()
    } catch {
        $sidstr = $null
    }
    Write-Host "Account: $($accountToAdd)" -ForegroundColor DarkCyan
    if( [string]::IsNullOrEmpty($sidstr) ) {
        Write-Host "Account not found!" -ForegroundColor Red
        exit -1
    }
    Write-Host "Account SID: $($sidstr)" -ForegroundColor DarkCyan
    $tmp = [System.IO.Path]::GetTempFileName()
    Write-Host "Export current Local Security Policy" -ForegroundColor DarkCyan
    secedit.exe /export /cfg "$($tmp)" 
    $c = Get-Content -Path $tmp 
    $currentSetting = ""
    foreach($s in $c) {
        if( $s -like "SECreateSymbolicLinkPrivilege*") {
            $x = $s.split("=",[System.StringSplitOptions]::RemoveEmptyEntries)
            $currentSetting = $x[1].Trim()
        }
    }
    if( $currentSetting -notlike "*$($sidstr)*" ) {
        Write-Host "Need to add permissions to SymLink" -ForegroundColor Yellow
        
        Write-Host "Modify Setting ""Create SymLink""" -ForegroundColor DarkCyan

        if( [string]::IsNullOrEmpty($currentSetting) ) {
            $currentSetting = "*$($sidstr)"
        } else {
            $currentSetting = "*$($sidstr),$($currentSetting)"
        }
        Write-Host "$currentSetting"
    $outfile = @"
[Unicode]
Unicode=yes
[Version]
signature="`$CHICAGO`$"
Revision=1
[Privilege Rights]
SECreateSymbolicLinkPrivilege = $($currentSetting)
"@
    $tmp2 = [System.IO.Path]::GetTempFileName()
        Write-Host "Import new settings to Local Security Policy" -ForegroundColor DarkCyan
        $outfile | Set-Content -Path $tmp2 -Encoding Unicode -Force
        Push-Location (Split-Path $tmp2)
        try {
            secedit.exe /configure /db "secedit.sdb" /cfg "$($tmp2)" /areas USER_RIGHTS 
        } finally { 
            Pop-Location
        }
    } else {
        Write-Host "NO ACTIONS REQUIRED! Account already in ""Create SymLink""" -ForegroundColor DarkCyan
        Write-Host "Account $accountToAdd already has permissions to SymLink" -ForegroundColor Green
        return $true;
    }
}

ssh

You can skip this if you will only be using the windows computer locally. In a local administrator powershell install OpenSSH. The rest can then be done remotely.

Get-WindowsCapability -Online | ? Name -like 'OpenSSH*'
Add-WindowsCapability -Online -Name OpenSSH.Client~~~~0.0.1.0
Add-WindowsCapability -Online -Name OpenSSH.Server~~~~0.0.1.0
Set-Service sshd -StartupType Automatic
Start-Service sshd
# add your ssh key to %programdata%\ssh\administrators_authorized_keys
# disable password login in %programdata%\ssh\sshd_config
Restart-Service sshd

Package manager

For managing a windows development/curation environment I highly recommend using the chocolatey package manager. Install chocolatey.

choco install `
autohotkey `
clisp `
emacs `
firefox `
GoogleChrome `
poshgit `
python `
racket `
vim

Update system Path to include packages that don’t add themselves. This needs to be run as administrator.

$path = [Environment]::GetEnvironmentVariable("Path", [EnvironmentVariableTarget]::Machine)
$prefix_path = "C:\Program Files\Racket;C:\Program Files\Git\cmd;C:\Program Files\Git\bin;"
[Environment]::SetEnvironmentVariable("Path",
                                      $prefix_path + $path,
                                      [EnvironmentVariableTarget]::Machine)

If you are logged in remotely restarting sshd is the easiest way to refresh the environment so commands are in PATH. This is because new shells inherit the environment of sshd at the time that it was started.

Restart-Service sshd

You will need to reconnect to a new ssh session in order to have access to git and other newly installed commands.

