[Debian-med-packaging] Bug#1019317: snakemake: HTML dashboard (--gui) is broken due to use of local jquery/bootstrap

[Olivier Aubert]

Package: snakemake
Version: 7.12.1-1
Severity: wishlist
X-Debbugs-Cc: contact at olivieraubert.net

Dear Maintainer,

as mentioned in README.Debian, the bootstrap and jquery references
in the GUI template have been replaced from the CDN URLs to file://
references. The GUI being loaded through a Flask server (so in http),
browsers apply security constraints preventing loading js from file://
URLs, which breaks the GUI code.

Some thoughts: the easy solution is to use the original CDN URLs.
Another one would be to have some Debian-blessed/-hosted CDN for such
js libs (which does not exist AFAIK). A last option, to build upon the
original modification, requires patching the gui.py code: define
an additional static route to serve the Debian javascript files.
This could easily be achieved by adding the `static` parameter when
instanciating Flask:

   app = Flask("snakemake", template_folder=os.path.dirname(__file__),
               static="/usr/share/javascript")

It will then make the whole local javascript directory available through
the local http server, and we can change the reference of jquery for
instance in the gui.html file to
`/static/jquery/jquery.min.js`

-- System Information:
Debian Release: bookworm/sid
  APT prefers testing
  APT policy: (990, 'testing'), (500, 'unstable'), (1, 'experimental')
merged-usr: no
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 5.18.0-4-amd64 (SMP w/8 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_FIRMWARE_WORKAROUND, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=C.UTF-8, LC_CTYPE=C (charmap=UTF-8) (ignored: LC_ALL set to C.UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages snakemake depends on:
ii  ca-certificates          20211016
ii  libjs-bootstrap          3.4.1+dfsg-2
ii  libjs-jquery             3.6.0+dfsg+~3.5.13-1
ii  python3                  3.10.6-1
ii  python3-appdirs          1.4.4-3
ii  python3-configargparse   1.5.3-1
ii  python3-connection-pool  0.0.3-2
ii  python3-datrie           0.8.2-2+b1
ii  python3-docutils         0.17.1+dfsg-2
ii  python3-git              3.1.27-1
ii  python3-jinja2           3.0.3-1
ii  python3-jsonschema       4.6.0-3
ii  python3-nbformat         5.4.0-2
ii  python3-pkg-resources    59.6.0-1.2
ii  python3-psutil           5.9.0-1+b1
ii  python3-pulp             2.6.0+dfsg-1
ii  python3-ratelimiter      1.2.0.post0-3
ii  python3-requests         2.27.1+dfsg-1
ii  python3-smart-open       5.2.1-4
ii  python3-stopit           1.1.2-2
ii  python3-tabulate         0.8.9-1
ii  python3-toposort         1.6-1
ii  python3-wrapt            1.13.3-1+b2
ii  python3-yaml             5.4.1-1+b2

Versions of packages snakemake recommends:
ii  cwltool                          3.1.20220224085855-1
ii  imagemagick                      8:6.9.11.60+dfsg-1.3+b3
ii  imagemagick-6.q16 [imagemagick]  8:6.9.11.60+dfsg-1.3+b3
ii  python3-azure-storage            20220407+git-1
pn  python3-biopython                <none>
ii  python3-boto3                    1.23.8+dfsg-1
ii  python3-botocore                 1.26.8+repack-1
pn  python3-dropbox                  <none>
ii  python3-flask                    2.0.3-1
pn  python3-ftputil                  <none>
pn  python3-irodsclient              <none>
pn  python3-kubernetes               <none>
ii  python3-pygments                 2.12.0+dfsg-2
ii  python3-tz                       2022.2.1-1
ii  python3-urllib3                  1.26.9-1
pn  python3-yappi                    <none>

Versions of packages snakemake suggests:
pn  snakemake-doc  <none>

-- no debconf information