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SID to CID rewrite function included.
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@meier-rene
meier-rene committed Jan 31, 2025
1 parent 0639986 commit 28d88ef
Showing 1 changed file with 205 additions and 20 deletions.
225 changes: 205 additions & 20 deletions MassBank-Project/MassBank-lib/src/main/java/massbank/cli/AddMetaData.java
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Original file line number Diff line number Diff line change
Expand Up @@ -475,11 +475,17 @@ else if (ret == InchiStatus.ERROR) {
}

public static String fetchCIDFromSID(String sid) {
String apiUrl = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/substance/sid/" + sid + "/cids/JSON";
String apiUrl = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/substance/sid/" + sid + "/JSON";
try {
HttpURLConnection connection = (HttpURLConnection) new URL(apiUrl).openConnection();
connection.setRequestMethod("GET");

int responseCode = connection.getResponseCode();
if (responseCode != 200) {
System.out.println("Error fetching CID: Server returned HTTP response code " + responseCode);
return null;
}

Scanner scanner = new Scanner(connection.getInputStream());
StringBuilder response = new StringBuilder();
while (scanner.hasNext()) {
Expand All @@ -488,38 +494,210 @@ public static String fetchCIDFromSID(String sid) {
scanner.close();

JsonObject jsonResponse = JsonParser.parseString(response.toString()).getAsJsonObject();
JsonArray cid = jsonResponse.getAsJsonObject("InformationList")
.getAsJsonArray("Information")
.get(0).getAsJsonObject()
.getAsJsonArray("CID");

if (cid.size() != 1) {
System.out.println("Error: More than one CID found for SID " + sid);
return null;
}

return cid.get(0).getAsString();
JsonObject information = jsonResponse.getAsJsonArray("PC_Substances")
.get(0).getAsJsonObject();

JsonArray compoundArray = information.getAsJsonArray("compound");
if (compoundArray.size() > 1) {
String cid = information.getAsJsonArray("compound")
.get(1).getAsJsonObject()
.getAsJsonObject("id")
.getAsJsonObject("id")
.getAsJsonPrimitive("cid").getAsString();

String sourceName = information.getAsJsonObject("source")
.getAsJsonObject("db")
.getAsJsonPrimitive("name").getAsString();

String sourceID = information.getAsJsonObject("source")
.getAsJsonObject("db")
.getAsJsonObject("source_id")
.getAsJsonPrimitive("str").getAsString();
return cid;
} else {
System.out.println("No valid CID found in the response.");
return null;
}
} catch (IOException e) {
e.printStackTrace();
System.out.println("Error fetching CID");
return null;
}
}

public static Map<String, String> fetchExternalDBIdFromPubchemCID(String cid) {
String apiUrl = "https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/" + cid + "/JSON";
Map<String, String> externalDatabaseInfo = new HashMap<>();
try {
HttpURLConnection connection = (HttpURLConnection) new URL(apiUrl).openConnection();
connection.setRequestMethod("GET");

Scanner scanner = new Scanner(connection.getInputStream());
StringBuilder response = new StringBuilder();
while (scanner.hasNext()) {
response.append(scanner.nextLine());
}
scanner.close();

JsonObject jsonResponse = JsonParser.parseString(response.toString()).getAsJsonObject();
JsonArray sections = jsonResponse.getAsJsonObject("Record").getAsJsonArray("Section");

for (int i = 0; i < sections.size(); i++) {
JsonObject section = sections.get(i).getAsJsonObject();
if (section.get("TOCHeading").getAsString().equals("Names and Identifiers")) {
JsonArray subSections = section.getAsJsonArray("Section");
for (int j = 0; j < subSections.size(); j++) {
JsonObject subSection = subSections.get(j).getAsJsonObject();
if (subSection.get("TOCHeading").getAsString().equals("Other Identifiers")) {
JsonArray identifiers = subSection.getAsJsonArray("Section");
for (int k = 0; k < identifiers.size(); k++) {
JsonObject identifier = identifiers.get(k).getAsJsonObject();
String dbName = identifier.get("TOCHeading").getAsString();
JsonArray information = identifier.getAsJsonArray("Information");
for (int l = 0; l < information.size(); l++) {
JsonObject info = information.get(l).getAsJsonObject();
if (info.has("Value")) {
JsonArray value = info.getAsJsonObject("Value").getAsJsonArray("StringWithMarkup");
for (int m = 0; m < value.size(); m++) {
JsonObject dbInfo = value.get(m).getAsJsonObject();
String dbValue = dbInfo.get("String").getAsString();
externalDatabaseInfo.put(dbName, dbValue);
}
}
}
}
} else if (subSection.get("TOCHeading").getAsString().equals("Computed Descriptors")) {
JsonArray identifiers = subSection.getAsJsonArray("Section");
for (int k = 0; k < identifiers.size(); k++) {
JsonObject identifier = identifiers.get(k).getAsJsonObject();
String dbName = identifier.get("TOCHeading").getAsString();
if (dbName.equals("InChI")) {
JsonArray information = identifier.getAsJsonArray("Information");
for (int l = 0; l < information.size(); l++) {
JsonObject info = information.get(l).getAsJsonObject();
if (info.has("Value")) {
String inchi = info.getAsJsonObject("Value").getAsJsonArray("StringWithMarkup")
.get(0).getAsJsonObject().get("String").getAsString();
externalDatabaseInfo.put("InChI", inchi);
}
}
}
if (dbName.equals("InChIKey")) {
JsonArray information = identifier.getAsJsonArray("Information");
for (int l = 0; l < information.size(); l++) {
JsonObject info = information.get(l).getAsJsonObject();
if (info.has("Value")) {
String inchi = info.getAsJsonObject("Value").getAsJsonArray("StringWithMarkup")
.get(0).getAsJsonObject().get("String").getAsString();
externalDatabaseInfo.put("INCHIKEY", inchi);
}
}
}
}
}
}
}
}
} catch (IOException e) {
e.printStackTrace();
System.out.println("Error fetching info for CID");
return new HashMap<>();
}
return externalDatabaseInfo;
}


