From 28908ca3b77a091d67a912641218d57d3dd11e73 Mon Sep 17 00:00:00 2001
From: sandyr <sandyr@ebi.ac.uk>
Date: Thu, 16 Nov 2023 11:30:04 +0000
Subject: [PATCH] escapes html chars in ebi search dump

---
 .../commands/ebi_search_analysis_dump.py      |  2 +-
 emgapi/templates/ebi_search/analysis.xml      | 30 +++++++++----------
 emgapi/templates/ebi_search/projects.xml      | 10 +++----
 emgcli/__init__.py                            |  2 +-
 pyproject.toml                                |  2 +-
 5 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/emgapi/management/commands/ebi_search_analysis_dump.py b/emgapi/management/commands/ebi_search_analysis_dump.py
index f2713f3fb..8514f98b1 100644
--- a/emgapi/management/commands/ebi_search_analysis_dump.py
+++ b/emgapi/management/commands/ebi_search_analysis_dump.py
@@ -129,7 +129,7 @@ def get_analysis_context(self, analysis: AnalysisJob):
                     try:
                         indexable_value = float(indexable_value.strip())
                     except ValueError:
-                        logger.warning(
+                        logger.debug(
                             f"Could not float-parse supposedly numeric field {indexable_name} : {indexable_value}")
                         continue
                 sample_metadata[
diff --git a/emgapi/templates/ebi_search/analysis.xml b/emgapi/templates/ebi_search/analysis.xml
index 841c2c079..578d24c12 100644
--- a/emgapi/templates/ebi_search/analysis.xml
+++ b/emgapi/templates/ebi_search/analysis.xml
@@ -9,57 +9,57 @@
             <additional_fields>
                 <field name="experiment_type">assembly</field>
                 <field name="pipeline_version">{{ analysis.pipeline.release_version }}</field>
-                <field name="sample_name">{{ analysis.sample.sample_name | safe }}</field>
-                <field name="project_name">{{ analysis.study.study_name | safe }}</field>
-                <field name="biome_name">{{ analysis.study.biome.biome_name | safe }}</field>
+                <field name="sample_name">{{ analysis.sample.sample_name | escape }}</field>
+                <field name="project_name">{{ analysis.study.study_name | escape }}</field>
+                <field name="biome_name">{{ analysis.study.biome.biome_name | escape }}</field>
 
                 {% if analysis.sample.species %}
-                <field name="species">{{ analysis.sample.species | safe }}</field>
+                <field name="species">{{ analysis.sample.species | escape }}</field>
                 {% endif %}
 
                 {% if analysis.sample.environment_feature %}
-                <field name="feature">{{ analysis.sample.environment_feature | safe }}</field>
+                <field name="feature">{{ analysis.sample.environment_feature | escape }}</field>
                 {% endif %}
 
                 {% if analysis.sample.environment_material %}
-                <field name="material">{{ analysis.sample.environment_material | safe }}</field>
+                <field name="material">{{ analysis.sample.environment_material | escape }}</field>
                 {% endif %}
 
-                <field name="sample_alias">{{ analysis.sample.sample_alias | safe }}</field>
-                <field name="project_name">{{ analysis.study.study_name | safe }}</field>
+                <field name="sample_alias">{{ analysis.sample.sample_alias | escape }}</field>
+                <field name="project_name">{{ analysis.study.study_name | escape }}</field>
 
                 <hierarchical_field name="biome">
                 {% for biome_element in analysis_biome %}
                     {% if forloop.first %}
-                    <root>{{ biome_element | safe }}</root>
+                    <root>{{ biome_element | escape }}</root>
                     {% else %}
-                    <child>{{ biome_element | safe }}</child>
+                    <child>{{ biome_element | escape }}</child>
                     {% endif %}
                 {% endfor %}
                 </hierarchical_field>
 
                 {% for metadata_key, metadata_value in sample_metadata.items %}
-                <field name="{{ metadata_key | safe }}">{{ metadata_value | safe }}</field>
+                <field name="{{ metadata_key | escape }}">{{ metadata_value | escape }}</field>
                 {% endfor %}
 
                 {% for taxonomy_lineage_elements in analysis_taxonomies %}
                 <hierarchical_field name="organism">
                     {% for taxonomy_element in taxonomy_lineage_elements %}
                         {% if forloop.first %}
-                        <root>{{ taxonomy_element | safe }}</root>
+                        <root>{{ taxonomy_element | escape }}</root>
                         {% else %}
-                        <child>{{ taxonomy_element | safe  }}</child>
+                        <child>{{ taxonomy_element | escape  }}</child>
                         {% endif %}
                     {% endfor %}
                 </hierarchical_field>
                 {% endfor %}
 
                 {% for go_slim in analysis_go_entries %}
-                <field name="go_term">{{ go_slim.description | safe }}</field>
+                <field name="go_term">{{ go_slim.description | escape }}</field>
                 {% endfor %}
 
                 {% for ips in analysis_ips_entries %}
-                <field name="interpro_entry">{{ ips.description | safe }}</field>
+                <field name="interpro_entry">{{ ips.description | escape }}</field>
                 {% endfor %}
             </additional_fields>
             <cross_references>
diff --git a/emgapi/templates/ebi_search/projects.xml b/emgapi/templates/ebi_search/projects.xml
index d8827e4a1..d8c9d2d04 100644
--- a/emgapi/templates/ebi_search/projects.xml
+++ b/emgapi/templates/ebi_search/projects.xml
@@ -7,8 +7,8 @@
         {% for addition in additions %}
         {% with addition.study as study %}
         <entry xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="{{ study.accession }}">
-            <name>{{ study.study_name | safe }}</name>
-            <description>{{ study.study_abstract | safe }}</description>
+            <name>{{ study.study_name | escape }}</name>
+            <description>{{ study.study_abstract | escape }}</description>
             <dates>
                 <date type="creation_date" value="{{ study.first_created|date:'Y-m-d' }}"/>
                 <date type="last_modification_date" value="{{ study.last_update|date:'Y-m-d' }}"/>
@@ -19,13 +19,13 @@
                 <hierarchical_field name="biome">
                 {% for biome_element in addition.biome_list %}
                     {% if forloop.first %}
-                    <root>{{ biome_element | safe }}</root>
+                    <root>{{ biome_element | escape }}</root>
                     {% else %}
-                    <child>{{ biome_element | safe }}</child>
+                    <child>{{ biome_element | escape }}</child>
                     {% endif %}
                 {% endfor %}
                 </hierarchical_field>
-                <field name="centre_name">{{ study.centre_name | safe }}</field>
+                <field name="centre_name">{{ study.centre_name | escape }}</field>
             </additional_fields>
             <cross_references>
                 <ref dbkey="{{ study.project_id }}" dbname="ena_project"/>
diff --git a/emgcli/__init__.py b/emgcli/__init__.py
index 8d1a700d2..48a6caa0d 100644
--- a/emgcli/__init__.py
+++ b/emgcli/__init__.py
@@ -1 +1 @@
-__version__: str = "2.4.38"
+__version__: str = "2.4.39"
diff --git a/pyproject.toml b/pyproject.toml
index cef87bf5b..780720c82 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -117,7 +117,7 @@ max-line-length = 119
 """
 
 [tool.bumpversion]
-current_version = "2.4.38"
+current_version = "2.4.39"
 
 [[tool.bumpversion.files]]
 filename = "emgcli/__init__.py"