Fixed to dump out the go qualifiers with underscores #250
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sagarjhaa
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Apr 2, 2020
kkarra
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Apr 29, 2020
* Merging changes back from master Retiring production proxy servers, so merging changes back from master that were hotfixed into production. Essentially an empty file, but keeping comments to provide sample formatting for future reference if needed. * From hotfixed master File created from master so it will be correct when qa is merged back into master. * script to dump RNA data in JSON format for RNACentral * fixed to get rid of trailing white spaces in note field (#210) * adding a missing space in the expt type pulldown * adding missing name field * added code to upload the file to s3 (#212) * Added keepalives More nginx changes lost from master_legacy. * Add redirects One more sync from master_legacy. * Change healthcheck URL Merge another change from master_legacy branch. * fixed some typos in gff and fixed the duplicate CHEBI term names (#215) * 5534 locus summaries (#216) * Add interaction and disease summary to dict * Add interaction summary, disease to form * Fix the return method for summaries * Add protein and sequence summaries * Add interaction and disease summary to dict * Add interaction summary, disease to form * Fix the return method for summaries * Add protein and sequence summaries * Add interaction and disease summary to dict * Add interaction summary, disease to form * Fix the return method for summaries * Add protein and sequence summaries * Add interaction and disease summary to dict * Add interaction summary, disease to form * Fix the return method for summaries * Add protein and sequence summaries * Add interaction and disease summary to dict * Add interaction summary, disease to form * Fix the return method for summaries * Add protein and sequence summaries * Add field for functional summary. * Add function summary to database. * Add function summary in return value for summaries * Add interaction and disease summary to dict * Add interaction summary, disease to form * Fix the return method for summaries * Add protein and sequence summaries * Add field for functional summary. * Add function summary to database. * Add function summary in return value for summaries * adding code to upload files to s3 or copy files between s3 buckets (#217) * Don't cache /search * Update urls for new/retired tools (#219) * get rid of html tags in pathway names (#218) * script to remove italic tag in pathway name * fixed to get rid of italic tag in pathway name before loading it into DB * commented out the debugging print statement * Updating from master * updated the crontab schedule and fixed the phenotype curation page to handle the non-condition annotation properly (#220) * fixed to handle null group_id properly * rescheduled the crontab * Change the loging format from basic. (#221) * adding new GO_REF IDs * Use taxid to find other strain. (#222) * fixed to point prod CI to preview server (#223) * 5651 ci count (#224) * Add log and rollback for CI count * Remove import of setError * listen for event only for loggedin user. * adding more GO reference IDs to config file * 5570 retire tools 2 (#225) * Add chromosome history and remove Gene registry * Add missing , * 5638 ci login (#226) * Update login api to log and with useful message. * Update flexiForm to show error message. * Fix the string formation for 3.5 * Log unauthorized user. * Add log module (#227) * Modify log module for tests, es-script, curator_views * remove script chemical cap * Revert "Add log module (#227)" This reverts commit 621a1b6. * Don't cache /webservice/get_search_results * Link production CI to preview server (#232) * adding more ENV * adding PREVIEW_URL * fixed PREVIEW URL * fixed PREVIEW URL * fixed PREVIEW URL * fixed PREVIEW URL * fixed PREVIEW URL * adding new class Dnasequenceannotation * getting rid of class Dnasequenceannotation * removed underscore from qualifiers (#233) * Rewrite www-2[ab] to www in prod. * Update the tools url and remove yeast lab (#235) * Update the tools url and remove yeast lab * Update the url for genome wide analysis paper * 5663 curation logs (#234) * Remove the logging setup from models.py * add curation log to write to curation.log in prod * Update to use curation.log for curation views. * Remove setting of log level on separate files. * Update the curation log to log level INFO for login * Scripts of generating sequences, running clustalo, processing data, & loading data for variant viewer project (#236) * adding readme file * adding sample data files * adding scripts for retriving/processing sequence data * adding scripts for running clustalO * adding script for generating variant data * adding scripts for generating variant data * adding scripts for loading seq align + variant data into db * adding classes for variant data * moved codon table to util.py * moved codon table to util.py * Performance config changes Remap more URLs to www.yeastgenome.org. 300/400 level return codes now use default TTL. 500 level codes still retain 15 second TTL. * 5674 ptm duplicate issue (#237) * Update queries to use Referencedbentity * Update to not use e.message * adding term name to SO and others (#238) * adding term_name to SO table * fixed to dump term_name instead of display_name * adding term_name to SO table * adding new script to copy active files to sgd-archive * added entries to crontab * get rid of print statement * adding code to get proper data for mito ncbi submission (#239) * 5688 sql logs (#240) * Remove root config from models.py * set bototcore to loglevel error in dev. * add sql.log