5db640d61b5495fb5a644885753ea37ff61dbb31 kent Mon Sep 2 08:46:09 2019 -0700 Fixing field names in output. diff --git src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c index e3b9bf1..39a548b 100644 --- src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c +++ src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c @@ -1,396 +1,397 @@ /* hcatTabUpdate - take the tabToTabDir result of the geo/sra import * and unpack a few fields that are just too hard in strex. * Put results in an output dir. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "fieldedTable.h" #include "portable.h" #include "csv.h" void usage() /* Explain usage and exit. */ { errAbort( "hcatTabUpdate - Update the hcat database given a tab seperated input and output dir.\n" "hcatTabUpdate - take the tabToTabDir result of the geo/sra import\n" "and unpack a few fields that are just too hard in strex. \n" "Put results in an output dir.\n" "usage:\n" " hcatTabUpdate inDir outDir\n" "options:\n" " -xxx=XXX\n" ); } /* Command line validation table. */ static struct optionSpec options[] = { {NULL, 0}, }; char *fieldedTableLookupNamedFieldInRow(struct fieldedTable *table, char *field, char **row) /* Look up field by name, not as effient as by index but what the heck. */ { int ix = fieldedTableFindFieldIx(table, field); if (ix < 0) return NULL; return row[ix]; } void addIfReal(int fieldIx, char *oldFieldNames[], char *newFields[], int newIxs[], int maxNewCount,int *pCurCount) /* If fieldIx is positive we consider it real anc add it to the newFields */ { if (fieldIx > 0) { char *oldName = cloneString(oldFieldNames[fieldIx]); char *newName = oldName; char *prefix = "contact_"; if (startsWith(prefix, oldName)) { newName += strlen(prefix);; } int curCount = *pCurCount; if (curCount >= maxNewCount) errAbort("Too many fields in addIfRead on %s, %d max", oldName, curCount); newIxs[curCount] = fieldIx; newFields[curCount] = newName; *pCurCount = curCount+1; } } struct slName *uniqVals(struct fieldedTable *table, char *field) /* Return list of all unique values in the field */ { struct dyString *scratch = dyStringNew(0); int fieldIx = fieldedTableFindFieldIx(table, field); if (fieldIx < 0) return NULL; struct hash *uniqHash = hashNew(0); struct slName *valList = NULL; struct fieldedRow *fr; for (fr = table->rowList; fr != NULL; fr = fr->next) { char *inTsv = fr->row[fieldIx]; char *val; while ((val = csvParseNext(&inTsv, scratch)) != NULL) { if (hashLookup(uniqHash, val) == NULL) { hashAdd(uniqHash, val, NULL); slNameAddHead(&valList, val); } } } slReverse(&valList); hashFree(&uniqHash); dyStringFree(&scratch); return valList; } char *slNameToCsv(struct slName *list) /* Convert slNames to a long string */ { struct dyString *dy = dyStringNew(0); struct slName *el; for (el = list; el != NULL; el = el->next) csvEscapeAndAppend(dy, el->name); return dyStringCannibalize(&dy); } struct fieldedTable *makeContributors(struct fieldedTable *inProject) /* Make a fielded table from project contact info and contributors list */ { char **projectRow = inProject->rowList->row; struct dyString *csvScratch = dyStringNew(0); /* Make the contributors list in two pieces first off of the contact */ int contact_email = fieldedTableFindFieldIx(inProject, "contact_email"); int contact_phone = fieldedTableFindFieldIx(inProject, "contact_phone"); //int contact_department = fieldedTableFindFieldIx(inProject, "contact_department"); //int contact_institute = fieldedTableFindFieldIx(inProject, "contact_institute"); //int contact_address = fieldedTableFindFieldIx(inProject, "contact_address"); //int contact_city = fieldedTableFindFieldIx(inProject, "contact_city"); //int contact_country = fieldedTableFindFieldIx(inProject, "contact_country"); //int contact_zip_postal_code = fieldedTableFindFieldIx(inProject, "contact_zip_postal_code"); /* Figure