Manual install

texlive

https://www.tug.org/texlive/windows.html https://www.tug.org/texlive/acquire-netinstall.html http://mirror.ctan.org/systems/texlive/tlnet/install-tl-windows.exe This takes quite a while, about 50 mins on a good connection with a fast computer.

protege

https://github.com/protegeproject/protege-distribution/releases/latest

redland

rdf tools http://librdf.org/raptor/INSTALL.html https://github.com/dajobe/raptor Unfortunately to get the latest version of these it seems you have to build them yourself.

old

add to PATH so we can just link everything there %HOMEPATH%\bin %APPDATA%\Python\Python37\Scripts

TODO -l %HOMEPATH%/opt/scimax/init.el setup.org in the shortcut … also %HOMEPATH% for the start in …

OS X

ssh

You can skip this if you will only be using the osx computer locally.

sudo systemsetup -setremotelogin on
# scp your key over to ~/.ssh/authorized_keys
# set PasswordAuthentication no in /etc/ssh/sshd_config
# set ChallengeResponseAuthentication no in /etc/ssh/sshd_config
sudo launchctl unload  /System/Library/LaunchDaemons/ssh.plist
sudo launchctl load -w /System/Library/LaunchDaemons/ssh.plist

Package manager

Install homebrew.

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/5ecca39372cffdc4c9fbacee6e22328a0dc61eac/install)"
brew cask install \
emacs \
firefox \
gimp \
google-chrome \
inkscape \
krita \
mactex \
macvim \
protege \
racket

brew install \
coreutils \
curl \
git \
htop \
hunspell \
pandoc \
postgres \
python \
redland \
rxvt-unicode \
sbcl \
sqlite \
tree

Add the following to your ~/.bash_profile

# This file is sourced by bash for login shells.  The following line
# runs your .bashrc and is recommended by the bash info pages.
[[ -f ~/.bashrc ]] && . ~/.bashrc

Add the following to your ~/.bashrc

export PATH=${HOME}/bin:${HAOME}/Library/Python/3.7/bin:${PATH}

Run the following to symlink python3 to python

mkdir ~/bin
ln -s /usr/local/bin/python3 ~/bin/python
ln -s /usr/local/bin/pip3 ~/bin/pip

Workflows

General

Updating an installation

pushd ~/git
for d in $(ls); do if [ -d $d/.git ]; then pushd $d; git pull || break; popd; fi; done
popd

SPARC

WARNINGS

DO NOT USE cp -a copy files with xattrs!
INSTEAD use rsync -X -u -v. \ cp does not remove absent fields from xattrs of the file previously occupying that name! OH NO (is this a cp bug!?)

Get data

If you have never retrieved the data before run.

pushd ~/files/blackfynn_local/
spc clone ${SPARC_ORG_ID} # initialize a new repo and pull existing structure
scp refresh -f
spc fetch  # actually download files
spc find -n '*.xlsx' -n '*.csv' -n '*.tsv' -n '*.msexcel'  # see what to fetch
spc find -n '*.xlsx' -n '*.csv' -n '*.tsv' -n '*.msexcel'-f  # fetch
spc find -n '*.xlsx' -n '*.csv' -n '*.tsv' -n '*.msexcel'-f -r 10  # slow down you are seeing errors!

ls -Q | xargs -P10 -r -n 1 sh -c 'spc refresh -r 4 "${1}"'

find -maxdepth 1 -type d -name '[C-Z]*' -exec spc refresh -r 8 {} \;

find \( -name '*.xlsx' -o -name '*.csv' -o -name '*.tsv' \) -exec ls -hlS {} \+

find -maxdepth 1 -type d -exec rmdir {} \;

Pull local copy of data to a new computer. Note the double escape needed for the space.

rsync -X -u -v -r -e ssh ${REMOTE_HOST}:/home/${DATA_USER}/files/blackfynn_local/SPARC\\\ Consortium ~/files/blackfynn_local/

-X copy extended attributes -u update files -v verbose -r recursive -e remote shell to use

Fetch missing files

fetching a whole dataset or a subset of a dataset spc ** -f

Export

pushd ${SPARCDATA}
spc export datasets
popd

Setup as root

mkdir -p /var/www/sparc/sparc/archive/exports/
chown -R nginx:nginx /var/www/sparc

# export vs exports, no wonder this is so confusing >_<
function sparc-export-to-server () {
    : ${SPARCUR_EXPORTS:=/var/lib/sparc/.local/share/sparcur/export}
    EXPORT_BASE=${SPARCUR_EXPORTS}/N:organization:618e8dd9-f8d2-4dc4-9abb-c6aaab2e78a0/
    FOLDERNAME=$(readlink ${EXPORT_BASE}/LATEST)
    FULLPATH=${EXPORT_BASE}/${FOLDERNAME}
    pushd /var/www/sparc/sparc
    cp -a "${FULLPATH}" archive/exports/ && chown -R nginx:nginx archive && unlink exports ; ln -sT "archive/exports/${FOLDERNAME}" exports
    popd
}

