4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/visiGene/hgVisiGene/visiSearch.c src/hg/visiGene/hgVisiGene/visiSearch.c index 4fe7fa1..4d0354b 100644 --- src/hg/visiGene/hgVisiGene/visiSearch.c +++ src/hg/visiGene/hgVisiGene/visiSearch.c @@ -1,797 +1,797 @@ /* visiSearch - free form search of visiGene database. */ /* Copyright (C) 2013 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "dystring.h" #include "bits.h" #include "obscure.h" #include "rbTree.h" #include "jksql.h" #include "visiGene.h" #include "visiSearch.h" #include "trix.h" char titleMessage[1024] = ""; struct visiMatch *visiMatchNew(int imageId, int wordCount) /* Create a new visiMatch structure, as yet with no weight. */ { struct visiMatch *match; AllocVar(match); match->imageId = imageId; match->wordBits = bitAlloc(wordCount); return match; } void visiMatchFree(struct visiMatch **pMatch) /* Free up memory associated with visiMatch */ { struct visiMatch *match = *pMatch; if (match != NULL) { bitFree(&match->wordBits); freez(pMatch); } } void visiMatchFreeList(struct visiMatch **pList) /* Free up memory associated with list of visiMatch */ { struct visiMatch *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; visiMatchFree(&el); } *pList = NULL; } static int visiMatchCmpImageId(void *va, void *vb) /* rbTree comparison function to tree on imageId. */ { struct visiMatch *a = va, *b = vb; return a->imageId - b->imageId; } int visiMatchCmpWeight(const void *va, const void *vb) /* Compare to sort based on match. */ { const struct visiMatch *a = *((struct visiMatch **)va); const struct visiMatch *b = *((struct visiMatch **)vb); double dif = b->weight - a->weight; if (dif > 0) return 1; else if (dif < 0) return -1; else return 0; } struct visiSearcher /* This collects together information for free format searches. */ { struct visiSearcher *next; /* Next search */ struct visiMatch *matchList; /* List of matching images. */ struct rbTree *tree; /* Tree for near random access. */ int wordCount; /* Number of words in search. */ }; static struct visiSearcher *visiSearcherNew(int wordCount) /* Create a new, empty search structure. */ { struct visiSearcher *searcher; AllocVar(searcher); searcher->tree = rbTreeNew(visiMatchCmpImageId); searcher->wordCount = wordCount; return searcher; } static void visiSearcherFree(struct visiSearcher **pSearcher) /* Free up memory associated with *pSearcher */ { struct visiSearcher *searcher = *pSearcher; if (searcher != NULL) { visiMatchFreeList(&searcher->matchList); rbTreeFree(&searcher->tree); freez(pSearcher); } } static struct visiMatch *visiSearcherAdd(struct visiSearcher *searcher, int imageId, double weight, int startWord, int wordCount) /* Add given weight to match involving imageId, creating * a fresh match if necessary for imageId. */ { struct visiMatch key, *match; key.imageId = imageId; match = rbTreeFind(searcher->tree, &key); if (match == NULL) { match = visiMatchNew(imageId, searcher->wordCount); slAddHead(&searcher->matchList, match); rbTreeAdd(searcher->tree, match); } match->weight += weight; assert(startWord + wordCount <= searcher->wordCount); bitSetRange(match->wordBits, startWord, wordCount); return match; } static void visiSearcherWeedResults(struct visiSearcher *searcher, struct sqlConnection *conn) /* Get rid of images that are just partial matches, and also * images that are private. This leaks a little memory - the * matches that are weeded out.