Oncotree mapper dev - Githubissues

cBioPortal / oncotree

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Oncotree mapper dev #170

Closed sheridancbio closed 5 years ago

sheridancbio commented 5 years ago

only let NA be a passthrough .. not blank and not N/A
do not bomb on an unrecognized oncotree code .. put a note in the oncotree_code_comments and move on
log unrecognized codes .. add a section in the summary
make the table of contents dependent on whether sections are populated
fix some outstanding syntax bugs
compare forward v. backwards mapping just by comparing release date .. not sorting
issue an error if the file has carriage returns in it
write a message when outputing to main output file
make headers bolder (H2 instead of H3)
drop "you may want to .." --> "you can .."

sheridancbio commented 5 years ago

making changes here from change requests

sheridancbio commented 5 years ago

from comment from @averyniceday : moving section reporting unrecognized oncotree codes to come first in the log/summary

sheridancbio commented 5 years ago

adding check from @averyniceday so that "???" is not added more than once when computing candidate codes. also testing for unrecognized code with (if ("???" in unrecognized_node[CHOICES_FIELD])) rather than len() == 1

sheridancbio commented 5 years ago

it looks like we tried to switch the program argument from "output_file" to "target_file" but the parser defined arguments still has output_file defined. Checking docs to see what we claimed should be there.

sheridancbio commented 5 years ago

The documentation page says we now take --source-file and --target-file as arguments ... so updating the script accordingly

sheridancbio commented 5 years ago

there are other broken references ... so standardizing all references to be to source_file and target_file rather than input_file and output_file

sheridancbio commented 5 years ago

Responding to issue raised by @averyniceday .. I tested the case of multiple occurrences of a "not found in source version" oncotree code. It was only reported once in the log/summary file, despite the code being used in three separate places in the input file.