Alliance files 6.0.0 #430
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Alliance files 6.0.0 #430
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sweng66
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Sep 6, 2023
* fixed to exclude transcripts for genome snapshot * changed 'null mutant' to 'null' * Code for Allele CI and all allele related backend changes (#316) * adding code for allele search & CI * adding code for new allele CI * new code for allele CI * adding code for allele CI * adding code for allele CI * adding code for allele CI * adding code for allele CI * fixed dbentity_id to allele_id * pass created_by around * checking to see if sgdid passed in * checking to see if sgdid passed in * checking to see if sgdid passed in * checking to see if updating desc/so term is working * checking to see if updating desc/so term is working * testing papers for allele name * testing papers for allele type * testing papers for allele type * testing papers... * testing papers... * testing papers... * testing papers... * testing papers... * testing papers... * testing aliases & papers... * testing aliases & papers... * testing aliases & papers... * testing aliases & papers... * testing aliases & papers... * testing aliases & papers... * testing aliases & papers... * testing aliases & papers... * testing aliases & papers... * testing aliases & papers... * testing aliases & papers... * passing parameters to delete web service * testing aliases & papers... * testing for deletion action... * testing for deletion action... * testing for deletion action... * testing for deletion action... * testing for deletion action... * testing for deletion action... * testing for deletion action... * testing for deletion action... * testing for deletion action... * adding preview link * new script for updating panther IDs * adding preview link * adding preview link * adding preview link * adding preview link * adding preview link * adding preview link * adding preview link * adding preview link * added check to make sure to ignore the duplicate rows * testing * testing * testing * testing * testing * adding preview link * testing * testing * get rid duplicate so term from the allele type list * added update url for newly added allele * get rid of other pmids and literatureannotation code * get rid of OneColTextField * added search_allele route * added allele search/update link * fixed to search allele name properly * fixing unmatched <span> tag * fixing unmatched <span> tag * adding logging * adding logging * testing * fixed to display allele search result * fixed to display allele search result * fixed to display allele search result * fixed to display allele search result * fixed to display allele search result * fixed to display allele search result * fixed to display allele search result * fixed to display allele search result * adding more checks * changed regulator_type from 'RNA-binding protein' to 'RNA binder' * adding code to handle alleles in lit triage * testing * added code to handle allele name * adding code to make genome snapshot work * get rid of unused variable * fixed to have proper reference_mapping for alleles * fixed text * adding all papers to literatureannotation for a new allele * fixed to display references only for basic info in allele pages * fixed to add new papers to literatureannotation table * fixed to get allele names that are listed in curation_reference table * fixed alleles with spaces * fixed to handle multiple taxonomy_id * fixed to get rid of quotes in allele names * fixed desc update message * fixed to only update domain data for reference genome * comment out the code for deleting old domains * fixed to return multiple affected genes for an allele * added code for complex facets * new versions of linkout files * adding transcripts to gff by Edith * Fixes to PTM/Regulation CI and complex web service (#319) * fixed complex webservice to accept SGDID * fixed PTM/regulation CI to accept complex as object * fixed typo * Update sgd-web Remove Strict-Transport-Security header. * Fix to phenotype CI to avoid duplicate alleles + code for cleaning up duplicate allele + updating alleles/scores etc (#320) * fixed phenotype CI * new scripts for updating alleles for interaction * new file for searching alleles * adding sgdid to complex web service * fixed a few bugs * fixed format name as well while display_name changed * script for adding missing yeastRGB links * fixed to check database directly if a paper ID is not in redis * Complement CI (#321) * save initial * save working version * save upload file initial * save * removed source; added info for overview * add triggers for funccomp table * fix hgnc url (#322) * can't update created_by (#323) * remove /hgnc in url (#324) * comment optional (#325) * cleaned up code