a44421a79fb36cc2036fe116b97ea3bc9590cd0c
braney
Fri Dec 2 09:34:39 2011 -0800
removed rcsid (#295)
diff --git src/hg/hgBlatTest/hgBlatTest.c src/hg/hgBlatTest/hgBlatTest.c
index da0563b..623e0f0 100644
--- src/hg/hgBlatTest/hgBlatTest.c
+++ src/hg/hgBlatTest/hgBlatTest.c
@@ -1,1380 +1,1379 @@
/* hgBlatTest - Test hgBlat web page. - was cloned from hgblatTest */
#include "common.h"
#include "memalloc.h"
#include "linefile.h"
#include "hash.h"
#include "htmshell.h"
#include "portable.h"
#include "options.h"
#include "errCatch.h"
#include "ra.h"
#include "fa.h"
#include "nib.h"
#include "htmlPage.h"
#include "../near/hgNear/hgNear.h"
#include "hdb.h"
#include "qa.h"
#include <time.h>
-static char const rcsid[] = "$Id: hgBlatTest.c,v 1.3 2004/11/07 05:26:30 kent Exp $";
/* Command line variables. */
char *dataDir = "./";
char *clOrg = NULL; /* Organism from command line. */
char *clDb = NULL; /* DB from command line */
char *clType = NULL; /* Type var from command line. */
char *clSort = NULL; /* Sort var from command line. */
char *clOutput = NULL; /* Output var from command line. */
int clRepeat = 3; /* Number of repetitions. */
char *raName = "hgBlatTest.ra";
struct hash *raList = NULL;
void usage()
/* Explain usage and exit. */
{
errAbort(
"hgBlatTest - Test hgBlat web page\n"
"usage:\n"
" hgBlatTest url log\n"
"options:\n"
" -org=Human - Restrict to Human (or Mouse, Fruitfly, etc.)\n"
" -db=hg16 - Restrict to particular database\n"
" -type=DNA - DNA query\n"
" -sort=query,score - sorty output by query and score, default\n"
" -output=query,score - sorty output by query and score, default\n"
" -dataDir=dataDir - Use selected data dir, default %s\n"
" -repeat=N - Number of times to repeat test (on random genes), default %d\n"
, dataDir, clRepeat);
}
static struct optionSpec options[] = {
{"org", OPTION_STRING},
{"db", OPTION_STRING},
{"type", OPTION_STRING},
{"sort", OPTION_STRING},
{"output", OPTION_STRING},
{"dataDir", OPTION_STRING},
{"repeat", OPTION_INT},
{NULL, 0},
};
struct blatTest
/* Test on one column. */
{
struct blatTest *next;
struct qaStatus *status; /* Result of test. */
char *info[6];
};
enum blatTestInfoIx {
ntiiTest = 0,
ntiiOrg = 1,
ntiiDb = 2,
ntiiType = 3,
ntiiSort = 4,
ntiiOutput = 5,
};
char *blatTestInfoTypes[] =
{
"test",
"organism",
"db",
"type",
"sort",
"output"
};
struct blatTest *blatTestList = NULL; /* List of all tests, latest on top. */
struct blatTest *blatTestNew(struct qaStatus *status, char *test,
char *org, char *db,
char *type, char *sort,
char *output )
/* Save away column test results. */
{
struct blatTest *bt;
AllocVar(bt);
bt->status = status;
bt->info[ntiiTest] = cloneString(naForNull(test));
bt->info[ntiiOrg] = cloneString(naForNull(org));
bt->info[ntiiDb] = cloneString(naForNull(db));
bt->info[ntiiType] = cloneString(naForNull(type));
bt->info[ntiiSort] = cloneString(naForNull(sort));
bt->info[ntiiOutput] = cloneString(naForNull(output));
slAddHead(&blatTestList, bt);
return bt;
}
void blatTestLogOne(struct blatTest *test, FILE *f)
/* Log test result to file. */
{
int i;
for (i=0; i<ArraySize(test->info); ++i)
fprintf(f, "%s ", test->info[i]);
fprintf(f, "%s\n", test->status->errMessage);
}
char *nearStartTablePat = "<!-- Start Rows -->";
char *nearEndTablePat = "<!-- End Rows -->";
char *nearEndRowPat = "<!-- Row -->";
int nearCountRows(struct htmlPage *page)
/* Count number of rows in big table. */
{
return qaCountBetween(page->htmlText, nearStartTablePat,
nearEndTablePat, nearEndRowPat);
}
int nearCountUniqAccRows(struct htmlPage *page)
/* Count number of unique rows in table containing just hyperlinked
* accessions. */
{
char *startTable, *endTable, *startRow;
char *s, *e, *row, *acc;
int count = 0;
struct hash *uniqHash = hashNew(0);
if (page == NULL)
return -1;
/* Set s to first row. */
s = stringIn(nearStartTablePat, page->htmlText);
if (s == NULL)
return -1;
s += strlen(nearStartTablePat);
for (;;)
{
e = stringIn(nearEndRowPat, s);
if (e == NULL)
break;
row = cloneStringZ(s, e-s);
acc = qaStringBetween(row, "_blank>", "</a>");
if (acc == NULL)
{
warn("Can't find between _blank> and </a> while counting uniq row %s",
row);
freez(&row);
break;
}
if (!hashLookup(uniqHash, acc))
{
hashAdd(uniqHash, acc, NULL);
++count;
}
freez(&row);
freez(&acc);
s = e + strlen(nearEndRowPat);
}
hashFree(&uniqHash);
return count;
}
struct htmlPage *quickSubmit(struct htmlPage *basePage,
