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* WGS assay 4.0 (#366) * cnv-purple-plugin * other updates for WGS 4.0 --------- Co-authored-by: Felix Beaudry <[email protected]> Co-authored-by: Aqsa Alam <[email protected]> Co-authored-by: Aqsa Alam <[email protected]> Co-authored-by: Felix Beaudry, Ph.D <[email protected]> * Replace input_params_tools with read_maybe_input_params in workspace; update tests (#367) * LOH data added to snv indel plugin * Changed rendering of LOH * Removed useless comments * Update all curated gene list for oncoKB * delete old curated genes file 2023116 * Fix gcgi 1317 write purple copy states (#369) * Fix indentation, imports and return statements * Fix imports, indentation, and return statements in main plugin * Add write_copy_states to purple plugin * Read by column headers instead of numbers * Refactoring: Less fragile handling of paths and validation of purity/ploidy, general cleanup * Fix gcgi 1320 cnv dependency (#370) * Create new wgts.common package and move tools.py there * move CNV code to common.cnv; simplify import path in process_CNA_data.r * Added if statement for X chromosome * Fixed tests for LOH * Update genomic landscape to read purity from PURPLE output; check for existence of input path in TMB calculation (#371) * Added test for when cnv data is missing * Added conditional for if MACN is greater than 0.5 it needs to be False * Fixed minor bug * Dev gcgi 993 multiple plugin packages (#373) * Support multiple top-level package names * Added r directory * Fixed metrix_cell to metric_cell * updated changelog * Support PWGS in mini-Djerba by making summary optional (#376) * Warning instead of error on inconsistent sample names (#377) * Added ARID2 to swi snf gene list * Removed copy state from snv indel plugin * Rewrite case_overview config; new core config method and assay constants; update changelog (#381) * Updated CHANGELOG * Remove obsolete provenance_tools from genomic_landscape (#384) * Import the traceback module in core.render (#383) * GCGI-1318, pWGS report improvements (#374) * first draft of changes * add detection cutoff constant to results_dict * Add introductory sentence * introductory sentence tweaks * introductory sentence tweaks * import case overview plugins * no message * no message * Add extraction step to plugin.py * include data from different plugin to the results dictionary * Pull parameters from full.config.ini * get path to the workspace directory * pull pc.results from json output file * write data to json * Different pattern for extracted fields * no message * using built in method to write to json * Use wrapper to access configuration parameters * Added file not found exception * file exist check and adjusting test * checksum update and testing for scenario when file exists * update summary/plugin_test.py checksum --------- Co-authored-by: Oumaima Hamza <[email protected]> * Edited definitions and disclaimers to include LOH * Edited md5sums for supplement and snv indel * Fixed sensitivity of CNVs from 30% to 100% * pWGS formatting fixes (#385) * Formatting fixes * Summary tweak * Update checksum * Extra formatting tweaks * Adjust padding * Adjust padding * Conditional page break * Syntax fix * no top margin * Adjust padding * no message * Adjust bottom margin * checksums update --------- Co-authored-by: Oumaima Hamza <[email protected]> * Write updated JSON by default, with a more informative name; update changelog and tests (#387) * Dev gcgi 1344 checksum fix (#388) * Update checksums after merging changes from release branch * Update checksums; tests on 1.6.0 release branch now pass (#389) * Update plugin lists for djerba.py setup mode * Added HRDetect to assay description * Updated CHANGELOG.md * Edited md5sums for supplementary * Added links for references * Fix gcgi 1348 benchmark tests (#391) * Update checksums; tests on 1.6.0 release branch now pass * First stage of fixes to benchmarking; can now generate GSICAPBENCH_1219 report * update changelog * Reinstate all but one GSICAPBENCH samples; update tests * Adjusting pWGS e-signature spacing (#392) * adjust space for signature * Checksum update * adjust padding bottom * no message * Checksum update --------- Co-authored-by: Oumaima Hamza <[email protected]> * Merge changes from release v1.5.6 and fix conflicts (#396) * GCGI-1346 setup.py and test/benchmark fixes (#397) * Update checksums * Add init file for alternate Djerba package * Add another init file * Update CNV plugins in setup script * More edits to package data list in setup script * Update setup script and data README * Add pwgs_cardea_helper to setup.py * Reinstate Sequenza CNV plugin to install list * Add HRD to list of plots for redaction * Fix gcgi 1352 update examples (#398) * Changed TERT protein annotation * Changed always to auto for whitespace option in gene information merger * Update CHANGELOG.md * Update version.py * Update WGTS examples * Update changelog and version for release 1.6.0 --------- Co-authored-by: Aqsa Alam <[email protected]> Co-authored-by: Aqsa Alam <[email protected]> --------- Co-authored-by: Felix Beaudry <[email protected]> Co-authored-by: Aqsa Alam <[email protected]> Co-authored-by: Aqsa Alam <[email protected]> Co-authored-by: Felix Beaudry, Ph.D <[email protected]> Co-authored-by: Oumaima Hamza <[email protected]> Co-authored-by: Oumaima Hamza <[email protected]>