for download gaf from go central and added an extra tab to the file * New files & new code for file metadata CI (#328) * new files for metadata CI * adding code for metadata CI * getting rid of unwanted prop * fixed to get around with go.owl format change * fixed minor bug * adding code for searching by PMID and GEO ID etc + plus fixing a few bugs (#329) * adding code to handle pmid/geo ID search * adding pmid to the edit page * minor text editing * fixing None bug * check for None previous file name and desc * added code to handle file with a dataset * New files/code for supplemental file uploading CI (#331) * adding new files for suppl uploading CI * adding new code for suppl uploading CI * adding 'Delete' button to file metadata CI and fixing code to reset multiple versions of old files in suppl CI (#332) * adding 'delele function' to file metadata CI * fixed to reset all old files that are matching the file names PMID.zip * adding delete message * adding code to add a row into Referencedeleted table when a paper is deleted * adding code to add a row into Referencedeleted table when a paper is deleted * adding code to add a row into Referencedeleted table when a paper is deleted * adding code to add a row into Referencedeleted table when a paper is deleted * adding reason_deleted * fixed typo * fixed typo * fixed typo * fixed to dump gaf in version2.2 format * fixed the reason for a paper to be deleted * Update varnish.vcl Change cache retention from 23.75h to 1s in prod. * New files + new code pieces for dataset/sample CI (#334) * new files for dataset CI * new code for dataset CI * adding keyword search box * fixed to not allow new keyword * skip transcripts * adding a new lab row * adding extra url & lab rows * getting 2nd lab info * fixing typo * fixing code to handle multiple labs for a dataset * fixing code to handle multiple labs for a dataset * fixing code to handle multiple labs for a dataset * fixing code to handle multiple labs for a dataset * fixing code to handle multiple labs for a dataset * formating the info text * formating the info text * make keywork search box smaller * fixing typo * making keyword search box smaller * getting rid of unused 'index' prop * getting rid of unused 'index' prop * getting rid of unused 'index' prop * fixing deepSacn warning * fixing deepSacn warning * fixing deepSacn warning * fixing deepSacn warning * get rid of any double spaces or trailing space in ncbi protein names + adding TPA protein ID for YPR099C if it is not in DB * adding TPA protein ID for YPR099C * new code/files for homology tab (#335) * adding code for homology tab * adding commit * making 'description' box larger for File Metadata CI * adding code to handle allele name for ORF * get rid of dataset CI link * fixed to make sure the S288C seq is on top of sequence_details web service * adding code for complementation data display (#339) * adding code for functional complementation annotations * adding code for functional complementation annotations * adding code for functional comp annots * adding/fixing code for functional compl * fixing code for functional compl * fixing/adding code for functional compl * script to copy URL files over to download site * Adding scripts/code for R64-3 annotation update (#340) * adding scripts for dumping data out for genome update * fixing code for genome annotation update * adding new scripts for updating variant data * adding scripts for adding the new domain data for genome update * adding scripts for R64-3 annotation update * fixed minor bug * updated genome version * fixing R64-2-1 to R64-3-1 * assay_id schema changes (#343) * Dataset/Sample batch loading CI + dataset/sample/track updating CI (#345) * fixed to move assay_id from dataset to datasetsample table + fixing bugs * adding uORF/other features and fixing bugs * fixed bug for regulation data loading * fixed regulator type allowed list + error message../../../curation_views.py * fixed regulator type allowed list + error message * fixed asn1 script option * updating release version for fsa files * updating release version for fsa files * updating release version for fsa files * new version of tbl2asn 2021-05-11 * update go_qualifier allowable values and add located in (#346) * fixed to only dump out main features that have seq in dnasequenceannotation table * fixed to handle pseudo genes properly * adding new regulation_type 'translation' * set a few ncRNA as antisense_RNA * return geo_url as well for dataset * set dataset condition to blank if it is null * adding dockerfile+scripts for BLAST server * adding dockerfile and program for patmatch docker image * getting rid of \ in the search query * move files around * move files around * adding json conf files for blast * adding wsgi file for blast * adding python code for blast * Stuart