Embed logos as base64 data URIs instead of remote URLs

README.md

@@ -1,5 +1,5 @@
 [![Build status](https://github.com/clinical-genomics/microsalt/actions/workflows/run_tests.yml/badge.svg)](https://github.com/clinical-genomics/microsalt/actions/workflows/run_tests.yml)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4026043.svg)](https://doi.org/10.5281/zenodo.4026043)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.4026043-blue)](https://doi.org/10.5281/zenodo.4026043)
 
 <p align="center">
   <a href="https://github.com/Clinical-Genomics/microSALT">
@@ -32,8 +32,8 @@ microSALT requires a SLURM cluster._
 ### Manual install
 
 1. Clone the repository and enter the directory
-2. Checkout the desired branch
-3. install package using `uv pip install .`
+1. Checkout the desired branch
+1. install package using `uv pip install .`
 
 ## Configuration
 
@@ -48,26 +48,28 @@ Copy the configuration file anywhere and.
 
 microSALT uses [Singularity](https://sylabs.io/singularity/) containers to run the various tools used in the analysis. These containers are available on Clinical Genomics' DockerHub, and can be pulled using the following command:
 
-`singularity pull docker://clinicalgenomics/microsalt-blast:latest`
-`singularity pull docker://clinicalgenomics/microsalt-bwa:latest`
-`singularity pull docker://clinicalgenomics/microsalt-picard:latest`
-`singularity pull docker://clinicalgenomics/microsalt-quast:latest`
-`singularity pull docker://clinicalgenomics/microsalt-samtools:latest`
-`singularity pull docker://clinicalgenomics/microsalt-skesa:latest`
-`singularity pull docker://clinicalgenomics/microsalt-trimmomatic:latest`
+```Console
+singularity pull docker://clinicalgenomics/microsalt-blast:latest
+singularity pull docker://clinicalgenomics/microsalt-bwa:latest
+singularity pull docker://clinicalgenomics/microsalt-picard:latest
+singularity pull docker://clinicalgenomics/microsalt-quast:latest
+singularity pull docker://clinicalgenomics/microsalt-samtools:latest
+singularity pull docker://clinicalgenomics/microsalt-skesa:latest
+singularity pull docker://clinicalgenomics/microsalt-trimmomatic:latest
+```
 
 > [!NOTE]
 > Remember to enter the correct path to the singularity images in the configuration file.
 
 ## Usage
 
 - `microsalt analyse` contains functions to start sbatch job(s) & produce
-  output to `folders['results']`. Afterwards the parsed results are uploaded
-  to the SQL back-end and produce reports (HTML), which are then automatically
-  e-mailed to the user.
+    output to `folders['results']`. Afterwards the parsed results are uploaded
+    to the SQL back-end and produce reports (HTML), which are then automatically
+    e-mailed to the user.
 - `microsalt utils` contains various functionality, including generating the
-  sample description json, manually adding new reference organisms and
-  re-generating reports.
+    sample description JSON, manually adding new reference organisms and
+    re-generating reports.
 
 ## Setup
 

microSALT/__init__.py

@@ -1,6 +1,6 @@
 import logging
 
-__version__ = "5.0.0"
+__version__ = "5.0.1"
 
 logger = None
 

microSALT/server/templates/STtracker_page.html

@@ -6,8 +6,7 @@
           <!-- Summary pages  -->
           <footer>
             <div class="panel"><div class="panel-body">
-              <a href="https://github.com/Clinical-Genomics/microSALT"><img src="https://github.com/Clinical-Genomics/microSALT/blob/master/artwork/microsalt.jpg?raw=true" alt="MicroSALT Logo" align="left" style="position:absolute;left:15px;width:400px;height:100px;display:flex;"></a>
-              <!--<img src="swedac.jpg" alt="Swedac Logo" align="right" style="display:flex;">-->
+                <a href="https://github.com/Clinical-Genomics/microSALT"><img src="{{read_jpg(file_path=microsalt_logo_path)}}" alt="MicroSALT Logo" align="left" style="position:absolute;left:15px;width:400px;height:100px;display:flex;"></a>
               <h2 class="page-header">
                 <small><br><br><br>Sekvenstypsuppdateringar</small>
               <small><p align="center">Rapport genererad: {{date}}</p></small></h2>