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| # alternate_djerba | ||
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| This package exists solely to test Djerba's functionality for loading plugins from multiple packages, added in release 1.6.0. It contains a single `demo4` plugin, which is a renamed version of the old `demo1` plugin. | ||
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| It is *not* intended for production plugins, which should go either go into the main `djerba` package, or an alternate package with a more descriptive name. |
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| """Simple Djerba plugin for demonstration and testing: Example 1""" | ||
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| import logging | ||
| from djerba.plugins.base import plugin_base | ||
| import djerba.core.constants as core_constants | ||
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| class main(plugin_base): | ||
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| PRIORITY = 200 | ||
| PLUGIN_VERSION = '1.0.0' | ||
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| # __init__ is inherited from the parent class | ||
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| def configure(self, config): | ||
| config = self.apply_defaults(config) | ||
| return config | ||
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| def extract(self, config): | ||
| wrapper = self.get_config_wrapper(config) | ||
| attributes = wrapper.get_my_attributes() | ||
| self.check_attributes_known(attributes) | ||
| data = { | ||
| 'plugin_name': self.identifier+' plugin', | ||
| 'version': self.PLUGIN_VERSION, | ||
| 'priorities': wrapper.get_my_priorities(), | ||
| 'attributes': attributes, | ||
| 'merge_inputs': { | ||
| 'gene_information_merger': [ | ||
| { | ||
| "Gene": "KRAS", | ||
| "Gene_URL": "https://www.oncokb.org/gene/KRAS", | ||
| "Chromosome": "12p12.1", | ||
| "Summary": "KRAS, a GTPase which functions as an upstream regulator of the MAPK and PI3K pathways, is frequently mutated in various cancer types including pancreatic, colorectal and lung cancers." | ||
| }, | ||
| { | ||
| "Gene": "PIK3CA", | ||
| "Gene_URL": "https://www.oncokb.org/gene/PIK3CA", | ||
| "Chromosome": "3q26.32", | ||
| "Summary": "PIK3CA, the catalytic subunit of PI3-kinase, is frequently mutated in a diverse range of cancers including breast, endometrial and cervical cancers." | ||
| } | ||
| ] | ||
| }, | ||
| 'results': {}, | ||
| } | ||
| question = 'What do you get if you multiply six by nine?' | ||
| self.workspace.write_string('question.txt', question) | ||
| return data | ||
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| def render(self, data): | ||
| super().render(data) # validate against schema | ||
| return "<h3>TODO demo1 plugin output goes here</h3>" | ||
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| def specify_params(self): | ||
| self.logger.debug("Specifying params for plugin demo1") | ||
| self.add_ini_required('question') | ||
| self.set_ini_default(core_constants.ATTRIBUTES, 'clinical') | ||
| self.set_ini_default('dummy_file', None) | ||
| self.set_priority_defaults(self.PRIORITY) |
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| [core] | ||
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| [demo1] | ||
| question = 'Who will win the Stanley Cup?' |
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| { | ||
| "attributes": ["clinical"], | ||
| "priorities": {"configure": 200, "extract": 200, "render": 200}, | ||
| "merge_inputs": { | ||
| "gene_information_merger": [ | ||
| { | ||
| "Chromosome": "12p12.1", | ||
| "Gene": "KRAS", | ||
| "Gene_URL": "https://www.oncokb.org/gene/KRAS", | ||
| "Summary": "KRAS, a GTPase which functions as an upstream regulator of the MAPK and PI3K pathways, is frequently mutated in various cancer types including pancreatic, colorectal and lung cancers." | ||
| }, | ||
| { | ||
| "Chromosome": "3q26.32", | ||
| "Gene": "PIK3CA", | ||
| "Gene_URL": "https://www.oncokb.org/gene/PIK3CA", | ||
| "Summary": "PIK3CA, the catalytic subunit of PI3-kinase, is frequently mutated in a diverse range of cancers including breast, endometrial and cervical cancers." | ||
| } | ||
| ] | ||
| }, | ||
| "plugin_name": "demo1 plugin", | ||
| "results": {}, | ||
| "version": "1.0.0" | ||
| } |
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