From 2a4c3db7689322ecc3219be32328b7a29e5792e1 Mon Sep 17 00:00:00 2001 From: ubyndr Date: Wed, 1 Nov 2023 13:15:33 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20INCATool?= =?UTF-8?q?s/pandasaurus=5Fcxg@cabb406b9fbeed79e29f5b557d9f43d13f57a8e1=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../pandasaurus_cxg/anndata_analyzer.html | 2 +- .../graph_generator/graph_generator.html | 6 ++++++ .../pandasaurus_cxg/utils/exceptions.html | 15 +++++++++++++-- genindex.html | 4 +++- objects.inv | Bin 1013 -> 1018 bytes pandasaurus_cxg/utils/exception.html | 6 ++++++ searchindex.js | 2 +- 7 files changed, 30 insertions(+), 5 deletions(-) diff --git a/_modules/pandasaurus_cxg/anndata_analyzer.html b/_modules/pandasaurus_cxg/anndata_analyzer.html index 8c86b64..d6522a2 100644 --- a/_modules/pandasaurus_cxg/anndata_analyzer.html +++ b/_modules/pandasaurus_cxg/anndata_analyzer.html @@ -258,7 +258,7 @@

Source code for pandasaurus_cxg.anndata_analyzer

def _enrich_co_annotation(enricher: AnndataEnricher): enriched_df = enricher.enricher.enriched_df if enriched_df.empty: - return pd.DataFrame() + return enriched_df return enriched_df[enriched_df["o"].isin(enricher.seed_list)][["s_label", "o_label"]] def _filter_data_and_drop_duplicates(self, field_name_1, field_name_2, disease): diff --git a/_modules/pandasaurus_cxg/graph_generator/graph_generator.html b/_modules/pandasaurus_cxg/graph_generator/graph_generator.html index 94496cc..22fc06b 100644 --- a/_modules/pandasaurus_cxg/graph_generator/graph_generator.html +++ b/_modules/pandasaurus_cxg/graph_generator/graph_generator.html @@ -83,6 +83,7 @@

Source code for pandasaurus_cxg.graph_generator.graph_generator

from rdflib.plugins.sparql import prepareQuery from pandasaurus_cxg.enrichment_analysis import ( + AnndataAnalyzer, AnndataEnricher, AnndataEnrichmentAnalyzer, ) @@ -102,6 +103,7 @@

Source code for pandasaurus_cxg.graph_generator.graph_generator

) from pandasaurus_cxg.utils.exceptions import ( InvalidGraphFormat, + MissingAnalysisProcess, MissingEnrichmentProcess, ) from pandasaurus_cxg.utils.logging_config import configure_logger @@ -130,6 +132,10 @@

Source code for pandasaurus_cxg.graph_generator.graph_generator

""" # TODO need to think about how to handle the requirement of enrichment and co_annotation_analysis methods self.ea = enrichment_analyzer + if self.ea.analyzer_manager.report_df.empty: + analysis_methods = [i for i in dir(AnndataAnalyzer) if "_report" in i] + analysis_methods.sort() + raise MissingAnalysisProcess(analysis_methods) # TODO need to handle invalid keys. We also need to discuss about keeping the keys param. DO NOT USE self.df = ( enrichment_analyzer.analyzer_manager.report_df[keys] diff --git a/_modules/pandasaurus_cxg/utils/exceptions.html b/_modules/pandasaurus_cxg/utils/exceptions.html index df13b93..cf80a17 100644 --- a/_modules/pandasaurus_cxg/utils/exceptions.html +++ b/_modules/pandasaurus_cxg/utils/exceptions.html @@ -116,14 +116,25 @@

Source code for pandasaurus_cxg.utils.exceptions

class MissingEnrichmentProcess(Exception): def __init__(self, enrichment_methods: List[str]): self.message = ( - f"Any of the following enrichment methods from AnndataEnricher must be used before " - f"using enriched_rdf_graph method: " + f"Any of the following enrichment methods from AnndataEnricher must be used first; " f"{', '.join(enrichment_methods)}" ) super().__init__(self.message)
+
+[docs] +class MissingAnalysisProcess(Exception): + def __init__(self, analysis_methods: List[str]): + self.message = ( + f"Any of the following analysis methods from AnndataAnalyser must be used first; " + f"{', '.join(analysis_methods)}" + ) + super().__init__(self.message)
+ + +
[docs] class SubclassWarning(Exception): diff --git a/genindex.html b/genindex.html index ca0b14a..f7c0f6f 100644 --- a/genindex.html +++ b/genindex.html @@ -232,10 +232,12 @@

M

  • (pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method)
    • -
  • MissingEnrichmentProcess +
  • MissingAnalysisProcess
      • +
    • MissingEnrichmentProcess +
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      +
      +
      +exception pandasaurus_cxg.utils.exceptions.MissingAnalysisProcess(analysis_methods: List[str])[source]
      +

      Bases: Exception

      +
      +
      exception pandasaurus_cxg.utils.exceptions.MissingEnrichmentProcess(enrichment_methods: List[str])[source]
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