to capture sql statements * Remove APP_LOG variable from deployment. * Set sql log to DEBUG level * add es queries to es.log (#241) * Updating SK1 sequence data, alignment, variant data, domain data for sequence variant viewer (#242) * adding code for web service to get data for variant viewer * adding logging & catching exception * adding logging & catching exception * 5384 traffic be (#243) * Fix the root to be DEBUG in dev. * add code to capture translogger traffic * use filehandler for wsgiapp logger * Add paste to requirements.txt * Update Paste package * Add react-datalist-field * use new DataList * Update setting to propagate = 0, (#245) sql to WARNING backend file to INFO * adding error catching for ref update process (#247) * adding error catching * adding more code into try/except block * Branch for PTM datalist (#246) The commits got on to qa directly * 5701 regulation datalist (#248) * Use new autocomplete package. * Remove datalist component * Add logs for Regulations insert,update,delete * update a log statement * Update e.message to str(e) * fixed to use newly updated datalist (#249) * fixed to dump out go qualifiers with underscore (#250) * Kk schema (#252) * bunch of schema changes * dnasequencealignment table DDL * new tables dnasequencealignment, proteinsequencealignment, sequencevariant #5603 * TOOLS table * bunch of schema changes * dnasequencealignment table DDL * new tables dnasequencealignment, proteinsequencealignment, sequencevariant #5603 * TOOLS table * file_type * Dci 5347 (#253) * working version * save * Fix the issue of blank page. * models.py - added association_type * fix deepscan fails Co-authored-by: Sagar <sagar.jhaa@gmail.com> * address 'has_disease' value for disease tab (#256) * insert/update has_disease={true/false} if new gene annotation or last annotation deleted * use .count() * Phenotype CI fixes + supplemental file uploading (#257) * added file_type to ReferenceFile class * fixed to work with newly fixed datalist * added code to handle the case while updating a pheno annotation to an existing one * fixed to work with newly fixed datalist * 5730 ptm encode issue (#258) * Fix encoding issue with file upload * Fix encoding issue with file upload * Fix encoding issue with file upload * adding case sensitive * fixed adding new pheno for non-std gene name issue (#259) * fixed to allow space/dot in the author names (#260) * NISS; DBXREF; COMPLEX/PATHWAY as new objects (#261) * fixed to handle genes with same protein seq properly * fixed to work with new complex/pathways objects * adding code for NISS data processing/loading * fixed code to work with pangenome+complex * rebrand and host bug fix (#263) Co-authored-by: stuartmiyasato <stuartmiyasato@users.noreply.github.com> Co-authored-by: sweng66 <sweng@stanford.edu> Co-authored-by: Sagar Jha <sagar.jhaa@gmail.com> Co-authored-by: Felix Gondwe <gondwefelix8@gmail.com>
kkarra
added a commit
that referenced
this pull request
Apr 29, 2020
* Merging changes back from master Retiring production proxy servers, so merging changes back from master that were hotfixed into production. Essentially an empty file, but keeping comments to provide sample formatting for future reference if needed. * From hotfixed master File created from master so it will be correct when qa is merged back into master. * script to dump RNA data in JSON format for RNACentral * fixed to get rid of trailing white spaces in note field (#210) * adding a missing space in the expt type pulldown * adding missing name field * added code to upload the file to s3 (#212) * Added keepalives More nginx changes lost from master_legacy. * Add redirects One more sync from master_legacy. * Change healthcheck URL Merge another change from master_legacy branch. * fixed some typos in gff and fixed the duplicate CHEBI term names (#215) * 5534 locus summaries (#216) * Add interaction and disease summary to dict * Add interaction summary, disease to form * Fix the return method for summaries * Add protein and sequence summaries * Add interaction and disease summary to dict * Add interaction summary, disease to form * Fix the return method for summaries * Add protein and sequence summaries * Add interaction and disease summary to dict * Add interaction summary, disease to form * Fix the return method for summaries * Add protein and sequence summaries * Add interaction and disease summary to dict * Add interaction summary, disease to form * Fix the return method for summaries * Add protein and sequence summaries * Add interaction and disease summary to dict * Add interaction summary, disease to form * Fix the return method for summaries * Add protein and sequence summaries * Add field for functional summary. * Add function summary to database. * Add function summary in return value for summaries * Add interaction and disease summary to dict * Add interaction summary, disease to form * Fix the return method for summaries * Add protein and sequence summaries * Add field for functional summary. * Add function summary to database. * Add function summary in return value for summaries * adding code to upload files to s3 or copy files between s3 buckets (#217) * Don't cache /search * Update urls for new/retired tools (#219) * get rid of html tags in pathway names (#218) * script to remove italic tag in pathway name * fixed to get rid of italic tag in pathway name before loading it into DB * commented out the debugging print statement * Updating from master * updated the crontab schedule and fixed the phenotype curation page to handle the non-condition annotation properly (#220) * fixed to handle null group_id properly * rescheduled the crontab * Change the loging format from basic. (#221) * adding new GO_REF IDs * Use taxid to find