char *org, char *db, char *type, char *sort, char *output, char *userSeq,
char *testName, char *button, char *buttonVal)
/* Submit page and record info. Return NULL if a problem. */
{
struct blatTest *test;
struct qaStatus *qs;
struct htmlPage *page;
if (basePage != NULL)
{
if (org != NULL)
htmlPageSetVar(basePage, NULL, "org", org);
if (db != NULL)
htmlPageSetVar(basePage, NULL, "db", db);
if (userSeq != NULL)
htmlPageSetVar(basePage, NULL, "userSeq", userSeq);
qs = qaPageFromForm(basePage, basePage->forms,
button, buttonVal, &page);
test = blatTestNew(qs, testName, org, db, type, sort, output);
}
return page;
}
void serialSubmit(struct htmlPage **pPage,
char *org, char *db, char *type, char *sort, char *output, char *userSeq,
char *testName, char *button, char *buttonVal)
/* Submit page, replacing old page with new one. */
{
struct htmlPage *oldPage = *pPage;
if (oldPage != NULL)
{
*pPage = quickSubmit(oldPage, org, db, type, sort, output, userSeq,
testName, button, buttonVal);
htmlPageFree(&oldPage);
}
}
void quickErrReport()
/* Report error at head of list if any */
{
struct blatTest *test = blatTestList;
if (test->status->errMessage != NULL)
blatTestLogOne(test, stderr);
}
void testCol(struct htmlPage *emptyConfig, char *org, char *db, char *col, char *gene)
/* Test one column. */
{
struct htmlPage *printPage = NULL;
struct blatTest *test;
struct qaStatus *qs;
char visVar[256];
safef(visVar, sizeof(visVar), "near.col.%s.vis", col);
htmlPageSetVar(emptyConfig, NULL, visVar, "on");
htmlPageSetVar(emptyConfig, NULL, orderVarName, "geneDistance");
htmlPageSetVar(emptyConfig, NULL, countVarName, "25");
//printPage = quickSubmit(emptyConfig, NULL, org, db, col, gene, "colPrint", "Submit", "on");
if (printPage != NULL)
{
int expectCount = 25;
int lineCount = nearCountRows(printPage);
if (lineCount != expectCount)
qaStatusSoftError(blatTestList->status,
"Got %d rows, expected %d", lineCount, expectCount);
}
quickErrReport();
htmlPageFree(&printPage);
htmlPageSetVar(emptyConfig, NULL, visVar, NULL);
}
struct htmlPage *emptyConfigPage(struct htmlPage *dbPage, char *org, char *db)
/* Get empty configuration page. */
{
//return quickSubmit(dbPage, NULL, org, db, NULL, NULL, "emptyConfig", hideAllConfName, "on");
return NULL; //debug
}
void testColInfo(struct htmlPage *dbPage, char *org, char *db, char *col)
/* Click on all colInfo columns. */
{
struct htmlPage *infoPage = NULL; //debug
// quickSubmit(dbPage, NULL, org, db, col, NULL, "colInfo", colInfoVarName, col);
if (infoPage != NULL)
{
if (stringIn("No additional info available", infoPage->htmlText))
qaStatusSoftError(blatTestList->status,
"%s failed - no %s.html?", colInfoVarName, col);
}
quickErrReport();
htmlPageFree(&infoPage);
}
void testDbColumns(struct htmlPage *dbPage, char *org, char *db,
struct slName *geneList)
/* Test on one database. */
{
struct htmlPage *emptyConfig;
struct slName *colList = NULL, *col;
struct htmlFormVar *var;
struct slName *gene;
uglyf("testDbColumns %s %s\n", org, db);
emptyConfig = emptyConfigPage(dbPage, org, db);
if (emptyConfig != NULL )
{
for (var = emptyConfig->forms->vars; var != NULL; var = var->next)
{
if (startsWith("near.col.", var->name) && endsWith(var->name, ".vis"))
{
char *colNameStart = var->name + strlen("near.col.");
char *colNameEnd = strchr(colNameStart, '.');
*colNameEnd = 0;
col = slNameNew(colNameStart);
slAddHead(&colList, col);
*colNameEnd = '.';
}
}
slReverse(&colList);
for (gene = geneList; gene != NULL; gene = gene->next)
{
htmlPageSetVar(emptyConfig, NULL, searchVarName, gene->name);
for (col = colList; col != NULL; col = col->next)
{
testCol(emptyConfig, org, db, col->name, gene->name);
}
}
for (col = colList; col != NULL; col = col->next)
{
testColInfo(dbPage, org, db, col->name);
}
}
htmlPageFree(&emptyConfig);
}
void testSortX(struct htmlPage *emptyConfig, char *org, char *db, char *sort, char *gene, char *accColumn)
/* Test one column. */
{
char accVis[256];
struct htmlPage *printPage = NULL;
safef(accVis, sizeof(accVis), "near.col.%s.vis", accColumn);
htmlPageSetVar(emptyConfig, NULL, accVis, "on");
htmlPageSetVar(emptyConfig, NULL, orderVarName, sort);
htmlPageSetVar(emptyConfig, NULL, countVarName, "25");
htmlPageSetVar(emptyConfig, NULL, searchVarName, gene);
//printPage = quickSubmit(emptyConfig, sort, org, db, NULL, gene, "sortType", "submit", "on");
if (printPage != NULL)
{
int lineCount = nearCountRows(printPage);
