867a3f8e1801a5e150dcc054a9f8b7b05fe6f428 kent Sat Sep 14 14:34:55 2019 -0700 Decided to go with a separate table for the tracker info since project was getting so big. No regrets! diff --git src/hca/hcat/hcatParseParth/hcatParseParth.c src/hca/hcat/hcatParseParth/hcatParseParth.c index a3c330b..634d193 100644 --- src/hca/hcat/hcatParseParth/hcatParseParth.c +++ src/hca/hcat/hcatParseParth/hcatParseParth.c @@ -1,273 +1,352 @@ /* hcatParseParth - Parse through Parth Shah's Project Tracker json and turn it into fodder for sqlUpdateRelated.. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "localmem.h" #include "dystring.h" #include "obscure.h" #include "portable.h" #include "jsonParse.h" #include "csv.h" void usage() /* Explain usage and exit. */ { errAbort( "hcatParseParth - Parse through Parth Shah's Project Tracker json and turn it into fodder for \n" "sqlUpdateRelated - that is a directory full of tab-separated files that'll update the SQL\n" "tables in a relationally correct way.\n" "usage:\n" " hcatParseParth inFile.json outDir\n" "options:\n" " -xxx=XXX\n" ); } /* Command line validation table. */ static struct optionSpec options[] = { {NULL, 0}, }; char *lookupSpecies(char *sciName) /* Some day we may query a decent database, for now * just have some of the most common */ { if (sameWord(sciName, "Homo sapiens")) return "human"; if (sameWord(sciName, "Mus musculus")) return "mouse"; if (sameWord(sciName, "Rattus norvegicus")) return "rat"; if (sameWord(sciName, "Danio rerio")) return "zebrafish"; if (sameWord(sciName, "Drosophila melanogaster")) return "fly"; if (sameWord(sciName, "Caenorhabditis elegans")) return "worm"; if (sameWord(sciName, "Saccharomyces cerevisiae")) return "yeast"; errAbort("Unknown species %s in lookup species", sciName); return NULL; } char *sciNameRefsToSpecies(struct slRef *refList, 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); struct slRef *ref; for (ref = refList; ref != NULL; ref = ref->next) { char *sciName = jsonStringVal(ref->val, "species"); csvEscapeAndAppend(result, lookupSpecies(sciName)); } return dyStringCannibalize(&result); } char *lookupAssayType(char *ingestSym) /* Convert ingest's representation of library_construction to something we put * in assayTech. */ { if (sameWord(ingestSym, "10x v2 sequencing") || sameWord(ingestSym, "10x 3' v2 sequencing") || sameWord(ingestSym, "10x 5' v2 sequencing")) // this one Paris's typo most likely return "10X Chromium V2"; if (sameWord(ingestSym, "smart-seq2") || sameWord(ingestSym, "smart-seq") || sameWord(ingestSym, "full length single cell rna sequencing") // Quake lab set I seen before || sameWord(ingestSym, "smart-seq2 paired-end")) return "smart-seq2 PE"; if (sameWord(ingestSym, "cite-seq")) return "cite-seq"; if (sameWord(ingestSym, "indrop")) return "inDrop"; if (sameWord(ingestSym, "mars-seq")) return "mars-seq"; if (sameWord(ingestSym, "drop-seq")) return "drop-seq"; if (sameWord(ingestSym, "dronc-seq")) return "dronc-seq"; if (sameWord(ingestSym, "10x 3' v1 sequencing")) return "10X Chromium V1"; if (sameWord(ingestSym, "10x 3' v3 sequencing")) return "10X Chromium V3"; // if (sameWord(ingestSym, "xyz")) return "xyz"; errAbort("Unknown ingest-info.library_construction_method %s", ingestSym); return NULL; } char *ingestConstructionRefsToAssayTech(struct slRef *refList, 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); struct slRef *ref; for (ref = refList; ref != NULL; ref = ref->next) { char *assayType = jsonStringVal(ref->val, "library_construction_methods"); csvEscapeAndAppend(result, lookupAssayType(assayType)); } return dyStringCannibalize(&result); } boolean isComplete(char *s) /* Return TRUE if jel is a string with a