cleaned up the steps * getting rid of debugging code * fixing some formattting bugs * moving files around * clean up dockerfile * adding files for patmatch docker image * fixed to handle bad Taxon ID * fixed to handle special characters in the datafile * fixed a few bugs * fixed a minor bug * adding new files/code for go tools * adding new files/code for go tools * adding new files/code for go tools * adding wsgi file for gotools * adding lib dir * fixing a minor bug * fixed jbrowse link parameters * fixed font size for blast search alignments * adding script for dumping gene to pmid mapping file for NCBI + adding the script to crontab (#350) * fixing the upload location * script for dumping gene/pmid pair for NCBI * adding gene2pmid mapping script * update documentation for setup, update Makefile, and travis to align test target (#351) * adding scripts for pdf downloading * scripts for pdf download related * fixed setup.py to work for both new/old pip versions (#353) * fixed URLeco.py * scripts for checking ontology data * fixed owl url * adding github actions qc workflow to run the python tests (#355) * adding github actions qc workflow to run the python tests * removing assay_id key from DatasetFactory * adding the needed factories and side effect function cases to make tests work * correcting errors and failures in tests * removing test_reference_tags_should_return_valid_reference * adding PREVIEW_URL to test environment variables * adding PREVIEW_URL to test environment variables to github actions qc.yaml * removing travis yaml * removing print statements, removing bad extra fields in models * rebased to QA version Co-authored-by: sweng66 <[email protected]> * checking scripts (#356) * adding facets for alleles * script for checking NTR terms * fixed interfaces & scripts to avoid dup'ed DOI (#358) * check to not add dup'ed doi * check to not add dup'ed doi * check to not add dup'ed doi * check to not add dup'ed doi * check to skip dup'ed doi * check to skip dup'ed doi * check to skip dup'ed doi * fixed to skip dup'ed doi * fixed to skip dup'ed doi * fixed email * running checking scripts * script for fixing bad goid in paragraph * fixed NULL created_by issue * fixed missing bad GOIDs in paragraphs * scripts for generating/updating genome count for GO Slim terms plus for adding extra complex terms to goslim (#361) * script for generating genome count * script for adding extra complex terms into goslim * script for updating genome_count in goslim * fixed created_by issue * adding one more obsolete id * adding missing FilePath * adding missing file * fixed a typo * adding alleles associated with gene to allele facet * script to NCBI link urls * adding ncbi link urls for new features * script for adding non-pubmed paper * adding allele/complex/pathway facets to Reference category * fixed to only update annotations for Active features * fixed to add complexes + NISS genes * upgrade capistrano to 3.8 for remote deploy to work on big sur (#362) * adding bad PMID check * fixed to handle non-pubmed ID properly * fixed a minor bug * adding code to get allele data for a locus * set lock to 3.4.0 in deploy.rb * fixed is_in_triage to false to new colleague rows * fixed to get around with missing go evidence code * scripts for generating/process/updating/dumping GO slim data (#365) * fixed to show all go slim terms on go tab * fixed to not load other parents * adding scripts for updating goslimannotation table * fixed to group slim terms * fixed to group slim terms * fixed to group slim terms * fixed to group slim terms * fixed to group slim terms * fixed to group slim terms * fixed to group slim terms * fixed to group slim terms * fixed to group slim terms * script for dumping goslim mapping file * fixed to take the slim type from command line * fixed to get allele Refs from literatureannotation table * fixed the NCBI record retrieval errors * fixed to take care of 'bad' records * removed the 2nd update script * fixed to update doi properly * fixed typo * adding HTP to search * scripts for updating goslim table * fixed allele search counting issue * get rid of special characters from gff file * script for dumping RNA dbxrefs * fixed to get papers for phenotype, htp, disease properly * one-off loading missing complex papers into literatureannotation table * fixed paper sorting for htp set and adding code to retrieve refs for complex * fixed typo * get rid of access / secret keys from backend codebase (#368) * fixed loading scripts to not use AWS access/secret keys and to use boto3 * fixed python modules to not use AWS access/secret keys and to use boto3 * fixed typo * adding scripts to goslim_update pipeline * adding entry to copy go slim mapping file * adding code to upload the file to s3 * fixed typo * adding row for copying rna_dbxref file * adding back * fixed s3 uploading code * adding more copy.. * cleaned up the code * change git:// to https:// in deploy script (#370) * testing * testing * testing * Complex tab pages + data updating + complex Go annotations (#371) * fixed to dump out data for complex * fixed to handle Deleted complex * fixed to mark deleted complexes as 'Deleted' in dbentity table * fixed to load annotations for complex as well * fixed to include complex go annotations in calculation * fixed a minor bug * added code for reading in complex go annotations as well * added code to get data for complex tab pages * changed Sequence page rsources link order * fixed to not change root term name in goslim * fixed to update systematic name properly * fixed uploading thing * fixed to dump go annots for complex * adding code to include complexes * adding format_name to dataset webservice * fixed to delete obsolete complex * fixing indentation error * fixed minor bugs * fixed to add papers for go annotations to literatureannotation table * fixed to delete obsolete complexes from db * adding a row to add any new papers for complex to literatureannotation table * fixed the gpi check * adding checks for suppl files and gene name reservation (#372) * 6143 disease CI minor mods (#373) * disease ci changes * save * save * fixed typo * adding missing go annotation papers to literatureannotation table * fixed to order the complex papers * fixed to handle obsolete pmid * fixed to map updated protein id to new/updated features * fixed to only retrieve PMCID for papers without PDF file * trigger_fct_colleague_relation fixed (#375) * fixed to exclude two papers from literatureannotation table * fixing subcomplex link * fixed rna subunit in complex to link to SGD page * fixed rna subunit in complex to link to SGD page * fixed rna subunit in complex to link to SGD page * fixed the chebi ID subunit for complex to link to chemical page * fixing strand = '0' to strand = '.' * excape = * add another allowed value for qualifier (#377) * adding a check * revert back change * revert back change * Fixed complex subunit (subcomplex and chemical) links + fixed strand col in gff file (#379) * fixed the complex subunit links and chemical unit link * fixed strand col from '0' to '.' and escape any '=' sign in desc * fixed the web services to return complex data for RNA + return protein and sequence summary. (#381) * adding multiple gene names for an alias in LitTriage * fixing code to return sequence/protein summary as well + return complex data for RNAs * adding data and logs dir * renamed the script * fixed to speed up seq section loading * adding 'UniProt' to source list for manually curated annotations * Fixed Ref Triage loading script (#386) * testing * testing * code to get metadata for blast datasets (#385) * testing * testing * testing * testing * fixed the webservice for sgd blast datasets * fixed typo * add back suppl file loading scripts * change to blast dataset metadata (#390) * testing * testing * testing * fixed to handle 'Δ' in allele name properly * fixed to deal with obsolete PMIDs * fixed the cutoff for gpa size check * fixed a go annotation loading bug * fixed the check for macromolecular complex terms * fixed to make gene reservation work * fixed to allow underscore and hyphen in the author names * fixed to skip complex go annotations with pmids not in our database * fixed to only report the missing PMIDs from noctua gpad * adding go_qualifier to the go annotation unique key check * fixed to use date_created as date_assigned * Author response (#405) * adding indicator on Author Response CI * fixing minor syntax error * moving author response up * moving author response up * Merge Stuart's change to qa (#407) * Change Redis server from localhost to prod. * Change Redis server from localhost to prod. Co-authored-by: stuartmiyasato <[email protected]> * fixed the redis url (#409) * adding dir and scripts for automatically download PMC packages * automate pmc download process * adding init file * adding no preprint to reference triage * adding pool_size when creating 'create_engine' for curation * setting pool_size to 100 * fixed gpi cutoff to 350,000 * fixed code to exclude the papers with eLife journal * fixed error message * fixed gpi cutoff size * adding prefix to UniProtKB and RefSeq IDs * fixed to add complex portal ID to col9 * fixed the path change for Noctua GO files * fixed the source URL * fixed the URL to retrieve complex data from EBI * save (#424) * Alliance files 6.0.0 (#430) * save * save * working gff4alliance script * save changes for sequence panel --------- Co-authored-by: Shuai Weng <[email protected]> Co-authored-by: stuartmiyasato <[email protected]> Co-authored-by: Eric Douglass <[email protected]>
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