if (lineCount < 1)
qaStatusSoftError(blatTestList->status, "No rows for sort %s", sort);
}
quickErrReport();
htmlPageFree(&printPage);
}
void testDbSorts(struct htmlPage *dbPage, char *org, char *db,
char *accColumn, struct slName *geneList)
/* Test on one database. */
{
struct htmlPage *emptyConfig;
struct slName *colList = NULL, *col;
struct htmlFormVar *sortVar = htmlFormVarGet(dbPage->forms, orderVarName);
struct slName *gene, *sort;
uglyf("testDbSorts %s %s\n", org, db);
if (sortVar == NULL)
errAbort("Couldn't find var %s", orderVarName);
emptyConfig = emptyConfigPage(dbPage, org, db);
if (emptyConfig != NULL)
{
for (sort = sortVar->values; sort != NULL; sort= sort->next)
{
for (gene = geneList; gene != NULL; gene = gene->next)
{
testSortX(emptyConfig, org, db, sort->name, gene->name, accColumn);
}
}
htmlPageFree(&emptyConfig);
}
}
void testDbFilters(struct htmlPage *dbPage, char *org, char *db,
char *accColumn, struct slName *geneList)
/* Test filter that returns just geneList. */
{
struct slName *gene;
int rowCount;
char accFilter[256];
safef(accFilter, sizeof(accFilter), "near.as.%s.wild", accColumn);
/* Start out with filter page. */
struct htmlPage *page = NULL; //debug
//quickSubmit(dbPage, NULL, org, db, accColumn, NULL,
// "accOneFilterPage", advFilterVarName, "on");
verbose(1, "testFilters %s %s\n", org, db);
if (page == NULL)
return;
/* Set up to filter exactly one gene. */
{
htmlPageSetVar(page, NULL, accFilter, geneList->name);
htmlPageSetVar(page, NULL, searchVarName, geneList->name);
//serialSubmit(&page, NULL, org, db, accColumn, geneList->name,
// "accOneFilterSubmit", "Submit", "on");
if (page == NULL)
return;
/* Make sure really got one gene. */
rowCount = nearCountUniqAccRows(page);
if (rowCount != 1)
{
qaStatusSoftError(blatTestList->status,
"Acc exact filter returned %d items", rowCount);
}
}
/* Set up filter for all genes in list. */
{
struct dyString *dy = newDyString(0);
int geneCount = slCount(geneList);
for (gene = geneList; gene != NULL; gene = gene->next)
dyStringPrintf(dy, "%s ", gene->name);
htmlPageSetVar(page, NULL, accFilter, dy->string);
htmlPageSetVar(page, NULL, countVarName, "all"); /* despite 3 genes requested, must see all if many dupes */
//serialSubmit(&page, NULL, org, db, accColumn, dy->string,
// "accMultiFilterSubmit", "Submit", "on");
dyStringFree(&dy);
if (page == NULL)
return;
rowCount = nearCountUniqAccRows(page);
if (rowCount != geneCount)
{
qaStatusSoftError(blatTestList->status,
"Acc multi filter expecting %d, got %d items", geneCount, rowCount);
}
}
/* Set up filter for wildcard in list. */
{
struct dyString *dy = newDyString(0);
char len = strlen(geneList->name);
dyStringAppendN(dy, geneList->name, len-1);
dyStringAppendC(dy, '*');
htmlPageSetVar(page, NULL, accFilter, dy->string);
// serialSubmit(&page, NULL, org, db, accColumn, dy->string,
// "accWildFilterSubmit", "Submit", "on");
dyStringFree(&dy);
if (page == NULL)
return;
rowCount = nearCountRows(page);
if (rowCount < 1)
{
qaStatusSoftError(blatTestList->status,
"Acc wild filter no match");
}
}
/* Clear out advanced filters. */
{
htmlPageFree(&page);
// page = quickSubmit(dbPage, NULL, org, db, NULL, NULL,
// "advFilterClear", advFilterClearVarName, "on");
}
htmlPageFree(&page);
}
// ==========================================================================
// testing mods to hdb.c: (hopefully compiler will resolve at linktime)
//struct dnaSeq *hGenBankGetMrnaC(struct sqlConnection *conn, char *acc, char *compatTable);
//aaSeq *hGenBankGetPepC(struct sqlConnection *conn, char *acc, char *compatTable);
void testOutput(struct htmlPage *sortPage, struct htmlForm *sortForm,
char *org, char *db, char *type, char *sort, char *output,
struct slName *geneList, char **dna, char **pro)
/* Test on one output. */
{
struct htmlPage *outputPage, *page;
struct htmlForm *mainForm;
struct slName *gene;
char *seq=NULL;
htmlPageSetVar(sortPage, sortForm, "org", org);
htmlPageSetVar(sortPage, sortForm, "db", db);
htmlPageSetVar(sortPage, sortForm, "type", type);
htmlPageSetVar(sortPage, sortForm, "sort", sort);
htmlPageSetVar(sortPage, sortForm, "output", output);
outputPage = htmlPageFromForm(sortPage, sortPage->forms, "submit", "Submit");
if ((mainForm = htmlFormGet(outputPage, "mainForm")) == NULL)
errAbort("Couldn't get main form on outputPage"); // we may want to report the error but try to keep going.