value COMPLETE */ { if (sameWord("COMPLETE", s)) return TRUE; else if (sameWord("INCOMPLETE", s)) return FALSE; else errAbort("Unexpected value %s in isComplete", s); return FALSE; } char *despaceAfterComma(char *tripleName) /* We return a possibly reduced version of input */ { char *in = tripleName; char *out = in; char c; while ((c = *in++) != 0) { if (c == ',' && *in == ' ') in += 1; *out++ = c; } *out=0; return tripleName; } char *nextContrib(char **pList) /* pList points to something looking like First1,Mid1,Last1; First2,Mid2,Last2; * We return the next name triple and and advance list pointer past it. * The parsing is destructive. */ { char *start = skipLeadingSpaces(*pList); if (isEmpty(start)) return NULL; /* Find end and update pointer. */ char *end = strchr(start, ';'); if (end != NULL) *end++ = 0; *pList = end; /* Return trimmed version of whats between start and end */ start = trimSpaces(start); despaceAfterComma(start); return start; } void outputContributors(FILE *f, char *semiList, char *type, struct dyString *csvOut, struct dyString *scratch) /* Parse throughs semicolon separated list of contributors of given * type and output to tab sep file */ { char *dupe = cloneString(semiList); // because of destructive parsing char *p = dupe; char *contrib; while ((contrib = nextContrib(&p)) != NULL) { if (!sameWord("n/a", contrib)) { fprintf(f, "%s\t%s\n", type, csvEscapeToDyString(scratch, contrib)); csvEscapeAndAppend(csvOut, contrib); } } freeMem(dupe); } +void outputTracker(FILE *f, char *projectName, char *submissionId, char *uuid, + struct hash *projectHash, int subBunCount, struct dyString *scratch) +/* Look for interesting state info from parth's tracker outside of ingest and output it */ +{ +/* Grab the dss-info and lots of pieces of it. It sees both primary and analysis, + * not sure about matrix */ +struct jsonElement *dssEl = hashMustFindVal(projectHash, "dss-info"); +struct jsonElement *awsPrimary = jsonMustFindNamedField(dssEl, + "dss-info", "aws_primary_bundle_count"); +int awsPrimaryCount = jsonDoubleVal(awsPrimary, "aws_primary_bundle_count"); +struct jsonElement *gcpPrimary = jsonMustFindNamedField(dssEl, + "dss-info", "gcp_primary_bundle_count"); +int gcpPrimaryCount = jsonDoubleVal(gcpPrimary, "gcp_primary_bundle_count"); +struct jsonElement *awsAnalysis = jsonMustFindNamedField(dssEl, + "dss-info", "aws_analysis_bundle_count"); +int awsAnalysisCount = jsonDoubleVal(awsAnalysis, "aws_analysis_bundle_count"); +struct jsonElement *gcpAnalysis = jsonMustFindNamedField(dssEl, + "dss-info", "gcp_analysis_bundle_count"); +int gcpAnalysisCount = jsonDoubleVal(gcpAnalysis, "gcp_analysis_bundle_count"); + +/* Grab just a little bit from azul-info */ +struct jsonElement *azulEl = hashMustFindVal(projectHash, "azul-info"); +struct jsonElement *azulBundle = jsonMustFindNamedField(azulEl, + "azul-info", "analysis_bundle_count"); +int azulBundleCount = jsonDoubleVal(azulBundle, "azul-info.analysis_bundle_count"); + +/* Grab a little bit from analysis-info */ +struct jsonElement *analysisEl = hashMustFindVal(projectHash, "analysis-info"); +struct jsonElement *succeededEl = jsonFindNamedField(analysisEl, + "analysis-info", "succeeded_workflows"); +int succeededWorkflows = 0; +if (succeededEl != NULL) + succeededWorkflows = jsonDoubleVal(succeededEl, "succeeded_workflows"); + +/* And get the matrix stuff! */ +struct jsonElement *matrixEl = hashMustFindVal(projectHash, "matrix-info"); +struct jsonElement *matBundle = jsonMustFindNamedField(matrixEl, + "matrix-info", "analysis_bundle_count"); +int matrixBundleCount = jsonDoubleVal(matBundle, "matrix-info.analysis_bundle_count"); +struct jsonElement *cellCountEl = jsonMustFindNamedField(matrixEl, + "matrix-info", "cell_count"); +int cellCount = jsonDoubleVal(cellCountEl, "cell_count"); + +fprintf(f, "%s\t%s\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", + projectName, uuid, submissionId, + subBunCount, awsPrimaryCount, gcpPrimaryCount, awsAnalysisCount, gcpAnalysisCount, + azulBundleCount, succeededWorkflows, matrixBundleCount, cellCount); +} + void hcatParseParth(char *inFile, char *outDir) /* hcatParseParth - Parse through Parth Shah's Project Tracker json and turn it into fodder * for sqlUpdateRelated.. */ { // These two are frankly unneeded speed optimizations for our purposes, but heck what // do you expect from the C code base? It was built to be fast more than easy. struct lm *lm = lmInit(0); struct dyString *scratch = dyStringNew(0); struct dyString *contribCsv = dyStringNew(0); // Here's stuff just to read in the input file in a big string and then parsed // out into jsonElements char *inAsString = NULL; size_t inStringSize = 0; readInGulp(inFile, &inAsString, &inStringSize); verbose(1, "Read %lld bytes from %s\n", (long long)inStringSize, inFile); struct jsonElement *rootEl = jsonParseLm(inAsString, lm); /* Check it is the type we expect - a list, and set up a bunch of stuff to help deduplicate * things. */ if (rootEl->type != jsonList) errAbort("Expecting first object in %s to be a [] but it's not", inFile); struct hash *uniqHash = hashNew(0), *uniqTitleHash = hashNew(0), *uniqShortNameHash = hashNew(0); /* Make output directories and files. */ makeDirsOnPath(outDir); char contribPath[PATH_LEN]; safef(contribPath, sizeof(contribPath), "%s/hcat_contributor.tsv", outDir); FILE *fContrib = mustOpen(contribPath, "w"); char projectPath[PATH_LEN]; safef(projectPath, sizeof(projectPath), "%s/hcat_project.tsv", outDir); FILE *fProject = mustOpen(projectPath, "w"); +char postPath[PATH_LEN]; +safef(postPath, sizeof(postPath), "%s/hcat_tracker.tsv", outDir); +FILE *fTracker = mustOpen(postPath, "w"); /* Write out file headers */ fprintf(fContrib, "#@type_id@hcat_contributortype@short_name@id ?name\n"); -fprintf(fProject, "#uuid\t?short_name\ttitle\t@@species@id@hcat_project_species@project_id@species_id@hcat_species@common_name@id\t@@assay_tech@id@hcat_project_assay_tech@project_id@assaytech_id@hcat_assaytech@short_name@id\t@@contributors@id@hcat_project_contributors@project_id@contributor_id@hcat_contributor@name@id\n"); +fprintf(fProject, "#?short_name\ttitle\t@@species@id@hcat_project_species@project_id@species_id@hcat_species@common_name@id\t@@assay_tech@id@hcat_project_assay_tech@project_id@assaytech_id@hcat_assaytech@short_name@id\t@@contributors@id@hcat_project_contributors@project_id@contributor_id@hcat_contributor@name@id\tsubmit_date\n"); +fprintf(fTracker, "#@project_id@hcat_project@short_name@id\t?uuid\tsubmission_id\tsubmission_bundles_exported_count\taws_primary_bundle_count\tgcp_primary_bundle_count\taws_analysis_bundle_count\tgcp_analysis_bundle_count\tazul_analysis_bundle_count\tsucceeded_workflows\tmatrix_bundle_count\tmatrix_cell_count\n"); /* Main loop - once through for each project (or in some cases project fragment */ struct slRef *projectRef; for (projectRef = rootEl->val.jeList; projectRef != NULL; projectRef = projectRef->next) { /* Each project is an object/hash/dictionary depending on your fave language. * Here we get that level object into a C hash, and extract the project_uuid */ struct hash *projectHash = jsonObjectVal(projectRef->val, "project"); struct jsonElement *uuidEl = hashMustFindVal(projectHash, "project_uuid"); char *projectUuid = uuidEl->val.jeString; /* Get the ingest-info subobject and make sure it's complete. */ struct jsonElement *ingestEl = hashFindVal(projectHash, "ingest-info"); if (ingestEl == NULL) errAbort("Can't find ingest-info for project_uuid %s", projectUuid); char *primaryState = jsonStringField(ingestEl, "primary_state"); if (!isComplete(primaryState)) continue; /* God help us even among the completes there are multiple projects associated * with the same thing. So far project_short_name is unique. We'll just take * the first (complete) one and warn about the rest. Some of the dupes have the * same uuid, some different. Yes, it's a little messy this input . */ char *shortName = jsonStringField(ingestEl, "project_short_name"); + // Abbreviate what is really and truly not a short name! + if (startsWith("Single cell RNAseq characterization of cell types produced over time in an in ", + shortName)) + { + shortName = "Single cell RNAseq characterization of cell types produced over time"; + verbose(2, "Abbreviated shortName to %s\n", shortName); + } if (hashLookup(uniqShortNameHash, shortName)) { verbose(2, "Skipping duplicate project named '%s'\n", shortName); continue; } hashAdd(uniqShortNameHash, shortName, NULL); - /* grab more string fields we like from ingest-info. */ + /* Grab more string fields we like from ingest-info. */ + char *submissionId = jsonStringField(ingestEl, "submission_id"); char *title = jsonStringField(ingestEl, "project_title"); char *wrangler = jsonStringField(ingestEl, "data_curator"); char *contributors = jsonStringField(ingestEl, "primary_investigator"); + char *submissionDateTime = jsonStringField(ingestEl, "submission_date"); + + /* Turn dateTime into just date */ + char *tStart = strchr(submissionDateTime, 'T'); + if (tStart == NULL) + errAbort("No T separator in submission_date %s", submissionDateTime); + char *submissionDate = cloneStringZ(submissionDateTime, tStart - submissionDateTime); /* Get species list, maybe.... */ struct jsonElement *speciesEl = jsonMustFindNamedField(ingestEl, "ingest-info", "species"); struct slRef *speciesRefList = jsonListVal(speciesEl, "species"); char *species = sciNameRefsToSpecies(speciesRefList, scratch); + struct jsonElement *subBunCountEl = jsonMustFindNamedField(ingestEl, + "ingest-info", "submission_bundles_exported_count"); + int subBunCount = jsonDoubleVal(subBunCountEl, "submission_bundles_exported_count"); /* Get assay techs maybe */ struct jsonElement *constructEl = jsonMustFindNamedField(ingestEl, "ingest-info", "library_construction_methods"); struct slRef *constructList = jsonListVal(constructEl, "library_construction_methods"); char *techs = ingestConstructionRefsToAssayTech(constructList, scratch); /* Still more error checking */ hashAddUnique(uniqHash, projectUuid, NULL); hashAddUnique(uniqTitleHash, title, NULL); /* Update contributors table */ dyStringClear(contribCsv); outputContributors(fContrib, contributors, "contributor", contribCsv, scratch); outputContributors(fContrib, wrangler, "wrangler", contribCsv, scratch); - fprintf(fProject, "%s\t%s\t%s\t", projectUuid, shortName, title); - fprintf(fProject, "%s\t%s\t%s\n", species, techs, contribCsv->string); + /* Update project table */ + fprintf(fProject, "%s\t%s\t", shortName, title); + fprintf(fProject, "%s\t%s\t%s\t", species, techs, contribCsv->string); + fprintf(fProject, "%s\n", submissionDate); + + /* We processed the heck out of the ingest-info, and this routine is so long, + * pass along what we parsed out that goes into the tracker table, and have it + * deal with the azul-info, matrix-info, etc, which are read-only to wranglers. */ + outputTracker(fTracker, shortName, submissionId, projectUuid, projectHash, + subBunCount, scratch); } } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 3) usage(); hcatParseParth(argv[1], argv[2]); return 0; }