Reporting

spc report completeness

spc server --latest --count

keywords = sorted(set([k for d in asdf['datasets'] if 'meta' in d and 'keywords' in d['meta']
                       for k in d['meta']['keywords']]))

Archiving files with xattrs

tar is the only one of the ‘usual’ suspects for file archiving that supports xattrs, zip cannot.

tar --force-local --xattrs -cvzf 2019-07-17T10\:44\:16\,457344.tar.gz '2019-07-17T10:44:16,457344/'

tar --force-local --xattrs -xvzf 2019-07-17T10\:44\:16\,457344.tar.gz

find 2019-07-17T10\:44\:16\,457344 -exec getfattr -d {} \;

Other random commands

Duplicate top level and ./.operations/objects

function sparc-copy-pull () {
    : ${SPARC_PARENT:=${HOME}/files/blackfynn_local/}
    local TODAY=$(date +%Y%m%d)
    pushd ${SPARC_PARENT} &&
        mv SPARC\ Consortium "SPARC Consortium_${TODAY}" &&
        rsync -ptgo -A -X -d --no-recursive --exclude=* "SPARC Consortium_${TODAY}/"  SPARC\ Consortium &&
        mkdir SPARC\ Consortium/.operations &&
        mkdir SPARC\ Consortium/.operations/trash &&
        rsync -X -u -v -r "SPARC Consortium_${TODAY}/.operations/objects" SPARC\ Consortium/.operations/ &&
        pushd SPARC\ Consortium &&
        spc pull || echo "spc pull failed"
    popd
    popd
}

Simplified error report

jq -r '[ .datasets[] |
         {id: .id,
          name: .meta.folder_name,
          se: [ .status.submission_errors[].message ] | unique,
          ce: [ .status.curation_errors[].message   ] | unique } ]' curation-export.json

File extensions

Get a list of all file extensions for symlinks (usually data)

find -type l | grep -o '\(\.[a-zA-Z0-9]\+\)\+$' | sort -u

Find datasets with unknown file types.

find -name '*.roi' -exec spc meta --context --uri {} \+

Sort of manifest generation

This is slow, but prototypes functionality useful for the curators.

find -type d -not -name 'ephys' -name 'ses-*' -exec bash -c \
'pushd $1 1>/dev/null; pwd >> ~/manifest-stuff.txt; spc report size --tab-table ./* >> ~/manifest-stuff.txt; popd 1>/dev/null' _ {} \;

Developer

Releases

DatasetTemplate

Commit any changes and push to master.

make-template-zip () {
    local CLEANROOM=/tmp/cleanroom/
    mkdir ${CLEANROOM} || return 1
    pushd ${CLEANROOM}
    git clone https://github.com/SciCrunch/sparc-curation.git &&
    pushd ${CLEANROOM}/sparc-curation/resources
    zip -r DatasetTemplate.zip DatasetTemplate
    mv DatasetTemplate.zip ${CLEANROOM}
    popd
    rm -rf ${CLEANROOM}/sparc-curation
    popd
}
make-template-zip

Once that is done open /tmp/cleanroom/DatasetTemplate.zip in file-roller or similar and make sure everything is as expected.

Create the GitHub release. The tag name should have the format dataset-template-1.1 where the version number should match the metadata version embedded in dataset_description.xlsx. Minor versions such as dataset-template-1.2.1 are allowed.

Attach ${CLEANROOM}/DatasetTemplate.zip as a release asset. Update https://github.com/Blackfynn/docs.sparc.science/blob/master/pages/data_submission/submit_data.md https://github.com/Blackfynn/docs.sparc.science/blob/master/pages/sparc_portal/sparc_data_format.md and with the new link. Link to the local copy. Link to the local copy.