int g = 0;
for (gene = geneList; gene != NULL; gene = gene->next)
{
if (sameWord(type,"BLAT's guess"))
{
if ((rand() % 2) == 0)
{
seq = dna[g];
}
else
{
seq = pro[g];
}
}
else if (sameWord(type,"DNA"))
{
seq = dna[g];
}
else if (sameWord(type,"Protein"))
{
seq = pro[g];
}
else if (sameWord(type,"translated RNA"))
{
seq = dna[g];
}
else if (sameWord(type,"translated DNA"))
{
seq = dna[g];
}
else
{
errAbort("unknown type=%s",type);
}
if (!seq)
{
uglyf("testOutput: seq value NULL for %s.%s.\n",org,db);
htmlPageFree(&outputPage);
return;
}
page = quickSubmit(outputPage, org, db, type, sort, output, seq, "BlatTest combos", "submit", "Submit");
quickErrReport();
if (page != NULL)
{
htmlPageFree(&page);
}
g++;
}
htmlPageFree(&outputPage);
}
void testSort(struct htmlPage *typePage, struct htmlForm *typeForm, char *org, char *db, char *type, char *sort,
struct slName *geneList, char **dna, char **pro)
/* Test on one sort. */
{
struct htmlPage *sortPage;
struct htmlForm *mainForm;
struct htmlFormVar *outputVar;
struct slName *output;
htmlPageSetVar(typePage, typeForm, "org", org);
htmlPageSetVar(typePage, typeForm, "db", db);
htmlPageSetVar(typePage, typeForm, "type", type);
htmlPageSetVar(typePage, typeForm, "sort", sort);
sortPage = htmlPageFromForm(typePage, typePage->forms, "submit", "Submit");
if ((mainForm = htmlFormGet(sortPage, "mainForm")) == NULL)
errAbort("Couldn't get main form on sortPage"); // we may want to report the error but try to keep going.
if ((outputVar = htmlFormVarGet(mainForm, "output")) == NULL)
errAbort("Couldn't get output var");
for (output = outputVar->values; output != NULL; output = output->next)
{
if (clOutput == NULL || sameString(clOutput, output->name))
{
uglyf("testSort: output->name=%s \n",output->name);
testOutput(sortPage, mainForm, org, db, type, sort, output->name, geneList, dna, pro);
}
}
htmlPageFree(&sortPage);
}
void testType(struct htmlPage *dbPage, struct htmlForm *dbForm, char *org, char *db, char *type,
struct slName *geneList, char **dna, char **pro)
/* Test on one type. */
{
struct htmlPage *typePage;
struct htmlForm *mainForm;
struct htmlFormVar *sortVar;
struct slName *sort;
htmlPageSetVar(dbPage, dbForm, "org", org);
htmlPageSetVar(dbPage, dbForm, "db", db);
htmlPageSetVar(dbPage, dbForm, "type", type);
typePage = htmlPageFromForm(dbPage, dbPage->forms, "submit", "Submit");
if ((mainForm = htmlFormGet(typePage, "mainForm")) == NULL)
errAbort("Couldn't get main form on typePage"); // we may want to report the error but try to keep going.
if ((sortVar = htmlFormVarGet(mainForm, "sort")) == NULL)
errAbort("Couldn't get sort var");
for (sort = sortVar->values; sort != NULL; sort = sort->next)
{
if (clSort == NULL || sameString(clSort, sort->name))
{
uglyf("testType: sort->name=%s \n",sort->name);
testSort(typePage, mainForm, org, db, type, sort->name, geneList, dna, pro);
}
}
htmlPageFree(&typePage);
}
struct hash *findRaSection(struct hash *raList, char *name)
/* find section in ra with this name */
{
struct hash *raHash,*result=NULL;
char *section = NULL;
char *targ = cloneString(name);
eraseWhiteSpace(targ); /* name entry at top of each group cannot have whitespace */
for (raHash = raList; raHash != NULL; raHash = raHash->next)
{
section = hashFindVal(raHash, "name");
//debug
//uglyf("section=%s\n",section);
if (section)
{
if (sameWord(section,targ))
{
result=raHash;
}
}
}
freez(&targ);
return result;
}
void inheritRa(char **pvar, struct hash *ra, char *name)
/* override previous value if non-null value found */
{
char *temp=NULL;
if (temp = hashFindVal(ra, name))
{
*pvar = temp;
}
}
char *getFieldWhereField(char *db, char *table, char *field, char *whereField, char *whereValue)
/* Get random sample from database. */
{
struct sqlConnection *conn = sqlConnect(db);
char query[256], **row;
struct sqlResult *sr;
char *result=NULL;
safef(query, sizeof(query), "select %s from %s where %s = '%s'",
field, table, whereField, whereValue);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
result = cloneString(row[0]);
}
sqlFreeResult(&sr);
sqlDisconnect(&conn);
return result;
}
int genePredCdnaSize(struct genePred *gp)
