UnboundLocalError: local variable 'mapped_data' referenced before assignment

[asaravia-butler]

Raw data only branch
OSD-375

pull metrics

2023-11-02 05:15:33.619 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmppux888ig
2023-11-02 05:15:33.639 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpy_n4mnvz
2023-11-02 05:15:33.659 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp5eaouu2x
2023-11-02 05:15:33.662 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp6ph8ktwh
2023-11-02 05:15:33.682 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpko10hv8f
2023-11-02 05:15:33.683 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpc58yq76u
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/datasets_w_raw_only_multiQC/OSD-375/../../../extract_dataset.py", line 36, in
main()
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/workspace/dp_tools/multiQC_output_ASB/datasets_w_raw_only_multiQC/OSD-375/../../../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

[asaravia-butler]

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

[asaravia-butler]

START OSD-243

pull metrics

2023-11-05 22:42:43.788 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpvp5mh_d1
2023-11-05 22:42:43.809 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpuyq3gyc2
2023-11-05 22:42:43.831 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpc1a3atit
2023-11-05 22:42:43.837 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpkq2jv6a3
2023-11-05 22:42:43.858 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpinjzicaz
2023-11-05 22:42:43.859 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp7yx7xb_o
/workspace/dp_tools/dp_tools/core/utilites/metrics_extractor.py:186: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
self.metrics = self.metrics.append(df_updated_metrics)
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/PE_datasets_w_raw_trim_align_multiQC/OSD-243/../../../extract_dataset.py", line 36, in
main()
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/workspace/dp_tools/multiQC_output_ASB/PE_datasets_w_raw_trim_align_multiQC/OSD-243/../../../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

[asaravia-butler]

START OSD-244

pull metrics

2023-11-05 22:42:45.311 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpcp7g1uux
2023-11-05 22:42:45.331 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp5zuhs0so
2023-11-05 22:42:45.354 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpo4rmyyd9
2023-11-05 22:42:45.360 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpt5nl70y_
2023-11-05 22:42:45.380 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpmvuymt9z
2023-11-05 22:42:45.381 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpotwv4oun
/workspace/dp_tools/dp_tools/core/utilites/metrics_extractor.py:186: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
self.metrics = self.metrics.append(df_updated_metrics)
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/PE_datasets_w_raw_trim_align_multiQC/OSD-244/../../../extract_dataset.py", line 36, in
main()
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/workspace/dp_tools/multiQC_output_ASB/PE_datasets_w_raw_trim_align_multiQC/OSD-244/../../../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

[asaravia-butler]

START OSD-245

pull metrics

2023-11-05 22:42:46.764 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp5ynpn16k
2023-11-05 22:42:46.784 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmppz1j8teh
2023-11-05 22:42:46.804 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmppcqy3o1b
2023-11-05 22:42:46.811 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpz6ukgscl
2023-11-05 22:42:46.832 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpnhf4hued
2023-11-05 22:42:46.833 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp88q3nv7b
/workspace/dp_tools/dp_tools/core/utilites/metrics_extractor.py:186: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
self.metrics = self.metrics.append(df_updated_metrics)
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/PE_datasets_w_raw_trim_align_multiQC/OSD-245/../../../extract_dataset.py", line 36, in
main()
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/workspace/dp_tools/multiQC_output_ASB/PE_datasets_w_raw_trim_align_multiQC/OSD-245/../../../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

[asaravia-butler]

START OSD-247

pull metrics

2023-11-05 22:42:50.101 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp4drzapy4
2023-11-05 22:42:50.124 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp6zez1nd6
2023-11-05 22:42:50.145 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpeiiqfsu4
2023-11-05 22:42:50.151 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp3aihntr0
2023-11-05 22:42:50.172 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmprgxmogp_
2023-11-05 22:42:50.173 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpebmbnstx
/workspace/dp_tools/dp_tools/core/utilites/metrics_extractor.py:186: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
self.metrics = self.metrics.append(df_updated_metrics)
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/PE_datasets_w_raw_trim_align_multiQC/OSD-247/../../../extract_dataset.py", line 36, in
main()
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/workspace/dp_tools/multiQC_output_ASB/PE_datasets_w_raw_trim_align_multiQC/OSD-247/../../../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