Getting to know the codebase

Use inspect.getclasstree along with pyontutils.utils.subclasses to display hierarchies of classes.

from inspect import getclasstree
from pyontutils.utils import subclasses
from IPython.lib.pretty import pprint

# classes to inspect
import pathlib
from sparcur import paths

def class_tree(root):
    return getclasstree(list(subclasses(root)))

pprint(class_tree(pathlib.PurePosixPath))

Viewing logs

View the latest log file with colors using less.

less -R $(ls -d ~sparc/files/blackfynn_local/export/log/* | tail -n 1)

For a permanent fix for less add

alias less='less -R'

Debugging terminal pipeline errors

You have an error!

maybe_size = c.cache.meta.size  # << AttributeError here

Modify to wrap code

try:
    maybe_size = c.cache.meta.size
except AttributeError as e:
    breakpoint()  # << investigate error

Temporary squash by logging as an exception with optional explanation

try:
    maybe_size = c.cache.meta.size
except AttributeError as e:
    log.exception(e)
    log.error(f'explanation for error and local variables {c}')

Dataset removed

If a dataset is removed, just move it manually to trash IF it is clear that it was supposed to be removed, otherwise to consult the curation team. You can confirm that it was actually removed by checking Blackfynn directly using DATASETID from the error trace.

spc meta -u "$(spc goto ${DATASETID})"

Example trace.

Future exception was never retrieved
future: <Future finished exception=Exception("No dataset matching name or ID 'N:dataset:83e0ebd2-dae2-4ca0-ad6e-81eb39cfc053'.",)>
Traceback (most recent call last):
  File "/usr/lib/python3.6/concurrent/futures/thread.py", line 56, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/var/lib/sparc/git/pyontutils/pyontutils/utils.py", line 416, in <lambda>
    generator = (lambda:list(limited_gen(chunk, smooth_offset=(i % lc)/lc, time_est=time_est, debug=debug, thread=i))  # this was the slowdown culpret
  File "/var/lib/sparc/git/pyontutils/pyontutils/utils.py", line 455, in limited_gen
    yield element()
  File "/var/lib/sparc/git/pyontutils/pyontutils/utils.py", line 376, in inner
    return function(*args, **kwargs)
  File "/var/lib/sparc/git/sparc-curation/sparcur/paths.py", line 1156, in refresh
    size_limit_mb=size_limit_mb)
  File "/var/lib/sparc/git/sparc-curation/sparcur/backends.py", line 816, in refresh
    old_meta = self.meta
  File "/var/lib/sparc/git/sparc-curation/sparcur/backends.py", line 872, in meta
    return PathMeta(size=self.size,
  File "/var/lib/sparc/git/sparc-curation/sparcur/backends.py", line 603, in size
    if isinstance(self.bfobject, File):
  File "/var/lib/sparc/git/sparc-curation/sparcur/backends.py", line 401, in bfobject
    bfobject = self._api.get(self._seed)
  File "/var/lib/sparc/git/sparc-curation/sparcur/blackfynn_api.py", line 795, in get
    thing = self.bf.get_dataset(id)  # heterogenity is fun!
  File "/var/lib/sparc/.local/lib/python3.6/site-packages/blackfynn/client.py", line 231, in get_dataset
    raise Exception("No dataset matching name or ID '{}'.".format(name_or_id))
Exception: No dataset matching name or ID 'N:dataset:83e0ebd2-dae2-4ca0-ad6e-81eb39cfc053'.
sparc@cassava:~/files/blackfynn_local/SPARC Consortium$ spc goto 'N:dataset:83e0ebd2-dae2-4ca0-ad6e-81eb39cfc053'
Hackathon Team Materials
sparc@cassava:~/files/blackfynn_local/SPARC Consortium$ mv Hackathon\ Team\ Materials ../.trash/
sparc@cassava:~/files/blackfynn_local/SPARC Consortium$ spc pull

Keep letsencrypt up to date

Variables

If you make any changes to this section be sure to run #+SRC and #+CALL: blocks below.

GitHub repositories

augpathlib idlib hyputils orthauth ontquery parsercomb pyontutils protc rrid-metadata rkdf orgstrap

NIF-Ontology scibot sparc-curation

Ophirr33/pda zussitarze/qrcode

Repository local roots. The ordering of the entries matters.

augpathlib idlib pyontutils/htmlfn pyontutils/ttlser hyputils orthauth ontquery parsercomb pyontutils pyontutils/nifstd pyontutils/neurondm protc/protcur sparc-curation scibot

qrcode/ pda/ protc/protc-lib protc/protc-tools-lib protc/protc protc/protc-tools rkdf/rkdf-lib rkdf/rkdf rrid-metadata/rrid NIF-Ontology/

