Embed logos as base64 data URIs instead of remote URLs

[karlnyr]

Description

Previously, the MicroSALT and Swedac logos in generated reports were loaded via remote GitHub URLs (raw=true links). This means reports required an active internet connection to display the logos, and would silently break if GitHub was unreachable or if the artwork paths changed.

This PR embeds both logos as base64-encoded inline data URIs at render time, reading the image files directly from the installed package. Reports are now fully self-contained.

Additionally, this PR includes a few dependabot alerts.

Primary function of PR

• Hot-fix
• Patch
• Minor functionality improvement
• New type of analysis
• Backward-breaking functionality improvement
• This change requires internal documents to be updated
• This change requires another repository to be updated

Changes:

• New microSALT/server/utils.py with read_jpg() (base64 encoder) and pre-resolved paths MICROSALT_LOGO_PATH / SWEDAC_LOGO_PATH pointing into the installed package's artwork/ directory.
• views.py injects these as Jinja2 globals so all templates can use them.
• typing_page.html, alignment_page.html, and STtracker_page.html updated to call read_jpg(file_path=...) instead of hardcoded remote src URLs.

Testing

• bash /home/proj/production/servers/resources/hasta.scilifelab.se/install-microsalt-stage.sh BRANCHNAME
• us
• conda activate S_microSALT
• microSALT analyse --input /path/to/fastq/ SAMPLEINFO_FILE

Quick local verification (no deployment needed):

from pathlib import Path
from datetime import datetime
from jinja2 import Environment, FileSystemLoader
from microSALT.server.utils import MICROSALT_LOGO_PATH, SWEDAC_LOGO_PATH, read_jpg

env = Environment(loader=FileSystemLoader("microSALT/server/templates"))
env.globals.update(read_jpg=read_jpg, microsalt_logo_path=MICROSALT_LOGO_PATH, swedac_logo_path=SWEDAC_LOGO_PATH)
rendered = env.get_template("typing_page.html").render(...)
assert "data:image/jpeg;base64," in rendered

Test results

Verified locally: rendered typing_page.html contains data:image/jpeg;base64,... inline data URIs for both logos. Opening the output HTML in a browser shows logos without any network requests.

Sign-offs

• Approved to run at Clinical-Genomics by @karlnyr or @Clinical-Genomics/micro

[Copilot]

Pull request overview

This PR makes generated MicroSALT HTML reports fully self-contained by embedding the MicroSALT and Swedac logos as inline data:image/jpeg;base64,... URIs instead of loading them from remote GitHub URLs.

Changes:

• Added microSALT/server/utils.py with logo resource paths and a read_jpg() helper to build JPEG data URIs.
• Injected read_jpg and the logo paths into the Jinja2 environment as globals from microSALT/server/views.py.
• Updated report templates to use read_jpg(...) rather than hardcoded remote raw=true image URLs.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
microSALT/server/views.py	Adds Jinja globals for logo embedding and minor formatting cleanups.
microSALT/server/utils.py	Introduces helper + constants for resolving and base64-encoding logo assets.
microSALT/server/templates/typing_page.html	Switches logo <img src> to embedded data URIs (including conditional Swedac logo).
microSALT/server/templates/STtracker_page.html	Switches MicroSALT logo <img src> to embedded data URI.
microSALT/server/templates/alignment_page.html	Switches MicroSALT logo <img src> to embedded data URI.

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[karlnyr]

Zenodo badge working in branch:

[karlnyr]

Reports before:

Typing:

QC:

Note

This is an old version of the QC reports where the Swedac logo was included. It was later removed, meaning we should not expect this in new versions of the QC reports.

Reports after:

Typing:

QC:

[jemten]

A couple of questions but otherwise it looks good.

[jemten]

Looks good!