itkdb 0.4.0rc13

Python wrapper to interface with ITk DB.

ITk DB v0.4.0rc13

To install as a user

pip install itkdb

or if you wish to develop/contribute

git clone ...
pip install -e .[develop]

or

git clone ...
pip install -e .[complete]

Using

Command line available via

itkdb --help

Environment Variables

See itkdb/settings/base.py for all environment variables that can be set. All environment variables for this package are prefixed with ITKDB_. As of now, there are:

• ITKDB_ACCESS_CODE1: access code #1 for authentication
• ITKDB_ACCESS_CODE2: access code #2 for authentication
• ITKDB_ACCESS_SCOPE: scope for the access token authentication request
• ITKDB_AUTH_URL: authentication server
• ITKDB_SITE_URL: API server
• ITKDB_CASSETTE_LIBRARY_DIR: for tests, where to store recorded requests/responses

Develop

Bump Version

Run bump2version x.y.z to bump to the next version. We will always tag any version we bump, and this creates the relevant commits/tags for you. All you need to do is git push --tags and that should be it.

Examples

import itkdb

client = itkdb.Client()
comps = client.get(
    "listComponents", json={"project": "P", "pageInfo": {"pageSize": 32}}
)

for i, comp in enumerate(comps):
    print(i, comp["code"])

FAQ

SSL Error with CERN websites

If you run into SSL errors with CERN websites, you might need the CERN certificate chain to sign the certificates correctly. Just add a verify keyword into your calls:

client.get(..., verify=itkdb.data / "CERN_chain.pem")

and it should work.

EOS Uploads?

To do EOS uploads, you need to install this package with the eos option like so

python -m pip install itkdb[eos]

If there are further errors, see below in the FAQ.

pycurl error

If you try running itkdb and run into an issue like:

Traceback (most recent call last):
  File "script.py", line 1, in <module>
    import itkdb
  File "/Users/kratsg/itkdb/src/itkdb/__init__.py", line 7, in <module>
    from .client import Client
  File "/Users/kratsg/itkdb/src/itkdb/client.py", line 8, in <module>
    import pycurl
ImportError: pycurl: libcurl link-time ssl backends (secure-transport, openssl) do not include compile-time ssl backend (none/other)

You will need to reinstall pycurl and force re-compilation. This can be done by first checking the config for curl on your machine:

$ curl-config --features
AsynchDNS
GSS-API
HTTPS-proxy
IPv6
Kerberos
Largefile
MultiSSL
NTLM
NTLM_WB
SPNEGO
SSL
UnixSockets
alt-svc
libz

and then setting the appropriate compile flags. For example, on a Mac, I have openssl so I do the following:

on MacOS

$ brew info openssl
...
...

For compilers to find openssl@3 you may need to set:
  export LDFLAGS="-L/usr/local/opt/openssl@3/lib"
  export CPPFLAGS="-I/usr/local/opt/openssl@3/include"

...

which tells me to export the above lines and then I can reinstall correctly:

$ export LDFLAGS="-L/usr/local/opt/openssl@3/lib"
$ export CPPFLAGS="-I/usr/local/opt/openssl@3/include"
$ python -m pip install --no-cache-dir --compile --ignore-installed --install-option="--with-openssl" pycurl

on lxplus (CC7)

Assuming a virtual environment like

$ lsetup "views dev4 latest/x86_64-centos7-gcc11-opt"
$ python3 -m venv venv
$ source venv/bin/activate

I looked up the locations of the installations on lxplus for you already:

$ export LDFLAGS="-L/usr/local/lib/openssl"
$ export CPPFLAGS="-I/usr/local/include/openssl"
$ export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/usr/lib/pkgconfig/
$ python -m pip install --no-cache-dir --compile --ignore-installed --install-option="--with-nss" pycurl

on SWAN

Assuming a virtual environment like

$ python3 -m venv venv
$ source venv/bin/activate

which came with python3.9 by default on swan, the installation flags needed are:

$ export LDFLAGS="-L/usr/lib64/openssl"
$ export CPPFLAGS="-I/usr/include/openssl"
$ export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/
$ python -m pip install --no-cache-dir --compile --ignore-installed --install-option="--with-nss" pycurl