out which contact data we actually have */ const int maxContacts = 32; char *contactFields[maxContacts+1]; // An extra for the project_role int contactIx[maxContacts]; char **oldFields = inProject->fields; // Add contact name field separately from the rest. We know it's there since it's a // required field, and also we need to decorate it's name contactFields[0] = "?name"; contactIx[0] = fieldedTableMustFindFieldIx(inProject, "contact_name"); int realFieldCount = 1; // The rest of the contact pieces are added just conditionally addIfReal(contact_email, oldFields, contactFields, contactIx, maxContacts, &realFieldCount); addIfReal(contact_phone, oldFields, contactFields, contactIx, maxContacts, &realFieldCount); //addIfReal(contact_department, oldFields, contactFields, contactIx, maxContacts, &realFieldCount); //#addIfReal(contact_institute, oldFields, contactFields, contactIx, maxContacts, &realFieldCount); //#addIfReal(contact_address, oldFields, contactFields, contactIx, maxContacts, &realFieldCount); //addIfReal(contact_city, oldFields, contactFields, contactIx, maxContacts, &realFieldCount); //addIfReal(contact_country, oldFields, contactFields, contactIx, maxContacts, &realFieldCount); //addIfReal(contact_zip_postal_code, oldFields, // contactFields, contactIx, maxContacts, &realFieldCount); contactFields[realFieldCount] = "project_role"; realFieldCount += 1; /* Make contributor output table. The first row of it will be seeded with the contact. * We can fill out names, but not other info on the other contributors, who will make * up the rest of the rows. */ struct fieldedTable *contributors = fieldedTableNew("contributor", contactFields, realFieldCount); contributors->startsSharp = inProject->startsSharp; /* Make up first row from contacts */ char *outVals[realFieldCount]; int outIx; struct dyString *scratch = dyStringNew(0); for (outIx=0; outIx<realFieldCount-1; ++outIx) { char *inTsv = projectRow[contactIx[outIx]]; char *inVal = emptyForNull(cloneString(csvParseNext(&inTsv, scratch))); outVals[outIx] = cloneString(csvEscapeToDyString(csvScratch, inVal)); } outVals[outIx] = "lab contact"; char *contactName = cloneString(outVals[0]); fieldedTableAdd(contributors, outVals, realFieldCount, 1); /* Unroll the contributors field into further rows*/ for (outIx=0; outIx<realFieldCount; ++outIx) outVals[outIx] = ""; // Empty out all rows. int inContribIx = fieldedTableMustFindFieldIx(inProject, "contributors"); int outContribIx = fieldedTableMustFindFieldIx(contributors, "?name"); char *inTsv = projectRow[inContribIx]; char *oneVal; while ((oneVal = csvParseNext(&inTsv, scratch)) != NULL) { - if (differentString(oneVal, contactName)) // We already got the contact as a contributor + char *escaped = csvEscapeToDyString(csvScratch, oneVal); + if (differentString(escaped, contactName)) // We already got the contact as a contributor { - outVals[outContribIx] = csvEscapeToDyString(csvScratch, oneVal); + outVals[outContribIx] = escaped; outVals[realFieldCount-1] = "contributor"; fieldedTableAdd(contributors, outVals, realFieldCount, contributors->rowCount+1); } } dyStringFree(&csvScratch); return contributors; } char *lookupSpecies(char *taxon) /* Some day we may query a decent database, for now * just have some of the most common */ { if (sameString(taxon, "9606")) return "human"; if (sameString(taxon, "10090")) return "mouse"; if (sameString(taxon, "10116")) return "rat"; if (sameString(taxon, "7955")) return "zebrafish"; if (sameString(taxon, "7227")) return "fly"; if (sameString(taxon, "6239")) return "worm"; if (sameString(taxon, "4932")) return "yeast"; errAbort("Unknown taxon %s", taxon); return NULL; } char *taxonsToSpecies(char *inVal, struct dyString *scratch) /* Convert a comma separated list of taxons in inVal to