/* Return total size of all exons. */
{
int totalSize = 0;
int exonIx;
for (exonIx = 0; exonIx < gp->exonCount; ++exonIx)
{
totalSize += (gp->exonEnds[exonIx] - gp->exonStarts[exonIx]);
}
return totalSize;
}
struct dnaSeq *hDnaFromSeqD(char *db, char *seqName, int start, int end, enum dnaCase dnaCase)
/* Fetch DNA (galt added db) */
{
char fileName[512];
char query[512];
struct dnaSeq *seq = NULL;
struct sqlConnection *conn = sqlConnect(db);
struct sqlResult *sr;
char **row;
safef(query, sizeof(query), "select fileName from chromInfo where chrom='%s'", seqName);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
safef(fileName,sizeof(fileName),"%s",row[0]);
}
sqlFreeResult(&sr);
sqlDisconnect(&conn);
seq = nibLoadPart(fileName, start, end-start);
if (dnaCase == dnaUpper)
touppers(seq->dna);
return seq;
}
struct dnaSeq *getCdnaSeqD(char *db, struct genePred *gp)
/* Load in cDNA sequence associated with gene prediction. */
{
int txStart = gp->txStart; // hDnaFromSeq
struct dnaSeq *genoSeq = hDnaFromSeqD(db, gp->chrom, txStart, gp->txEnd, dnaLower);
struct dnaSeq *cdnaSeq;
int cdnaSize = genePredCdnaSize(gp);
int cdnaOffset = 0, exonStart, exonSize, exonIx;
AllocVar(cdnaSeq);
cdnaSeq->dna = needMem(cdnaSize+1);
cdnaSeq->size = cdnaSize;
for (exonIx = 0; exonIx < gp->exonCount; ++exonIx)
{
exonStart = gp->exonStarts[exonIx];
exonSize = gp->exonEnds[exonIx] - exonStart;
memcpy(cdnaSeq->dna + cdnaOffset, genoSeq->dna + (exonStart - txStart), exonSize);
cdnaOffset += exonSize;
}
assert(cdnaOffset == cdnaSeq->size);
freeDnaSeq(&genoSeq);
return cdnaSeq;
}
void getCdsInMrna(struct genePred *gp, int *retCdsStart, int *retCdsEnd)
/* Given a gene prediction, figure out the
* CDS start and end in mRNA coordinates. */
{
int missingStart = 0, missingEnd = 0;
int exonStart, exonEnd, exonSize, exonIx;
int totalSize = 0;
for (exonIx = 0; exonIx < gp->exonCount; ++exonIx)
{
exonStart = gp->exonStarts[exonIx];
exonEnd = gp->exonEnds[exonIx];
exonSize = exonEnd - exonStart;
totalSize += exonSize;
missingStart += exonSize - positiveRangeIntersection(exonStart, exonEnd, gp->cdsStart, exonEnd);
missingEnd += exonSize - positiveRangeIntersection(exonStart, exonEnd, exonStart, gp->cdsEnd);
}
*retCdsStart = missingStart;
*retCdsEnd = totalSize - missingEnd;
}
struct dnaSeq *htcGeneMrna(char *db, char * table, char *geneName)
/* Display cDNA predicted from genome */
{
char query[512];
struct sqlConnection *conn = sqlConnect(db);
struct sqlResult *sr;
char **row;
struct genePred *gp;
struct dnaSeq *seq=NULL;
int cdsStart, cdsEnd;
int rowOffset = 0;
char *fld=NULL;
int f = 0;
safef(query, sizeof(query), "select * from %s where name = '%s'", table, geneName);
sr = sqlGetResult(conn, query);
while ((fld = sqlFieldName(sr)) != NULL)
{
if (sameString(fld,"bin"))
{
rowOffset = f+1;
}
f++;
}
uglyf("rowOffset=%d \n",rowOffset);
if ((row = sqlNextRow(sr)) != NULL)
{
gp = genePredLoad(row+rowOffset);
seq = getCdnaSeqD(db, gp);
getCdsInMrna(gp, &cdsStart, &cdsEnd);
toUpperN(seq->dna + cdsStart, cdsEnd - cdsStart);
if (gp->strand[0] == '-')
{
reverseComplement(seq->dna, seq->size);
}
genePredFree(&gp);
//freeDnaSeq(&seq); don't free it, return it.
}
sqlFreeResult(&sr);
sqlDisconnect(&conn);
return seq;
}
void testDb(struct htmlPage *orgPage, struct htmlForm *orgForm, char *org, char *db)
/* Test on one database. */
{
struct hash *genomeRa=NULL;
char *dnaTable = NULL;
char *lnkTable = NULL;
char *proTable = NULL;
char *dnaColumn = NULL;
char *lnkColumn = NULL;
char *proColumn = NULL;
char *method = NULL;
char *temp = NULL;
genomeRa=findRaSection(raList,"global");
if (!genomeRa)
{
errAbort("testDb: .ra has no global section \n");
}
inheritRa(&dnaTable, genomeRa, "dna");
inheritRa(&lnkTable, genomeRa, "lnk");
inheritRa(&proTable, genomeRa, "pro");
inheritRa(&dnaColumn, genomeRa, "dnaColumn");
inheritRa(&lnkColumn, genomeRa, "lnkColumn");
inheritRa(&proColumn, genomeRa, "proColumn");
inheritRa(&method, genomeRa, "method");
genomeRa=findRaSection(raList,org);
if (!genomeRa)
{
uglyf("testDb: skipping org=%s, has no .ra section \n",org);