public static String doNormalizeCompoundIdentifier(Record record) {
Map<String, String> inRecord = new HashMap<>();
inRecord.put("Inchi", record.CH_IUPAC());
inRecord.put("InChI", record.CH_IUPAC());
inRecord.put("SMILES", record.CH_SMILES());
if (record.CH_LINK().get("PUBCHEM") != null) {
inRecord.put("PUBCHEM", record.CH_LINK().get("PUBCHEM"));
if (record.CH_LINK() != null) {
inRecord.putAll(record.CH_LINK());
}

Map<String, String> externalDBInfo = new HashMap<>();
String cid = "";
if (inRecord.containsKey("PUBCHEM")) {
String pubchem = inRecord.get("PUBCHEM");
if (pubchem.startsWith("SID:")) {
String sid = pubchem.substring(4); // Extract the identifier after "SID:"
cid = fetchCIDFromSID(sid);
if (cid != null) {
externalDBInfo = fetchExternalDBIdFromPubchemCID(cid);
} else {
return record.toString();
}
}
}

// Rename keys
Map<String, String> renamedExternalDBInfo = new HashMap<>();
for (Entry<String, String> entry : externalDBInfo.entrySet()) {
String key = entry.getKey();
if (key.equals("ChEBI ID")) {
key = "CHEBI";
}
if (key.equals("HMDB ID")) {
key = "HMDB";
}
if (key.equals("KEGG ID")) {
key = "KEGG";
}
if (key.equals("Lipid Maps ID (LM_ID)")) {
key = "LIPIDMAPS";
}
if (key.equals("ChEMBL ID")) {
key = "CHEMBL";
}
renamedExternalDBInfo.put(key, entry.getValue());
}
if (record.CH_LINK().get("CAS") != null) {
inRecord.put("CAS", record.CH_LINK().get("CAS"));
externalDBInfo = renamedExternalDBInfo;

if (inRecord.get("InChI") != null) {
for (Entry<String, String> entry : inRecord.entrySet()) {
String key = entry.getKey();
if (externalDBInfo.containsKey(key)) {
String inRecordValue = entry.getValue();
String externalDBInfoValue = externalDBInfo.get(key);
if (!inRecordValue.equals(externalDBInfoValue)) {
System.out.println("Mismatch found for key: " + key);
System.out.println("inRecord value: " + inRecordValue);
System.out.println("externalDBInfo value: " + externalDBInfoValue);
}
}
}
}
if (inRecord.get("InChI") != null && externalDBInfo.get("InChI") != null &&
inRecord.get("InChI").substring(0, 14).equals(externalDBInfo.get("InChI").substring(0, 14))) {
Map<String, String> chlink = record.CH_LINK();
chlink.put("PUBCHEM", "CID:" + cid);
} else {
System.out.println("InChI does not match.");
System.out.println("InChIKey in Record: " + inRecord.get("INCHIKEY"));
System.out.println("InChIKey for compound in CID: " + externalDBInfo.get("INCHIKEY"));
System.out.println("Rewrite SID to CID? (y/n/s): ");
Scanner scanner = new Scanner(System.in);
String response = scanner.nextLine();
Map<String, String> chlink = record.CH_LINK();
if (response.equalsIgnoreCase("y")) {
chlink.put("PUBCHEM", "CID:" + cid);
}
// for (Entry<String, String> entry : chlink.entrySet()) {
// String key = entry.getKey();
// if (externalDBInfo.containsKey(key)) {
// chlink.put(key, externalDBInfo.get(key));
// }
// }
// record.CH_LINK(chlink);
// } else if (response.equalsIgnoreCase("n")) {
// chlink.put("PUBCHEM", "CID:" + cid);
// } else {
// return record.toString();
// }
// }
}

System.out.println(inRecord);

System.out.println(fetchCIDFromSID("5689"));

return record.toString();
}
Expand All @@ -542,11 +720,12 @@ public static void main(String[] arguments) throws Exception {
}

RecordParser recordparser = new RecordParser(new HashSet<>());
recordFiles.parallelStream()
recordFiles.stream()
.map(Validator::readFile)
.filter(Objects::nonNull)
.forEach(recordString -> {
logger.info("Working on {}.", recordString.getKey());
System.out.println("Working on " + recordString.getKey());
Record record = parseRecord(recordString, recordparser);
if (record == null || record.DEPRECATED()) return;

Expand All @@ -561,6 +740,11 @@ public static void main(String[] arguments) throws Exception {
//}

recordStringAfterMod = doNormalizeCompoundIdentifier(record);
try {
Thread.sleep(100);
} catch (InterruptedException e) {
throw new RuntimeException(e);
}


// if (doAddPubchemCid.get()) {
Expand Down Expand Up @@ -595,6 +779,7 @@ public static void main(String[] arguments) throws Exception {
}
}
});
System.out.println();
}

private static CommandLine parseCommandLine(String[] arguments) {
Expand Down

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