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UnboundLocalError affecting multiQC metrics for OSD-379 #34

Closed asaravia-butler closed 12 months ago

asaravia-butler commented 1 year ago

pull metrics command: python extract_dataset.py --osd-id OSD-379

Output / stderr:

2023-10-31 08:39:18.196 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmprih50im1 2023-10-31 08:39:18.229 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpdfu6saus 2023-10-31 08:39:18.254 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpbynk41sr 2023-10-31 08:39:18.264 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpqgqqd6ky 2023-10-31 08:39:18.292 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpyd29povf 2023-10-31 08:39:18.293 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp4efvdd7v Not implemented for dataframe extraction: heatmap, skipping this plot with Title: FastQC: Status Checks Traceback (most recent call last): File "/workspace/dp_tools/multiQC_output_ASB/OSD-379/../../extract_dataset.py", line 36, in main() File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1130, in call return self.main(args, kwargs) File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 760, in invoke return __callback(args, **kwargs) File "/workspace/dp_tools/multiQC_output_ASB/OSD-379/../../extract_dataset.py", line 29, in main metricsExtractor.extract_sections() File "/workspace/dp_tools/dp_tools/core/utilites/metrics_extractor.py", line 266, in extract_sections _extract_section_from_json( File "/workspace/dp_tools/dp_tools/core/utilites/metrics_extractor.py", line 150, in _extract_section_from_json df_plot_data = multiqc_tools.format_plots_as_dataframe( File "/workspace/dp_tools/dp_tools/core/utilites/multiqc_tools.py", line 187, in format_plots_as_dataframe flat_plot_dict = format_plot_data(mqc_rep) File "/workspace/dp_tools/dp_tools/core/utilites/multiqc_tools.py", line 330, in format_plot_data clean_data = __clean_mapped_data(mapped_data, messy_to_clean_map) UnboundLocalError: local variable 'mapped_data' referenced before assignment