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 @@ assembly {{ analysis.pipeline.release_version }} - {{ analysis.sample.sample_name | safe }} - {{ analysis.study.study_name | safe }} - {{ analysis.study.biome.biome_name | safe }} + {{ analysis.sample.sample_name | escape }} + {{ analysis.study.study_name | escape }} + {{ analysis.study.biome.biome_name | escape }} {% if analysis.sample.species %} - {{ analysis.sample.species | safe }} + {{ analysis.sample.species | escape }} {% endif %} {% if analysis.sample.environment_feature %} - {{ analysis.sample.environment_feature | safe }} + {{ analysis.sample.environment_feature | escape }} {% endif %} {% if analysis.sample.environment_material %} - {{ analysis.sample.environment_material | safe }} + {{ analysis.sample.environment_material | escape }} {% endif %} - {{ analysis.sample.sample_alias | safe }} - {{ analysis.study.study_name | safe }} + {{ analysis.sample.sample_alias | escape }} + {{ analysis.study.study_name | escape }} {% for biome_element in analysis_biome %} {% if forloop.first %} - {{ biome_element | safe }} + {{ biome_element | escape }} {% else %} - {{ biome_element | safe }} + {{ biome_element | escape }} {% endif %} {% endfor %} {% for metadata_key, metadata_value in sample_metadata.items %} - {{ metadata_value | safe }} + {{ metadata_value | escape }} {% endfor %} {% for taxonomy_lineage_elements in analysis_taxonomies %} {% for taxonomy_element in taxonomy_lineage_elements %} {% if forloop.first %} - {{ taxonomy_element | safe }} + {{ taxonomy_element | escape }} {% else %} - {{ taxonomy_element | safe }} + {{ taxonomy_element | escape }} {% endif %} {% endfor %} {% endfor %} {% for go_slim in analysis_go_entries %} - {{ go_slim.description | safe }} + {{ go_slim.description | escape }} {% endfor %} {% for ips in analysis_ips_entries %} - {{ ips.description | safe }} + {{ ips.description | escape }} {% endfor %} 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 %} - {{ study.study_name | safe }} - {{ study.study_abstract | safe }} + {{ study.study_name | escape }} + {{ study.study_abstract | escape }} @@ -19,13 +19,13 @@ {% for biome_element in addition.biome_list %} {% if forloop.first %} - {{ biome_element | safe }} + {{ biome_element | escape }} {% else %} - {{ biome_element | safe }} + {{ biome_element | escape }} {% endif %} {% endfor %} - {{ study.centre_name | safe }} + {{ study.centre_name | escape }} 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"