*/ { struct visiMatch *newList = NULL, *match, *next, key; int wordCount = searcher->wordCount; struct dyString *query = dyStringNew(0); struct sqlResult *sr; char **row; int passCount = 0; /* Construct query to fetch all non-private imageId's in matchList. */ sqlDyStringPrintf(query, "select image.id from image,submissionSet " "where submissionSet.privateUser = 0 " "and submissionSet.id = image.submissionSet " "and image.id in ("); for (match = searcher->matchList; match != NULL; match = next) { next = match->next; if (bitCountRange(match->wordBits, 0, wordCount) == wordCount) { if (passCount != 0) sqlDyStringPrintf(query, ","); sqlDyStringPrintf(query, "%d", match->imageId); ++passCount; } } sqlDyStringPrintf(query, ")"); /* Execute query, and put corresponding images on newList. */ if (passCount > 0) { sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { key.imageId = sqlUnsigned(row[0]); match = rbTreeFind(searcher->tree, &key); if (match == NULL) internalErr(); slAddHead(&newList, match); } slReverse(&newList); } searcher->matchList = newList; dyStringFree(&query); } static struct visiMatch *visiSearcherSortResults(struct visiSearcher *searcher, struct sqlConnection *conn) /* Get sorted list of match results from searcher. * You don't own the list returned though. It will evaporate * with visiSearcherFree. */ { visiSearcherWeedResults(searcher, conn); return searcher->matchList; } static char *stripSpacesEtc(char *s) /* Return a copy of s with spaces, periods, and dashes removed */ { char *d = cloneString(s); stripChar(d, ' '); stripChar(d, '.'); stripChar(d, '-'); touppers(d); return d; } static int countPartsUsedInName(char *name, struct slName *wordList) /* The name here is last name followed by initials with a * period after each initial and no space between initials. * The last name may contain multiple words. Some complex * examples are "van den Eijnden-van Raaij A.J." and * "Van De Water T." A typical example "Kwong W.H." * The word list is just space separated words. We'd * Want the last example to be matched by "Kwong" "W.H." * as well as "Kwong WH" as well as "Kwong W H". */ { int count = 0; struct slName *word; char *stripped = stripSpacesEtc(name); char *pt = stripped; for (word = wordList; word != NULL; word = word->next) { char *w = stripSpacesEtc(word->name); if (startsWith(w, pt)) { count += 1; pt += strlen(w); freeMem(w); } else { freeMem(w); break; } } freeMem(stripped); return count; } static int countWordsUsedInPhrase(char *phrase, struct slName *wordList) /* Count the number of words in wordList that are used in phrase. * The words are in order and space-separated in phrase. */ { int count = 0; struct slName *word; char *dupe = cloneString(phrase); char *s = dupe, *w; for (word = wordList; word != NULL; word = word->next) { w = nextWord(&s); if (w == NULL) break; if (sameWord(w, word->name)) count += 1; else break; } freeMem(dupe); return count; } typedef void AdderFunc(struct visiSearcher *searcher, struct sqlConnection *conn, struct dyString *dy, char *exactMatch, int startWord, int wordCount); /* Typedef of function to add things that are exact matches of * some type to searcher. This is broken out separately * so that the visiGeneMatchMultiWord function below can be * used in many contexts. */ static void visiGeneMatchMultiWord(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList, char *table, char *field, AdderFunc adder) /* This helps cope with matches that may involve more than * one word. It will preferentially match as many words * as possible, and if there is a multiple-word match it * will take that over a single-word match. */ { struct slName *word; struct dyString *query = dyStringNew(0); int wordIx; for (word = wordList, wordIx=0; word != NULL; ++wordIx) { struct slName *nameList = NULL, *name; int maxWordsUsed = 0; if (strlen(word->name) >= 3) /* Logic could be expensive on small words */ { dyStringClear(query); sqlDyStringPrintf(query, "select %s from %s where %s like '%s%%'", field, table, field, word->name); nameList = sqlQuickList(conn, query->string); if (nameList != NULL) { for (name = nameList; name != NULL; name = name->next) { int wordsUsed = countWordsUsedInPhrase(name->name, word); if (wordsUsed > maxWordsUsed) maxWordsUsed = wordsUsed; } } } if (maxWordsUsed > 0) { for (name = nameList; name != NULL; name = name->next) { if (countWordsUsedInPhrase(name->name, word) == maxWordsUsed) (*adder)(searcher, conn, query, name->name, wordIx, maxWordsUsed); } while (--maxWordsUsed >= 0) word = word->next; } else word = word->next; slFreeList(&nameList); } dyStringFree(&query); } static void addImagesMatchingQuery(struct visiSearcher *searcher, struct sqlConnection *conn, char *query, struct hash *uniqHash, char *searchTerm, int startWord, int wordCount) /* Add images that match query */ { struct sqlResult *sr; char **row; sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { boolean skip = FALSE; if (uniqHash) { char uniqString[512]; safef(uniqString, sizeof(uniqString), "%s#%s", row[0], searchTerm); if (hashLookup(uniqHash, uniqString)) skip = TRUE; else hashAdd(uniqHash, uniqString, NULL); } if (!skip) visiSearcherAdd(searcher, sqlUnsigned(row[0]), 1.0, startWord, wordCount); } sqlFreeResult(&sr); } static void addImagesMatchingName(struct visiSearcher *searcher, struct sqlConnection *conn, struct dyString *dy, char *contributor, int startWord, int wordCount) /* Add images that are contributed by given contributor to * searcher with a weight of one. Use dy for scratch space for * the query. */ { dyStringClear(dy); sqlDyStringPrintf(dy, "select image.id from " "contributor,submissionContributor,imageFile,image " "where contributor.name = '%s' " "and contributor.id = submissionContributor.contributor " "and submissionContributor.submissionSet = imageFile.submissionSet " "and imageFile.id = image.imageFile" , contributor); addImagesMatchingQuery(searcher, conn, dy->string, NULL, NULL, startWord, wordCount); } static void visiGeneMatchContributor(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Put images from contributors in wordList into searcher. * We want the behavior to be such that if you give it two names * say "Smith Mahoney" it will weigh those that match both * names. We also want it so that if you include the initials * after the last name either with or without periods that will * set those matching the last name and initials. For * instance "Smith JJ" or "Smith J.J." or "Smith J. J." all would * match a particular John Jacob Smith, but not Francis K. Smith. * Making this a little more interesting is a case like * "smith li" which could either be two last names, or a last * name followed by initials. We would want to match both * cases. Finally, making it even more interesting, is the * case where the last name is compound, like "Van Koppen" or * "de la Cruz" and the like. Also don't forget the apostrophe * containing names like O'Shea. */ { struct slName *word; struct dyString *query = dyStringNew(0); int wordIx; for (word = wordList, wordIx=0; word != NULL; wordIx++) { struct slName *nameList, *name; int maxWordsUsed = 0; dyStringClear(query); sqlDyStringPrintf(query, "select name from contributor where name like '%s %%'", word->name); nameList = sqlQuickList(conn, query->string); if (nameList != NULL) { for (name = nameList; name != NULL; name = name->next) { int wordsUsed = countPartsUsedInName(name->name, word); if (wordsUsed > maxWordsUsed) maxWordsUsed = wordsUsed; } for (name = nameList; name != NULL; name = name->next) { if (countPartsUsedInName(name->name, word) == maxWordsUsed) addImagesMatchingName(searcher, conn, query, name->name, wordIx, maxWordsUsed); } while (--maxWordsUsed >= 0) word = word->next; } else word = word->next; slFreeList(&nameList); } dyStringFree(&query); } static void addImageListAndFree(struct visiSearcher *searcher, struct slInt *imageList, int startWord, int wordCount) /* Add images in list to searcher with weight one. * Then free imageList */ { struct slInt *image; for (image = imageList; image != NULL; image = image->next) visiSearcherAdd(searcher, image->val, 1.0, startWord, wordCount); slFreeList(&imageList); } static void visiGeneMatchGene(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Add images matching genes in wordList to searcher. * The wordList can include wildcards. */ { struct slName *word; int wordIx; for (word = wordList, wordIx=0; word != NULL; word = word->next, ++wordIx) { char *sqlPat = sqlLikeFromWild(word->name); struct slInt *imageList; if (sqlWildcardIn(sqlPat)) imageList = visiGeneSelectNamed(conn, sqlPat, vgsLike); else imageList = visiGeneSelectNamed(conn, sqlPat, vgsExact); addImageListAndFree(searcher, imageList, wordIx, 1); freez(&sqlPat); } } static void visiGeneMatchAccession(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Add images matching RefSeq, LocusLink, GenBank, or UniProt * accessions to searcher. */ { struct slName *word; int wordIx; for (word = wordList, wordIx=0; word != NULL; word = word->next, ++wordIx) { addImageListAndFree(searcher, visiGeneSelectRefSeq(conn, word->name), wordIx, 1); addImageListAndFree(searcher, visiGeneSelectLocusLink(conn, word->name), wordIx, 1); addImageListAndFree(searcher, visiGeneSelectGenbank(conn, word->name), wordIx, 1); addImageListAndFree(searcher, visiGeneSelectUniProt(conn, word->name), wordIx, 1); } } static void visiGeneMatchSubmitId(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Add images matching submitId accessions to searcher. */ { struct slName *word; int wordIx; for (word = wordList, wordIx=0; word != NULL; word = word->next, ++wordIx) { char query[512]; sqlSafef(query, sizeof(query), "select image.id from image,imageFile " "where imageFile.submitId = '%s' " "and imageFile.id = image.imageFile", word->name); addImageListAndFree(searcher, sqlQuickNumList(conn, query), wordIx, 1); } } static void addImagesMatchingBodyPart(struct visiSearcher *searcher, struct sqlConnection *conn, struct dyString *dy, char *bodyPart, int startWord, int wordCount) /* Add images that are contributed by given contributor to * searcher with a weight of one. Use dy for scratch space for * the query. */ { struct hash *uniqHash = newHash(0); dyStringClear(dy); sqlDyStringPrintf(dy, "select imageProbe.image from " "bodyPart,expressionLevel,imageProbe " "where bodyPart.name = '%s' " "and bodyPart.id = expressionLevel.bodyPart " "and expressionLevel.imageProbe = imageProbe.id " "and expressionLevel.level > 0" , bodyPart); addImagesMatchingQuery(searcher, conn, dy->string, uniqHash, bodyPart, startWord, wordCount); dyStringClear(dy); sqlDyStringPrintf(dy, "select image.id from bodyPart,specimen,image " "where bodyPart.name = '%s' " "and bodyPart.id = specimen.bodyPart " "and specimen.id = image.specimen", bodyPart); addImagesMatchingQuery(searcher, conn, dy->string, uniqHash, bodyPart, startWord, wordCount); hashFree(&uniqHash); } static void visiGeneMatchBodyPart(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Add images matching bodyPart to searcher. * This is a little complicated by some body parts containing * multiple words, like "choroid plexus". */ { visiGeneMatchMultiWord(searcher, conn, wordList, "bodyPart", "name", addImagesMatchingBodyPart); } static void visiGeneMatchSex(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Add images matching bodyPart to searcher. * This is a little complicated by some body parts containing * multiple words, like "choroid plexus". */ { struct dyString *query = dyStringNew(0); struct slName *word; int wordIx; for (word = wordList, wordIx=0; word != NULL; word = word->next, ++wordIx) { dyStringClear(query); sqlDyStringPrintf(query, "select image.id from sex,specimen,image "); sqlDyStringPrintf(query, "where sex.name = '%s' ", word->name); sqlDyStringPrintf(query, "and sex.id = specimen.sex "); sqlDyStringPrintf(query, "and specimen.id = image.specimen"); addImagesMatchingQuery(searcher, conn, query->string, NULL, NULL, wordIx, 1); } } void addImagesMatchingStage(struct visiSearcher *searcher, struct sqlConnection *conn, int schemeId, int taxon, char *minAge, int wordIx, int wordCount) /* Given a developmental stage scheme (schemeId) and a specific * stage, return all images that match stage */ { struct dyString *dy = dyStringNew(0); char *maxAge; // note in the code below minAge and maxAge are strings // but they should contain float values. Putting single-quotes // around them and escaping their contents is something that will // protect against sql injection. dyStringClear(dy); sqlDyStringPrintf(dy, "select age from lifeStage where lifeStageScheme = %d ", schemeId); sqlDyStringPrintf(dy, "and age > '%s' order by age", minAge); maxAge = sqlQuickString(conn, dy->string); dyStringClear(dy); sqlDyStringPrintf(dy, "select image.id from specimen,image "); sqlDyStringPrintf(dy, "where specimen.age >= '%s' ", minAge); if (maxAge != NULL) sqlDyStringPrintf(dy, "and specimen.age < '%s' ", maxAge); sqlDyStringPrintf(dy, "and specimen.taxon = %d ", taxon); sqlDyStringPrintf(dy, "and specimen.id = image.specimen"); addImagesMatchingQuery(searcher, conn, dy->string, NULL, NULL, wordIx, wordCount); dyStringFree(&dy); } static void visiGeneMatchStage(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Add images matching Theiler or other developmental stage */ { struct slName *word; struct dyString *dy = dyStringNew(0); struct sqlResult *sr; char **row; int wordIx; for (word = wordList, wordIx=0; word != NULL && word->next != NULL; word = word->next, ++wordIx) { int schemeId = 0,taxon=0; dyStringClear(dy); sqlDyStringPrintf(dy, "select id,taxon from lifeStageScheme where name = '%s'", word->name); sr = sqlGetResult(conn, dy->string); if ((row = sqlNextRow(sr)) != NULL) { schemeId = sqlUnsigned(row[0]); taxon = sqlUnsigned(row[1]); } sqlFreeResult(&sr); if (schemeId > 0) { char *specificStage = word->next->name; char *minAge; dyStringClear(dy); sqlDyStringPrintf(dy, "select age from lifeStage where name = '%s' ", specificStage); sqlDyStringPrintf(dy, "and lifeStageScheme = %d\n", schemeId); minAge = sqlQuickString(conn, dy->string); if (minAge != NULL) addImagesMatchingStage(searcher, conn, schemeId, taxon, minAge, wordIx, 2); freez(&minAge); } } dyStringFree(&dy); } static void addImagesMatchingYears(struct visiSearcher *searcher, struct sqlConnection *conn, int minYear, int maxYear, int wordIx) /* Fold in images that are published between given years */ { struct dyString *dy = dyStringNew(0); sqlDyStringPrintf(dy, "select image.id from submissionSet,imageFile,image " "where submissionSet.year >= %d and submissionSet.year <= %d " "and submissionSet.id = imageFile.submissionSet " "and imageFile.id = image.imageFile" , minYear, maxYear); addImagesMatchingQuery(searcher, conn, dy->string, NULL, NULL, wordIx, 1); dyStringFree(&dy); } static void visiGeneMatchYear(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Fold in matches to a year. */ { struct slName *word; char *now = sqlQuickString(conn, NOSQLINJ "select now()"); int currentYear = atoi(now); int maxYear = currentYear+1; /* May be slightly ahead of publication */ int minYear = 1988; /* Oldest record in Jackson Labs database. */ int wordIx; for (word = wordList, wordIx=0; word != NULL; word = word->next, ++wordIx) { char *name = word->name; if (strlen(name) == 4 && isdigit(name[0])) { int year = atoi(name); if (year >= minYear && year <= maxYear) addImagesMatchingYears(searcher, conn, year, year, wordIx); } } } static void visiGeneMatchProbeId(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Fold in matches to a probe ID. */ { struct slName *word; int wordIx; for (word = wordList, wordIx=0; word != NULL; word = word->next, ++wordIx) { char *name = word->name; char *pat = "vgPrb_"; if (startsWith(pat, name)) { struct sqlResult *sr; char **row, query[256]; int probeId = atoi(name + strlen(pat)); sqlSafef(query, sizeof(query), "select ip.image from imageProbe ip, vgPrbMap m, vgPrb e" " where ip.probe = m.probe and m.vgPrb = e.id" " and e.id=%d", probeId); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) visiSearcherAdd(searcher, sqlUnsigned(row[0]), 1.0, wordIx, 1); sqlFreeResult(&sr); } } } static void addImagesMatchingBinomial(struct visiSearcher *searcher, struct sqlConnection *conn, struct dyString *dy, char *binomial, int startWord, int wordCount) /* Add images that match binomial name. */ { dyStringClear(dy); sqlDyStringPrintf(dy, "select distinct image.id from " "image,specimen,uniProt.taxon " "where uniProt.taxon.binomial = '%s' " "and specimen.taxon = uniProt.taxon.id " "and image.specimen = specimen.id" , binomial); addImagesMatchingQuery(searcher, conn, dy->string, NULL, binomial, startWord, wordCount); } static void addImagesMatchingCommonName(struct visiSearcher *searcher, struct sqlConnection *conn, struct dyString *dy, char *commonName, int startWord, int wordCount) /* Add images that match common name. */ { dyStringClear(dy); sqlDyStringPrintf(dy, "select distinct image.id from " "image,specimen,uniProt.commonName " "where uniProt.commonName.val = '%s' " "and specimen.taxon = uniProt.commonName.taxon " "and image.specimen = specimen.id" , commonName); addImagesMatchingQuery(searcher, conn, dy->string, NULL, commonName, startWord, wordCount); } static void visiGeneMatchOrganism(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Fold in matches to organism. */ { visiGeneMatchMultiWord(searcher, conn, wordList, "uniProt.taxon", "binomial", addImagesMatchingBinomial); visiGeneMatchMultiWord(searcher, conn, wordList, "uniProt.commonName", "val", addImagesMatchingCommonName); } static void visiGeneMatchDescription(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Fold in matches to description - using full text index. */ { struct trix *trix = NULL; struct slName *word; int wordIx; if (!fileExists("visiGeneData/visiGene.ix")) { safef(titleMessage,sizeof(titleMessage), " - visiGene.ix not found, run vgGetText"); fprintf(stderr,"%s\n",titleMessage); return; } trix = trixOpen("visiGeneData/visiGene.ix"); for (word=wordList, wordIx=0; word != NULL; word = word->next, ++wordIx) { char *s = cloneString(word->name); struct trixSearchResult *tsr, *tsrList; tolowers(s); tsrList = trixSearch(trix, 1, &s, tsmExact); for (tsr = tsrList; tsr != NULL; tsr = tsr->next) visiSearcherAdd(searcher, sqlUnsigned(tsr->itemId), 1.0, wordIx, 1); trixSearchResultFreeList(&tsrList); freez(&s); } trixClose(&trix); } struct visiMatch *visiSearch(struct sqlConnection *conn, char *searchString) /* visiSearch - return list of images that match searchString sorted * by how well they match. This will search most fields in the * database. */ { struct visiMatch *matchList; struct slName *wordList = stringToSlNames(searchString); int wordCount = slCount(wordList); struct visiSearcher *searcher = visiSearcherNew(wordCount); visiGeneMatchContributor(searcher, conn, wordList); visiGeneMatchYear(searcher, conn, wordList); visiGeneMatchProbeId(searcher, conn, wordList); visiGeneMatchGene(searcher, conn, wordList); visiGeneMatchAccession(searcher, conn, wordList); visiGeneMatchBodyPart(searcher, conn, wordList); visiGeneMatchSex(searcher, conn, wordList); visiGeneMatchStage(searcher, conn, wordList); visiGeneMatchSubmitId(searcher, conn, wordList); visiGeneMatchOrganism(searcher, conn, wordList); visiGeneMatchDescription(searcher, conn, wordList); matchList = visiSearcherSortResults(searcher, conn); searcher->matchList = NULL; /* Transferring memory ownership to return val. */ visiSearcherFree(&searcher); slFreeList(&wordList); return matchList; }