Make repos

from itertools import chain
urs = chain((('tgbugs', r) for tr in trl for rs in tr for r in rs.split(' ')),
            (('SciCrunch', r) for sr in srl for rs in sr for r in rs.split(' ')),
            (ur.split('/') for o_r in orl for urs in o_r for ur in urs.split(' ')))
#print(trl, srl, orl)
#print(list(urs))  # will express the generator so there will be no result

out = []
for user, repo in urs:
    out.append(f'https://github.com/{user}/{repo}')
return [' '.join(out)]

Variables testing

for repo in ${REPOS}; do echo ${repo}; done
echo '-------------'
for repo in ${PYROOTS}; do echo ${repo}; done
echo '-------------'
for repo in ${RKTROOTS}; do echo ${repo}; done

Remote exports code

export REPOS='
https://github.com/tgbugs/augpathlib
https://github.com/tgbugs/idlib
https://github.com/tgbugs/hyputils
https://github.com/tgbugs/orthauth
https://github.com/tgbugs/ontquery
https://github.com/tgbugs/parsercomb
https://github.com/tgbugs/pyontutils
https://github.com/tgbugs/protc
https://github.com/tgbugs/rrid-metadata
https://github.com/tgbugs/rkdf
https://github.com/tgbugs/orgstrap
https://github.com/SciCrunch/NIF-Ontology
https://github.com/SciCrunch/scibot
https://github.com/SciCrunch/sparc-curation
https://github.com/Ophirr33/pda
https://github.com/zussitarze/qrcode
'
export PYROOTS='
augpathlib
idlib
pyontutils/htmlfn
pyontutils/ttlser
hyputils
orthauth
ontquery
parsercomb
pyontutils
pyontutils/nifstd
pyontutils/neurondm
protc/protcur
sparc-curation
scibot
'
export RKTROOTS='
qrcode/
pda/
protc/protc-lib
protc/protc-tools-lib
protc/protc
protc/protc-tools
rkdf/rkdf-lib
rkdf/rkdf
rrid-metadata/rrid
NIF-Ontology/
'

Appendix

Code

Bootstrap code

user.el

Tangle the following blocks with C-c C-v C-t in vanilla emacs or paste it into scimax’s

;; silence ob-ipython complaining about missing command
;; THIS CAN CAUSE RUNTIME ERRORS
(setq ob-ipython-html-to-image-program "/dev/null")

;; requires
(require 'cl)  ;; needed for case

;; org goto heading
(defun org-goto-section (heading)
  "\`heading' should be a string matching the desired heading"
  (goto-char (org-find-exact-headline-in-buffer heading)))

;; workaround for powershell cmd windows braindead handling of strings
(defvar *section-per-user-setup* "Per user setup")
(defvar *section-accounts-and-api-access* "Accounts and API access")

;; recenter a line set using --eval to be at the top of the buffer
(add-hook 'emacs-startup-hook (lambda () (recenter-top-bottom 0)))

;; line numbers so it is harder to get lost in a big file
(when (>= emacs-major-version 26)
  (setq display-line-numbers-grow-only 1)
  (global-display-line-numbers-mode 1))

;; open setup.org symlink without prompt
(setq vc-follow-symlinks 1)

;; sane python indenting
(setq-default indent-tabs-mode nil)
(setq tab-width 4)
(setq org-src-preserve-indentation nil)
(setq org-src-tab-acts-natively nil)

;; don't hang on tlmgr since it is broken on ubuntu
(setq scimax-installed-latex-packages t)

;; save command history
(setq history-length t)
(savehist-mode 1)
(setq savehist-additional-variables '(kill-ring search-ring regexp-search-ring))

;; racket
(when (fboundp 'use-package)
  (use-package racket-mode
    :mode "\\.ptc\\'" "\\.rkt\\'" "\\.sxml\\'"
    :bind (:map racket-mode-map
                ("<f5>" . recompile-quietly))
    :init
    (defun my/buffer-local-tab-complete ()
      "Make \`tab-always-indent' a buffer-local variable and set it to 'complete."
      (make-local-variable 'tab-always-indent)
      (setq tab-always-indent 'complete))
    (defun rcc ()
      (set (make-local-variable 'compile-command)
           (format "raco make %s" (file-name-nondirectory buffer-file-name))))
    (add-hook 'racket-mode-hook 'rcc)
    (add-hook 'racket-mode-hook 'hs-minor-mode)
    (add-hook 'racket-mode-hook 'goto-address-mode)
    (add-hook 'racket-mode-hook 'my/buffer-local-tab-complete)
    (add-hook 'racket-repl-mode-hook 'my/buffer-local-tab-complete)))