microSALT/server/templates/alignment_page.html

@@ -7,7 +7,7 @@
           <footer>
             <div class="panel"><div class="panel-body">
               <a href="https://github.com/Clinical-Genomics/microSALT">
-              <img src="https://github.com/Clinical-Genomics/microSALT/blob/master/artwork/microsalt.jpg?raw=true" \
+                <img src="{{read_jpg(file_path=microsalt_logo_path)}}" \
               alt="MicroSALT Logo" align="left" \
               style="position:absolute;left:15px;width:400px;height:100px;display:flex;"></a>
               <h2 class="page-header">

microSALT/server/templates/typing_page.html

@@ -7,11 +7,11 @@
           <footer>
             <div class="panel"><div class="panel-body">
               <a href="https://github.com/Clinical-Genomics/microSALT">
-              <img src="https://github.com/Clinical-Genomics/microSALT/blob/master/artwork/microsalt.jpg?raw=true" \
+                <img src="{{read_jpg(file_path=microsalt_logo_path)}}" \
               alt="MicroSALT Logo" align="left" \
               style="position:absolute;left:15px;width:400px;height:100px;display:flex;"></a>
               {% if topsample.application_tag and 'MW' in topsample.application_tag %}
-                <img src="https://github.com/Clinical-Genomics/microSALT/blob/master/artwork/swedac.jpg?raw=true" alt="Swedac Logo" align="right" style="display:flex;">
+              <img src="{{read_jpg(file_path=swedac_logo_path)}}" alt="Swedac Logo" align="right" style="display:flex;">
               {% endif %}
               <h2 class="page-header">
                 <small><br><br><br>Typningsrapport</small>
@@ -263,7 +263,7 @@ <h3>Signatur f&ouml;r godk&auml;nnande av rapport<br></h3>
         	  <h2 class="page-header"><div class="row"></div>Detaljresultat
                   {% if sample.organism is not none %}
                     {% if sample.priority == 'standard' and sample.organism.replace('_', ' ').capitalize() in verified_organisms %}
-                      <img src="https://github.com/Clinical-Genomics/microSALT/blob/master/artwork/swedac.jpg?raw=true" alt="Swedac Logo" \
+                      <img src="{{read_jpg(file_path=swedac_logo_path)}}" alt="Swedac Logo" \
                       align="right" style="width:40px;height:60px;display:flex;">
                     {% endif %}
                   {% endif %}

microSALT/server/utils.py

@@ -0,0 +1,13 @@
+import base64
+from importlib.resources import files
+from importlib.resources.abc import Traversable
+
+SWEDAC_LOGO_PATH: Traversable = files("microSALT").joinpath("artwork", "swedac.jpg")
+MICROSALT_LOGO_PATH: Traversable = files("microSALT").joinpath("artwork", "microsalt.jpg")
+
+
+def read_jpg(file_path: Traversable) -> str:
+    """Return a base64-encoded data URI for a JPEG image."""
+    with file_path.open("rb") as jpg_file:
+        encoded_string: str = base64.b64encode(jpg_file.read()).decode("utf-8")
+    return f"data:image/jpeg;base64,{encoded_string}"

microSALT/server/views.py

@@ -8,15 +8,15 @@
 
 from microSALT import __version__
 from microSALT.config import Threshold
+from microSALT.server.utils import MICROSALT_LOGO_PATH, SWEDAC_LOGO_PATH, read_jpg
+from microSALT.store.database import get_session
 from microSALT.store.orm_models import (
     Collections,
     Reports,
     Samples,
     Versions,
 )
 