[asaravia-butler]

START OSD-248

pull metrics

2023-11-05 22:42:51.515 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp50_r5d16
2023-11-05 22:42:51.537 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpwtgxcfx9
2023-11-05 22:42:51.559 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpssa60c5k
2023-11-05 22:42:51.565 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpc4ktfun8
2023-11-05 22:42:51.586 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp8qax31aq
2023-11-05 22:42:51.587 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp9dk6ttjw
/workspace/dp_tools/dp_tools/core/utilites/metrics_extractor.py:186: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
self.metrics = self.metrics.append(df_updated_metrics)
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/PE_datasets_w_raw_trim_align_multiQC/OSD-248/../../../extract_dataset.py", line 36, in
main()
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/workspace/dp_tools/multiQC_output_ASB/PE_datasets_w_raw_trim_align_multiQC/OSD-248/../../../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

[asaravia-butler]

START OSD-253

pull metrics

2023-11-05 22:42:54.669 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmppxjme93r
2023-11-05 22:42:54.690 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpj5up4x6l
2023-11-05 22:42:54.711 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp_onh5ck5
2023-11-05 22:42:54.718 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpcxrhwsbt
2023-11-05 22:42:54.740 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp7tcjbo5u
2023-11-05 22:42:54.742 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp7u6mc35f
/workspace/dp_tools/dp_tools/core/utilites/metrics_extractor.py:186: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
self.metrics = self.metrics.append(df_updated_metrics)
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/PE_datasets_w_raw_trim_align_multiQC/OSD-253/../../../extract_dataset.py", line 36, in
main()
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/workspace/dp_tools/multiQC_output_ASB/PE_datasets_w_raw_trim_align_multiQC/OSD-253/../../../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

[asaravia-butler]

START OSD-254

pull metrics

2023-11-05 22:42:56.087 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp02ue84xa
2023-11-05 22:42:56.110 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpzo3xi7o7
2023-11-05 22:42:56.132 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpjq5grzi1
2023-11-05 22:42:56.139 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpriajkkm7
2023-11-05 22:42:56.162 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpz3mdc06f
2023-11-05 22:42:56.164 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp444_nw9b
/workspace/dp_tools/dp_tools/core/utilites/metrics_extractor.py:186: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
self.metrics = self.metrics.append(df_updated_metrics)
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/PE_datasets_w_raw_trim_align_multiQC/OSD-254/../../../extract_dataset.py", line 36, in
main()
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/workspace/dp_tools/multiQC_output_ASB/PE_datasets_w_raw_trim_align_multiQC/OSD-254/../../../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

[asaravia-butler]

START OSD-272

pull metrics

2023-11-05 22:42:57.589 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp6opy84_f
2023-11-05 22:42:57.610 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp87lmqv68
2023-11-05 22:42:57.631 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpmqh1yu7o
2023-11-05 22:42:57.637 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpr_hqlt_t
2023-11-05 22:42:57.658 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpb6do5fnp
2023-11-05 22:42:57.659 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp0un24rdm
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/PE_datasets_w_raw_trim_align_multiQC/OSD-272/../../../extract_dataset.py", line 36, in
main()
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/workspace/dp_tools/multiQC_output_ASB/PE_datasets_w_raw_trim_align_multiQC/OSD-272/../../../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

[asaravia-butler]

START OSD-273

pull metrics

2023-11-05 22:42:58.853 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpkr67moxr
2023-11-05 22:42:58.873 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpspxbaclu
2023-11-05 22:42:58.894 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpw42sgs3s
2023-11-05 22:42:58.899 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmpa9vuvcgr
2023-11-05 22:42:58.919 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp3ty9q49u
2023-11-05 22:42:58.919 | DEBUG | dp_tools.core.files.isa_archive:fetch_isa_files:29 - Extracting ISA Archive to temp directory: /tmp/tmp02kp_urs
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/PE_datasets_w_raw_trim_align_multiQC/OSD-273/../../../extract_dataset.py", line 36, in
main()
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/gitpod/miniconda3/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/workspace/dp_tools/multiQC_output_ASB/PE_datasets_w_raw_trim_align_multiQC/OSD-273/../../../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