other strain. (#222) * fixed to point prod CI to preview server (#223) * 5651 ci count (#224) * Add log and rollback for CI count * Remove import of setError * listen for event only for loggedin user. * adding more GO reference IDs to config file * 5570 retire tools 2 (#225) * Add chromosome history and remove Gene registry * Add missing , * 5638 ci login (#226) * Update login api to log and with useful message. * Update flexiForm to show error message. * Fix the string formation for 3.5 * Log unauthorized user. * Add log module (#227) * Modify log module for tests, es-script, curator_views * remove script chemical cap * Revert "Add log module (#227)" This reverts commit 621a1b6. * Don't cache /webservice/get_search_results * Link production CI to preview server (#232) * adding more ENV * adding PREVIEW_URL * fixed PREVIEW URL * fixed PREVIEW URL * fixed PREVIEW URL * fixed PREVIEW URL * fixed PREVIEW URL * adding new class Dnasequenceannotation * getting rid of class Dnasequenceannotation * removed underscore from qualifiers (#233) * Rewrite www-2[ab] to www in prod. * Update the tools url and remove yeast lab (#235) * Update the tools url and remove yeast lab * Update the url for genome wide analysis paper * 5663 curation logs (#234) * Remove the logging setup from models.py * add curation log to write to curation.log in prod * Update to use curation.log for curation views. * Remove setting of log level on separate files. * Update the curation log to log level INFO for login * Scripts of generating sequences, running clustalo, processing data, & loading data for variant viewer project (#236) * adding readme file * adding sample data files * adding scripts for retriving/processing sequence data * adding scripts for running clustalO * adding script for generating variant data * adding scripts for generating variant data * adding scripts for loading seq align + variant data into db * adding classes for variant data * moved codon table to util.py * moved codon table to util.py * Performance config changes Remap more URLs to www.yeastgenome.org. 300/400 level return codes now use default TTL. 500 level codes still retain 15 second TTL. * 5674 ptm duplicate issue (#237) * Update queries to use Referencedbentity * Update to not use e.message * adding term name to SO and others (#238) * adding term_name to SO table * fixed to dump term_name instead of display_name * adding term_name to SO table * adding new script to copy active files to sgd-archive * added entries to crontab * get rid of print statement * adding code to get proper data for mito ncbi submission (#239) * 5688 sql logs (#240) * Remove root config from models.py * set bototcore to loglevel error in dev. * add sql.log to capture sql statements * Remove APP_LOG variable from deployment. * Set sql log to DEBUG level * add es queries to es.log (#241) * Updating SK1 sequence data, alignment, variant data, domain data for sequence variant viewer (#242) * adding code for web service to get data for variant viewer * adding logging & catching exception * adding logging & catching exception * 5384 traffic be (#243) * Fix the root to be DEBUG in dev. * add code to capture translogger traffic * use filehandler for wsgiapp logger * Add paste to requirements.txt * Update Paste package * Add react-datalist-field * use new DataList * Update setting to propagate = 0, (#245) sql to WARNING backend file to INFO * adding error catching for ref update process (#247) * adding error catching * adding more code into try/except block * Branch for PTM datalist (#246) The commits got on to qa directly * 5701 regulation datalist (#248) * Use new autocomplete package. * Remove datalist component * Add logs for Regulations insert,update,delete * update a log statement * Update e.message to str(e) * fixed to use newly updated datalist (#249) * fixed to dump out go qualifiers with underscore (#250) * Kk schema (#252) * bunch of schema changes * dnasequencealignment table DDL * new tables dnasequencealignment, proteinsequencealignment, sequencevariant #5603 * TOOLS table * bunch of schema changes * dnasequencealignment table DDL * new tables dnasequencealignment, proteinsequencealignment, sequencevariant #5603 * TOOLS table * file_type * Dci 5347 (#253) * working version * save * Fix the issue of blank page. * models.py - added association_type * fix deepscan fails Co-authored-by: Sagar <sagar.jhaa@gmail.com> * address 'has_disease' value for disease tab (#256) * insert/update has_disease={true/false} if new gene annotation or last annotation deleted * use .count() * Phenotype CI fixes + supplemental file uploading (#257) * added file_type to ReferenceFile class * fixed to work with newly fixed datalist * added code to handle the case while updating a pheno annotation to an existing one * fixed to work with newly fixed datalist * 5730 ptm encode issue (#258) * Fix encoding issue with file upload * Fix encoding issue with file upload * Fix encoding issue with file upload * adding case sensitive * fixed adding new pheno for non-std gene name issue (#259) * fixed to allow space/dot in the author names (#260) * NISS; DBXREF; COMPLEX/PATHWAY as new objects (#261) * fixed to handle genes with same protein seq properly * fixed to work with new complex/pathways objects * adding code for NISS data processing/loading * fixed code to work with pangenome+complex * rebrand and host bug fix (#263) * fix duplicate logging caused by master merge into qa * extra line in models.py Co-authored-by: stuartmiyasato <stuartmiyasato@users.noreply.github.com> Co-authored-by: sweng66 <sweng@stanford.edu> Co-authored-by: Sagar Jha <sagar.jhaa@gmail.com> Co-authored-by: Felix Gondwe <gondwefelix8@gmail.com>
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