-from microSALT.store.database import get_session
-
 # Removes server start messages
 log = logging.getLogger("werkzeug")
 log.setLevel(logging.CRITICAL)
@@ -48,6 +48,10 @@ def render_template(template_folder, template_name, **context):
     """Renders a template using Jinja2 directly to avoid Flask overhead"""
     template_loader = FileSystemLoader(searchpath=str(template_folder))
     jinja_env = Environment(loader=template_loader)
+    jinja_env.globals["read_jpg"] = read_jpg
+    jinja_env.globals["microsalt_logo_path"] = MICROSALT_LOGO_PATH
+    jinja_env.globals["swedac_logo_path"] = SWEDAC_LOGO_PATH
+
     template = jinja_env.get_template(template_name)
     if "url_for" not in context:
         context["url_for"] = _make_url_for()
@@ -93,7 +97,13 @@ def render_alignment_page(project, threshold: Threshold, template_folder: Path =
     return alignment_page(project, threshold=threshold, template_folder=template_folder)
 
 
-def typing_page(project, organism_group, threshold: Threshold, verified_organisms: list, template_folder: Path = TEMPLATE_FOLDER):
+def typing_page(
+    project,
+    organism_group,
+    threshold: Threshold,
+    verified_organisms: list,
+    template_folder: Path = TEMPLATE_FOLDER,
+):
     sample_info = gen_reportdata(project, organism_group, threshold=threshold)
 
     return render_template(
@@ -111,8 +121,20 @@ def typing_page(project, organism_group, threshold: Threshold, verified_organism
     )
 
 
-def render_typing_page(project, organism_group, threshold: Threshold, verified_organisms: list, template_folder: Path = TEMPLATE_FOLDER):
-    return typing_page(project, organism_group, threshold=threshold, verified_organisms=verified_organisms, template_folder=template_folder)
+def render_typing_page(
+    project,
+    organism_group,
+    threshold: Threshold,
+    verified_organisms: list,
+    template_folder: Path = TEMPLATE_FOLDER,
+):
+    return typing_page(
+        project,
+        organism_group,
+        threshold=threshold,
+        verified_organisms=verified_organisms,
+        template_folder=template_folder,
+    )
 
 
 def STtracker_page(customer, threshold: Threshold, template_folder: Path = TEMPLATE_FOLDER):
@@ -123,7 +145,7 @@ def STtracker_page(customer, threshold: Threshold, template_folder: Path = TEMPL
             if s.pubmlst_ST != -1 and s.ST < 0:
                 final_samples.append(s)
 
-    final_samples = sorted(final_samples, key=lambda sample: (sample.CG_ID_sample))
+    final_samples = sorted(final_samples, key=lambda sample: sample.CG_ID_sample)
 
     return render_template(
         template_folder=template_folder,
@@ -219,8 +241,7 @@ def gen_add_info(sample_info=dict(), threshold: Optional[Threshold] = None):
                         seq_type.st_predictor
                         and seq_type.identity >= threshold.mlst_novel_id
                         and threshold.mlst_id > seq_type.identity
-                        and 1 - abs(1 - seq_type.span)
-                        >= (threshold.mlst_span / 100.0)
+                        and 1 - abs(1 - seq_type.span) >= (threshold.mlst_span / 100.0)
                     ):
                         near_hits = near_hits + 1
                     elif (
@@ -245,18 +266,12 @@ def gen_add_info(sample_info=dict(), threshold: Optional[Threshold] = None):
         # Resistence filter
         if threshold is not None:
             for r in s.resistances:
-                if (
-                    r.identity >= threshold.motif_id
-                    and r.span >= threshold.motif_span / 100.0
-                ):
+                if r.identity >= threshold.motif_id and r.span >= threshold.motif_span / 100.0:
                     r.threshold = "Passed"
                 else:
                     r.threshold = "Failed"
             for v in s.expacs:
-                if (
-                    v.identity >= threshold.motif_id
-                    and v.span >= threshold.motif_span / 100.0
-                ):
+                if v.identity >= threshold.motif_id and v.span >= threshold.motif_span / 100.0:
                     v.threshold = "Passed"
                 else:
                     v.threshold = "Failed"

pyproject.toml

@@ -44,10 +44,10 @@ include = ["microSALT*"]
 
 [dependency-groups]
 dev = [
-    "black>=23.0",
+    "black>=26.3.1",
     "flake8>=6.0",
     "gitlint>=0.19.1",
-    "pytest>=7.4",
+    "pytest>=9.0.3",
     "pylint>=3.0",
     "yamllint>=1.32",
 ]