;; config paths

(defun config-paths (&optional os)
  (case (or os system-type)
    ;; ucp udp uchp ulp
    (gnu/linux '("~/.config"
                 "~/.local/share"
                 "~/.cache"
                 "~/.cache/log"))
    (darwin '("~/Library/Application Support"
              "~/Library/Application Support"
              "~/Library/Caches"
              "~/Library/Logs"))
    (windows-nt (let ((ucp "~/AppData/Local"))
                  (list ucp ucp ucp (concat ucp "/Logs"))))
    (otherwise (error (format "Unknown OS %s" (or os system-type))))))

(eval-when-compile (defvar *config-paths* (config-paths)))

(defun fcp (position &optional suffix)
  (let ((base-path (funcall position *config-paths*)))
    (if suffix
        (format "%s/%s" base-path suffix)
      base-path)))

(defun user-config-path (&optional suffix) (fcp #'first  suffix))
(defun user-data-path   (&optional suffix) (fcp #'second suffix))
(defun user-cache-path  (&optional suffix) (fcp #'third  suffix))
(defun user-log-path    (&optional suffix) (fcp #'fourth suffix))

;; vim bindings if you need them
;; if undo-tree fails to install for strange reasons M-x list-packages C-s undo-tree
;; to manually install, mega gnu elpa weirdness
(setq evil-want-keybinding nil)
(when (fboundp 'use-package)
  (require 'scimax-evil))

scimax launch scripts

emacs -q -l ~/opt/scimax/init.el $args

emacs -q -l ~/opt/scimax/init.el $@

Developer setup code

# implicit check for bash by being able to run this block at all

# git check on the off chance that we made it here without cloning this repo
git --version || exit 1

# python version check
python -c "print('python ok') if __import__('sys').version_info.major >= 3 else __import__('sys').exit(1)" || exit 2
pip --version || exit 3

# git email check
[[ -n "$(git config --list | grep user.email)" ]] || exit 4

pushd ~/git
for repo_url in ${REPOS}; do git clone ${repo_url}.git 2>&1; done
popd

pushd ~/git
for repo in ${PYROOTS}; do pushd ${repo}; pip install --user --editable . 2>&1 || break; popd; done
popd

ln -s ~/git/rkdf/bin/ttl-to-rkt ~/bin/ttl-to-rkt
ln -s ~/git/rkdf/bin/rkdf-convert-all ~/bin/rkdf-convert-all
pushd ~/git/NIF-Ontology
git checkout dev
rkdf-convert-all
git checkout master
popd

pushd ~/git
raco pkg install --skip-installed --auto --batch ${RKTROOTS} 2>&1
popd

Remote exports

Paste the results of this block into your shell if you are running the code from this file by pasting it into a terminal.

*NOTE: DO NOT EDIT THE CODE BELOW IT WILL BE OVERWRITTEN.*

Files

setup.org

Latest commit

History

setup.org

File metadata and controls

Developer and curator setup guide

Introduction

Setup

User

Git name and email

Bootstrapping this setup.org file

Per user setup

Configuration files

Accounts and API access

Ontology

SciGraph

Data

Blackfynn

Human workflows

Google

Protocol annotation set up

Hypothes.is

protocols.io

Developer extras

One shot

Gentoo

Ubuntu

Windows

Symlinks

ssh

Package manager

Manual install

texlive

protege

redland

old

OS X

ssh

Package manager

Workflows

General

Updating an installation

SPARC

WARNINGS

Get data

Fetch missing files

Export

Reporting

Archiving files with xattrs

Other random commands

Duplicate top level and ./.operations/objects

Simplified error report

File extensions

Sort of manifest generation

Developer

Releases

DatasetTemplate

Getting to know the codebase

Viewing logs

Debugging terminal pipeline errors

Dataset removed

Keep letsencrypt up to date

Variables

Make repos

Variables testing

Remote exports code

Appendix

Code

Bootstrap code

user.el

scimax launch scripts

Developer setup code

Remote exports

Bootstrapping this `setup.org` file