return; /* if there's no section for the organism, assume it should be skipped. */
}
inheritRa(&dnaTable, genomeRa, "dna");
inheritRa(&lnkTable, genomeRa, "lnk");
inheritRa(&proTable, genomeRa, "pro");
inheritRa(&dnaColumn, genomeRa, "dnaColumn");
inheritRa(&lnkColumn, genomeRa, "lnkColumn");
inheritRa(&proColumn, genomeRa, "proColumn");
inheritRa(&method, genomeRa, "method");
genomeRa=findRaSection(raList,db);
if (!genomeRa)
{
uglyf("testDb: skipping db=%s, has no .ra section \n",db);
return; /* if there's no section for the db, assume it should be skipped. */
}
inheritRa(&dnaTable, genomeRa, "dna");
inheritRa(&lnkTable, genomeRa, "lnk");
inheritRa(&proTable, genomeRa, "pro");
inheritRa(&dnaColumn, genomeRa, "dnaColumn");
inheritRa(&lnkColumn, genomeRa, "lnkColumn");
inheritRa(&proColumn, genomeRa, "proColumn");
inheritRa(&method, genomeRa, "method");
uglyf("dnaTable=%s \n",dnaTable);
if (!dnaTable)
{
uglyf("testDb: dnaTable missing for org=%s db=%s line, skipping \n",org,db);
return;
}
uglyf("lnkTable=%s \n",lnkTable);
if (!lnkTable)
{
uglyf("testDb: lnkTable missing for org=%s db=%s line, skipping \n",org,db);
return;
}
uglyf("proTable=%s \n",proTable);
if (!proTable)
{
uglyf("testDb: proTable missing for org=%s db=%s line, skipping \n",org,db);
return;
}
uglyf("dnaColumn=%s \n",dnaColumn);
if (!dnaColumn)
{
uglyf("testDb: dnaColumn missing for org=%s db=%s, skipping \n",org,db);
return;
}
uglyf("lnkColumn=%s \n",lnkColumn);
if (!lnkColumn)
{
uglyf("testDb: lnkColumn missing for org=%s db=%s, skipping \n",org,db);
return;
}
uglyf("proColumn=%s \n",proColumn);
if (!proColumn)
{
uglyf("testDb: proColumn missing for org=%s db=%s, skipping \n",org,db);
return;
}
uglyf("method=%s \n",method);
if (!method)
{
uglyf("testDb: method missing for org=%s db=%s, skipping \n",org,db);
return;
}
struct slName *geneList = NULL;
char **dna;
char **pro;
// debug
//clRepeat = 1;
dna=needMem(clRepeat*sizeof(char*));
pro=needMem(clRepeat*sizeof(char*));
if (sameWord(method,"1"))
geneList = sqlRandomSample(db, dnaTable, dnaColumn, clRepeat);
else if (sameWord(method,"2"))
geneList = sqlRandomSample(db, proTable, dnaColumn, clRepeat);
else
errAbort("unknown method %s in .ra",method);
if (!geneList)
{
uglyf("testDb: sqlRandomSample returned empty geneList for %s.%s \n",db,dnaTable);
return;
}
struct htmlPage *dbPage;
//debug
struct dyString *dy = newDyString(0);
int geneCount = slCount(geneList);
struct slName *gene;
//char *dna = NULL;
//HGID retId = 0;
char *tempdna = NULL;
struct dnaSeq *dnaseq=NULL;
aaSeq *proseq=NULL;
struct sqlConnection *conn = hAllocOrConnect(db);
uglyf("sqlGetDatabase(conn) = %s\n", sqlGetDatabase(conn) );
//uglyf("host=%s, db=%s, user=%s, pwd=%s \n", hGetDbHost(), hGetDbName(), hGetDbUser(), hGetDbPassword());
char *acc = NULL;
int g = 0;
for (gene = geneList; gene != NULL; gene = gene->next)
{
//uglyf("testDb: got to top of geneList loop for %s.%s \n",db,dnaTable);
acc = gene->name;
//uglyf("testDb: got past acc=gene->name for %s.%s \n",db,dnaTable);
//acc = "NM_020967";
//acc = "AB002332";
dyStringPrintf(dy, "%s ", acc);
//dna = hGetSeqAndId(conn, acc, &retId);
//uglyf("testDb: about to call hgGetSeqAndId for %s.%s \n",db,dnaTable);
//tempdna = hGetSeqAndId(conn, acc, NULL);
//if (tempdna)
// {
// dnaseq = faFromMemText(tempdna);
// //uglyf("\ntestDb: gene = %s. size=%d.\n tempdna=%s.\n",acc,strlen(tempdna),tempdna);
// //uglyf("\ntestDb: dnaseq->dna=%s.\n",dnaseq->dna);
// }
//else
// {
// uglyf("testDb: hGetSeqAndId returned empty result for %s.%s \n",db,dnaTable);
// return;
// }
if (sameWord(method,"1"))
{
//uglyf("testDb: about to call hgGenBankGetMrnaC for %s.%s \n",db,dnaTable);
dnaseq = hGenBankGetMrnaC(conn, acc, NULL);
if (!dnaseq)
{
uglyf("testDb: hGenBankGetMrnaC returned empty result for %s.%s \n",db,dnaTable);
return;
}
}
else if (sameWord(method,"2"))
{
//uglyf("testDb: about to call htcGeneMrna for %s.%s.%s \n",db,dnaTable,acc);
dnaseq = htcGeneMrna(db, dnaTable, acc);
if (!dnaseq)
{
uglyf("testDb: htcGeneMrna returned empty result for %s.%s.%s \n",db,dnaTable,acc);
return;
}
}
else
{
errAbort("unknown method %s in .ra",method);
}