a * comma separated species list, using scratch. */ { struct dyString *result = dyStringNew(64); char *taxon; char *s = inVal; while ((taxon = csvParseNext(&s, scratch)) != NULL) { char *species = lookupSpecies(taxon); csvEscapeAndAppend(result, species); } return dyStringCannibalize(&result); } void addListFieldIfNonempty(char *field, struct slName *list, char *newFields[], char *newVals[], int maxNewCount,int *pCurCount) /* Add field to newFields if list is non-empty, taking care not to go past end. */ { if (list != NULL) { int curCount = *pCurCount; if (curCount >= maxNewCount) errAbort("Too many fields in addListFieldIfNonempty on %s, %d max", field, curCount); char fieldName[256]; char *strippedField = cloneString(field); stripChar(strippedField, '_'); safef(fieldName, sizeof(fieldName), - "@@%s@hcat_project_%s@project_id@%s_id@hcat_%s.short_name@id", + "@@%s@id@hcat_project_%s@project_id@%s_id@hcat_%s.short_name@id", field, strippedField, field, strippedField); newFields[curCount] = cloneString(fieldName); newVals[curCount] = slNameToCsv(list); *pCurCount = curCount+1; freez(&strippedField); } } struct fieldedTable *makeProject(struct fieldedTable *inProject, struct fieldedTable *inSample) /* Make output project table. This is the big one - 35 fields now * probably twice that by the time HCA is done. Fortunately we only need * to deal with some of the fields and it only has one row. */ { char **inFields = inProject->fields; char **inRow = inProject->rowList->row; int inFieldCount = inProject->fieldCount; struct dyString *scratch = dyStringNew(0); int outFieldMax = inFieldCount + 16; // Mostly we remove fields but we do add a few. Gets checked char *outFields[outFieldMax]; char *outRow[outFieldMax]; int outFieldCount = 0; /* First we make up the basics of the outProject table. Mostly this is just * passing through from the inProject, but there's exceptions like contacts. */ int inIx; for (inIx=0; inIx<inFieldCount; ++inIx) { /* Fetch input name and value */ char *inName = inFields[inIx]; char *inVal = inRow[inIx]; /* Go through list of input fields we tweak slightly */ if (sameString("taxons", inName)) { // its many-to-many, whoot! - inName = "@@species@hcat_project_species@project_id@species_id@hcat_species@common_name@id"; + inName = "@@species@id@hcat_project_species@project_id@species_id@hcat_species@common_name@id"; inVal = taxonsToSpecies(inVal, scratch); } /* We might modify names of some fields */ char nameBuf[128]; if (sameString("state_reached", inName) || sameString("cur_state", inName)) { safef(nameBuf, sizeof(nameBuf), "@%s_id@hcat_project_state.state@id", inName); inName = cloneString(nameBuf); } else if (sameString("consent", inName) || sameString("effort", inName)) { safef(nameBuf, sizeof(nameBuf), "@%s_id@hcat_%s.short_name@id", inName, inName); inName = cloneString(nameBuf); } /* Output all the ones we haven't dealt with already or will deal with later */ if (!startsWith("contact_", inName) && !sameString("contributors", inName)) { outFields[outFieldCount] = inName; outRow[outFieldCount] = inVal; ++outFieldCount; } } /* Add in contributors as a multi to multi field */ -outFields[outFieldCount] = "@@contributors@hcat_project_contributors@project_id@contributor_id@hcat_contributor.name@id"; +outFields[outFieldCount] = "@@contributors@hcat_project_contributors@id@project_id@contributor_id@hcat_contributor@name@id"; outRow[outFieldCount] = fieldedTableLookupNamedFieldInRow(inProject, "contributors", inRow); /* Add the fields we scan and merge from sample at end */ struct slName *organList = uniqVals(inSample, "organ"); struct slName *organPartList = uniqVals(inSample, "organ_part"); struct slName *assayTypeList = uniqVals(inSample, "assay_type"); struct slName *diseaseList = uniqVals(inSample, "disease"); addListFieldIfNonempty("organ", organList, outFields, outRow, outFieldMax, &outFieldCount); addListFieldIfNonempty("organ_part", organPartList, outFields, outRow, outFieldMax, &outFieldCount); addListFieldIfNonempty("assay_type", assayTypeList, outFields, outRow, outFieldMax, &outFieldCount); addListFieldIfNonempty("disease", diseaseList, outFields, outRow, outFieldMax, &outFieldCount); struct fieldedTable *outTable = fieldedTableNew("project", outFields, outFieldCount); outTable->startsSharp = inProject->startsSharp; fieldedTableAdd(outTable, outRow, outFieldCount, 1); dyStringFree(&scratch); return outTable; } struct fieldedTable *makeLab(struct fieldedTable *inProject) /* If there's a lab field we make a lab table and seed it with the contacts. */ { int labIx = fieldedTableFindFieldIx(inProject, "lab"); if (labIx >= 0) { char **inRow = inProject->rowList->row; char *short_name = inRow[labIx]; char *contact = fieldedTableLookupNamedFieldInRow(inProject, "contact_name", inRow); char *contributors = fieldedTableLookupNamedFieldInRow(inProject, "contributors", inRow); char *institute = emptyForNull(fieldedTableLookupNamedFieldInRow(inProject, "contact_institute", inRow)); char labName[256]; if (strlen(short_name) < 20) // Unlikely to be unique, may cause trouble safef(labName, sizeof(labName), "%s %s", short_name, institute); else safef(labName, sizeof(labName), "%s", short_name); labName[50] = 0; // not too long - char *outFields[4] = {"?short_name", "institute", "@contact@hcat_contributor.name@id", - "@@contributors@hcat_lab_contributors@lab_id@contributor_id@hcat_contributor.name@id"}; + char *outFields[4] = {"?short_name", "institution", "@contact_id@hcat_contributor@name@id", + "@@contributors@id@hcat_lab_contributors@lab_id@contributor_id@hcat_contributor@name@id"}; struct fieldedTable *labTable = fieldedTableNew("lab", outFields, ArraySize(outFields)); char *outRow[4] = {labName, institute, contact, contributors}; fieldedTableAdd(labTable, outRow, ArraySize(outRow), 1); return labTable; } else return NULL; } void hcatTabUpdate(char *inDir, char *outDir) /* hcatTabUpdate - Update the hcat database given a tab seperated input and output dir. */ { // We are actually just looking for specific files in inDir. */ /* Load up input projects table */ char *projectFile = "hcat_project.tsv"; char inPath[PATH_LEN]; safef(inPath, sizeof(inPath), "%s/%s", inDir, projectFile); char *projectRequired[] = {"short_name", "contact_name", "contributors"}; struct fieldedTable *inProject = fieldedTableFromTabFile(inPath, inPath, projectRequired, ArraySize(projectRequired)); /* Load up samples table */ char *sampleFile = "hcat_sample.tsv"; safef(inPath, sizeof(inPath), "%s/%s", inDir, sampleFile); char *sampleRequired[] = {"short_name",}; struct fieldedTable *inSample = fieldedTableFromTabFile(inPath, inPath, sampleRequired, ArraySize(sampleRequired)); /* Make sure inProject table makes sense by having exactly one row */ if (inProject->rowCount != 1) errAbort("Expected one row in %s, got %d\n", projectFile, inProject->rowCount); struct fieldedTable *outContributor = makeContributors(inProject); struct fieldedTable *outProject = makeProject(inProject, inSample); struct fieldedTable *outLab = makeLab(inProject); /* Write output from lowest level to highest level tables. */ makeDirsOnPath(outDir); char outPath[PATH_LEN]; safef(outPath, sizeof(outPath), "%s/hcat_%s", outDir, "contributor.tsv"); fieldedTableToTabFile(outContributor, outPath); if (outLab != NULL) { safef(outPath, sizeof(outPath), "%s/hcat_%s", outDir, "lab.tsv"); fieldedTableToTabFile(outLab, outPath); } safef(outPath, sizeof(outPath), "%s/hcat_%s", outDir, "project.tsv"); fieldedTableToTabFile(outProject, outPath); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 3) usage(); hcatTabUpdate(argv[1], argv[2]); return 0; }