def relate_structures(cfg,log,db, pm): try: log.info('Merging Training and Result Sets...') rows = db.getData(cfg.sqlCopyTrainingSetIntoLiterature).fetchall() for row in rows: article = pm.get_pubmed_article(row['pubmed_id']) pm.save_pubmed_article(row['pubmed_id'], article, 'Literature') if cfg.FullReload: db.executeCommand(cfg.sqlTruncateRel) candidates = db.getData(cfg.sqlSelectCandidates).fetchall() for addFile in candidates: key = addFile['pdbID'] f = PDB.parse_prody(cfg,key) if f.journal.pmid != "": db.executeCommand(cfg.sqlInsertRel, (addFile['pdbID'], f.journal.pmid, 'Originator')) log.info('Opening article to find references to structures...') fileName = pm.get_related_pubmed_articles(f.journal.pmid) for item in fileName[0]['LinkSetDb'][0]['Link']: db.executeCommand(cfg.sqlInsertRel, (addFile['pdbID'], item['Id'], 'Related')) db.commit() except: db.rollback() log.error(traceback.format_exc()) raise Exception('Training Set was not built.')
def relate_structures(cfg, log, db, pm): try: log.info('Merging Training and Result Sets...') rows = db.getData(cfg.sqlCopyTrainingSetIntoLiterature).fetchall() for row in rows: article = pm.get_pubmed_article(row['pubmed_id']) pm.save_pubmed_article(row['pubmed_id'], article, 'Literature') if cfg.FullReload: db.executeCommand(cfg.sqlTruncateRel) candidates = db.getData(cfg.sqlSelectCandidates).fetchall() for addFile in candidates: key = addFile['pdbID'] f = PDB.parse_prody(cfg, key) if f.journal.pmid != "": db.executeCommand( cfg.sqlInsertRel, (addFile['pdbID'], f.journal.pmid, 'Originator')) log.info('Opening article to find references to structures...') fileName = pm.get_related_pubmed_articles(f.journal.pmid) for item in fileName[0]['LinkSetDb'][0]['Link']: db.executeCommand( cfg.sqlInsertRel, (addFile['pdbID'], item['Id'], 'Related')) db.commit() except: db.rollback() log.error(traceback.format_exc()) raise Exception('Training Set was not built.')
def build_training_set(cfg, log, db, pm): try: listAdded = [] if cfg.FullReload: db.executeCommand(cfg.sqlTruncateTrainingSet) log.info('Getting Reference articles...') candidates = db.getData(cfg.sqlSelectCandidates).fetchall() for addFile in candidates: key = addFile[0] f = PDB.parse_prody(cfg, key) if f.status == 'Imported' and ( f.journal.pmid not in listAdded) and f.journal.pmid != "": article = pm.get_pubmed_article(f.journal.pmid) pm.save_pubmed_article(f.journal.pmid, article, 'Training') listAdded.append(f.journal.pmid) db.commit() except: log.error(traceback.format_exc()) db.rollback() raise Exception('Training Set was not built.')
try: listAdded = [] <<<<<<< HEAD ======= >>>>>>> origin/master if cfg.FullReload: db.executeCommand(cfg.sqlTruncateTrainingSet) log.info('Getting Reference articles...') candidates = db.getData(cfg.sqlSelectCandidates).fetchall() for addFile in candidates: key = addFile['pdbID'] f = PDB.parse_prody(cfg,key) if (f.journal.pmid not in listAdded) and f.journal.pmid != "": article = pm.get_pubmed_article(f.journal.pmid) pm.save_pubmed_article(f.journal.pmid,article,'Training') listAdded.append(f.journal.pmid) db.commit() except: log.error(traceback.format_exc()) db.rollback() raise Exception('Training Set was not built.') def search_literature(cfg,log,db,pm): try: if cfg.FullReload: db.executeCommand(cfg.sqlTruncateLiterature)