char *protAcc = getFieldWhereField(db, lnkTable, proColumn, lnkColumn, acc);
uglyf("testDb: protAcc=%s for %s.%s.%s='%s' \n",protAcc,db,dnaTable,dnaColumn,acc);
//debug: restore this line:
proseq = hGenBankGetPepC (conn, protAcc, proTable);
if (!proseq)
{
uglyf("\n testDb: hGenBankGetPepC returned empty result for %s.%s \n",db,proTable);
return;
}
//dna = dnaseq->dna;
//uglyf("testDb: gene = %s. dnasize=%d. retId=%u.\n",acc,strlen(dna),retId);
//uglyf("testDb: gene = %s. dna=%lu. retId=%u.\n",acc,(unsigned long)dna,retId);
///uglyf("testDb: gene = %s. dna=%s. \n",acc,dna);
if (dnaseq != NULL)
{
if (dnaseq->dna != NULL)
{
//uglyf("\n testDb: gene = %s. size=%d.\n dnaseq->dna=%s.\n",acc,strlen(dnaseq->dna),dnaseq->dna);
//struct htmlForm *mainForm;
//if ((mainForm = htmlFormGet(orgPage, "mainForm")) == NULL)
// errAbort("Couldn't get main form");
/*
uglyf("\nbefore: org=%s, db=%s, type=%s, sort=%s, output=%s, userSeq=%s\n",
(htmlFormVarGet(mainForm, "org"))->curVal,
(htmlFormVarGet(mainForm, "db"))->curVal,
(htmlFormVarGet(mainForm, "type"))->curVal,
(htmlFormVarGet(mainForm, "sort"))->curVal,
(htmlFormVarGet(mainForm, "output"))->curVal,
(htmlFormVarGet(mainForm, "userSeq"))->curVal
);
*/
/*
struct htmlFormVar *var;
var = htmlFormVarGet(form, name);
if (var == NULL)
{
AllocVar(var);
var->type = "TEXT";
var->tagName = "INPUT";
var->name = name;
var->curVal;
}
*/
//if (org != NULL)
// htmlPageSetVar(orgPage, mainForm, "org", org);
//if (db != NULL)
// htmlPageSetVar(orgPage, mainForm, "db", db);
//htmlPageSetVar(orgPage, mainForm, "type", "DNA");
//htmlPageSetVar(orgPage, mainForm, "sort", "score");
//htmlPageSetVar(orgPage, mainForm, "output", "psl");
//htmlPageSetVar(orgPage, mainForm, "userSeq", dnaseq->dna);
//htmlPageSetVar(orgPage, mainForm, "seqFile", dnaseq->dna);
/*
uglyf("\nafter: org=%s, db=%s, type=%s, sort=%s, output=%s, userSeq=%s\n",
(htmlFormVarGet(mainForm, "org"))->curVal,
(htmlFormVarGet(mainForm, "db"))->curVal,
(htmlFormVarGet(mainForm, "type"))->curVal,
(htmlFormVarGet(mainForm, "sort"))->curVal,
(htmlFormVarGet(mainForm, "output"))->curVal,
(htmlFormVarGet(mainForm, "userSeq"))->curVal
);
*/
/*
struct htmlFormVar *var;
var = htmlFormVarGet(mainForm, "seqFile");
if (var == NULL)
{
uglyf("var=htmlFormVarGet returned %lu \n",(unsigned long)var);
}
else
{
uglyf("\ntype=%s, tagName=%s, name=%s, curVal=%s \n",
var->type,
var->tagName,
var->name,
var->curVal
);
}
*/
//struct qaStatus *qs;
//struct htmlPage *page;
//qs = qaPageFromForm(orgPage, orgPage->forms, "Submit", "Submit", &page);
//qs = qaPageFromForm(orgPage, htmlFormGet(orgPage, "mainForm"), "Submit", "Submit", &page);
//page = htmlPageFromForm(orgPage, mainForm, "Submit", "Submit");
//uglyf("qs.errMessage=%s, qs.hardError=%d \n",qs->errMessage,qs->hardError);
//uglyf("%s\n",page->htmlText);
}
}
if (proseq != NULL)
{
if (proseq->dna != NULL)
{
//uglyf("\n testDb: gene = %s. size=%d. \n proseq->dna=%s.\n",acc,strlen(proseq->dna),proseq->dna);
}
}
//freez(&dna);
//save for later
dna[g]=cloneString(dnaseq->dna);
pro[g]=cloneString(proseq->dna);
freez(&dnaseq);
freez(&proseq);
//uglyf("dbg: got here3 \n");
g++;
}
uglyf("testDb: genelist = %s.\n",dy->string);
dyStringFree(&dy);
//uglyf("host=%s, db=%s, user=%s, pwd=%s \n", hGetDbHost(), hGetDbName(), hGetDbUser(), hGetDbPassword());
hFreeOrDisconnect(&conn);
htmlPageSetVar(orgPage, orgForm, "db", db);
//dbPage = quickSubmit(orgPage, org, db, NULL, NULL, NULL, NULL, "dbEmptyPage", "submit", "Submit");
//quickErrReport();
//uglyf("dbg: got here5 \n");
dbPage = htmlPageFromForm(orgPage, orgPage->forms, "submit", "Submit");
//uglyf("dbg: got here6 \n dbPage->htmlText=%s\n",dbPage->htmlText);
if (dbPage != NULL)
{
struct htmlForm *mainForm;
struct htmlFormVar *typeVar;
struct slName *type;
//testDbColumns(dbPage, org, db, geneList);
//testDbSorts(dbPage, org, db, dnaColumn, geneList);
//testDbFilters(dbPage, org, db, dnaColumn, geneList);
// uglyf("dbg: got here4 \n");
if ((mainForm = htmlFormGet(dbPage, "mainForm")) == NULL)
errAbort("Couldn't get main form on dbPage"); // we may want to report the error but try to keep going.
if ((typeVar = htmlFormVarGet(mainForm, "type")) == NULL)
errAbort("Couldn't get type var");
for (type = typeVar->values; type != NULL; type = type->next)
{
if (clType == NULL || sameString(clType, type->name))
{
uglyf("testDb: type->name=%s \n",type->name);
testType(dbPage, mainForm, org, db, type->name, geneList, dna, pro);
}
}
}
// uglyf("dbg: got here7 \n");
htmlPageFree(&dbPage);
for (g=0;g<clRepeat;g++)
{
freez(&dna[g]);
freez(&pro[g]);
}
freez(&dna);
freez(&pro);
// uglyf("dbg: got here8 \n");
}
void testOrg(struct htmlPage *rootPage, struct htmlForm *rootForm, char *org)
/* Test on organism. If forceDb is non-null, only test on
* given database. */
{
struct htmlPage *orgPage;
struct htmlForm *mainForm;
struct htmlFormVar *dbVar;
struct slName *db;
htmlPageSetVar(rootPage, rootForm, "org", org);
htmlPageSetVar(rootPage, rootForm, "db", NULL);
if (!findRaSection(raList,org))
{
uglyf("testOrg: skipping org=%s, has no .ra section \n",org);
return; /* if there's no section for the organism, assume it should be skipped. */
}
printf("\n"); // separation
orgPage = htmlPageFromForm(rootPage, rootPage->forms, "submit", "Submit");
if ((mainForm = htmlFormGet(orgPage, "mainForm")) == NULL)
errAbort("Couldn't get main form on orgPage"); // we may want to report the error but try to keep going.
if ((dbVar = htmlFormVarGet(mainForm, "db")) == NULL)
errAbort("Couldn't get db var");
for (db = dbVar->values; db != NULL; db = db->next)
{
if (clDb == NULL || sameString(clDb, db->name))
{
uglyf("testOrg: db->name=%s \n",db->name);
testDb(orgPage, mainForm, org, db->name);
}
}
htmlPageFree(&orgPage);
}
void statsOnSubsets(struct blatTest *list, int subIx, FILE *f)
/* Report tests of certain subtype. */
{
struct blatTest *test;
struct hash *hash = newHash(0);
struct slName *typeList = NULL, *type;
fprintf(f, "\n%s subtotals\n", blatTestInfoTypes[subIx]);
/* Get list of all types in this field. */
for (test = list; test != NULL; test = test->next)
{
char *info = test->info[subIx];
if (!hashLookup(hash, info))
{
type = slNameNew(info);
hashAdd(hash, info, type);
slAddHead(&typeList, type);
}
}
slNameSort(&typeList);
hashFree(&hash);
for (type = typeList; type != NULL; type = type->next)
{
struct qaStatistics *stats;
AllocVar(stats);
for (test = list; test != NULL; test = test->next)
{
if (sameString(type->name, test->info[subIx]))
{
qaStatisticsAdd(stats, test->status);
}
}
qaStatisticsReport(stats, type->name, f);
freez(&stats);
}
}
void reportSummary(struct blatTest *list, FILE *f)
/* Report summary of test results. */
{
struct qaStatistics *stats;
struct blatTest *test;
AllocVar(stats);
int i;
for (i=0; i<=ntiiOutput; ++i)
statsOnSubsets(list, i, f);
for (test = list; test != NULL; test = test->next)
qaStatisticsAdd(stats, test->status);
qaStatisticsReport(stats, "Total", f);
}
void reportAll(struct blatTest *list, FILE *f)
/* Report all tests. */
{
struct blatTest *test;
for (test = list; test != NULL; test = test->next)
{
if (test->status->errMessage != NULL)
blatTestLogOne(test, f);
}
}
void hgBlatTest(char *url, char *log)
/* hgblatTest - Test hgBlat web page. */
{
struct htmlPage *rootPage = htmlPageGet(url);
struct htmlForm *mainForm;
struct htmlFormVar *orgVar;
FILE *f = mustOpen(log, "w");
htmlPageValidateOrAbort(rootPage);
/* global settings?
htmlPageSetVar(rootPage, NULL, orderVarName, "geneDistance");
htmlPageSetVar(rootPage, NULL, countVarName, "25");
*/
if ((mainForm = htmlFormGet(rootPage, "mainForm")) == NULL)
errAbort("Couldn't get main form");
if ((orgVar = htmlFormVarGet(mainForm, "org")) == NULL)
errAbort("Couldn't get org var");
if (clOrg != NULL)
{
uglyf("clOrg=%s\n",clOrg);
testOrg(rootPage, mainForm, clOrg);
}
else
{
struct slName *org;
for (org = orgVar->values; org != NULL; org = org->next)
{
uglyf("clOrg=%s\n",org->name);
testOrg(rootPage, mainForm, org->name);
}
}
htmlPageFree(&rootPage);
slReverse(&blatTestList);
reportSummary(blatTestList, stdout);
reportAll(blatTestList, f);
fprintf(f, "---------------------------------------------\n");
reportSummary(blatTestList, f);
}
void hgBlatTestX(char *url, char *log)
{
struct htmlPage *page;
struct qaStatus *qs;
qs = qaPageGet(url, &page);
qaStatusReportOne(stdout, qs, url);
htmlPageFree(&page);
}
int main(int argc, char *argv[])
/* Process command line. */
{
pushCarefulMemHandler(200000000);
/* Set initial seed */
srand( (unsigned)time( NULL ) );
optionInit(&argc, argv, options);
if (argc != 3)
usage();
clDb = optionVal("db", clDb);
clOrg = optionVal("org", clOrg);
clType = optionVal("type", clType);
clSort = optionVal("sort", clSort);
clOutput = optionVal("output", clOutput);
dataDir = optionVal("dataDir", dataDir);
clRepeat = optionInt("repeat", clRepeat);
raList = hgReadRa("org", "db", dataDir, raName, NULL);
if (raList == NULL)
errAbort("Couldn't find anything from %s", raName);
hgBlatTest(argv[1], argv[2]);
//hgBlatTestX(argv[1], argv[2]);
hashFreeList(&raList);
carefulCheckHeap();
return 0;
}