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Fix bug in globals.d.ts: error TS1357: An enum member name must be fo… #126

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41d0655
Fix bug in globals.d.ts: error TS1357: An enum member name must be fo…
Apr 29, 2023
2085c91
fix bug. Can't close hdf5 file
May 2, 2023
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4 changes: 4 additions & 0 deletions .devcontainer/devcontainer.json
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@@ -0,0 +1,4 @@
{
"image": "mcr.microsoft.com/devcontainers/typescript-node:0-18",
"remoteUser":"root"
}
6 changes: 3 additions & 3 deletions lib/globals.d.ts
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Expand Up @@ -14,11 +14,11 @@ export declare enum Access {
/** print debug info */
ACC_DEBUG,
/** create non-existing files */
ACC_CREAT
ACC_CREAT,
/** read/write in SWMR mode*/
ACC_SWMR_WRITE
ACC_SWMR_WRITE,
/** read in SWMR mode*/
ACC_SWMR_READ
ACC_SWMR_READ,
}

export declare enum CreationOrder {
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13 changes: 7 additions & 6 deletions package.json
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@@ -1,14 +1,14 @@
{
"name": "hdf5",
"version": "0.4.0",
"description": "Native Abstractions for hdf5 file io",
"name": "hdf5.node18",
"description": "Native Abstractions for hdf5 file io, forked from https://github.com/HDF-NI/hdf5.node.git, upgrade to node18",
"version": "0.0.4",
"main": "./index.js",
"repository": {
"type": "git",
"url": "https://github.com/HDF-NI/hdf5.node.git"
"url": "https://github.com/HanyuITK/hdf5-node18.node"
},
"engines": {
"node": ">=12.0.0"
"node": ">=18.0.0"
},
"devDependencies": {
"mocha": "8.1.1",
Expand All @@ -21,7 +21,8 @@
},
"contributors": [
"Ryan Cole <ryan@rycole.com> (https://github.com/ryancole/)",
"Roger I Martin <mathmldashx@yahoo.com> (https://github.com/rimmartin/)"
"Roger I Martin <mathmldashx@yahoo.com> (https://github.com/rimmartin/)",
"Hanyu <hanyu.sun@itk-engineering.de>"
],
"license": "MIT",
"keywords": [],
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100 changes: 50 additions & 50 deletions src/h5_file.cc
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Expand Up @@ -493,58 +493,58 @@ namespace NodeHDF5 {
}

H5Pclose(file->gcpl);
ssize_t size = 0;
//ssize_t size = 0;
std::stringstream ss;
bool allClosed=true;
if (H5Fget_obj_count(file->id, H5F_OBJ_FILE) == 1) {
if ((size = H5Fget_obj_count(file->id, H5F_OBJ_GROUP)) > 0) {
allClosed=false;
std::unique_ptr<hid_t[]> groupList(new hid_t[size]);
H5Fget_obj_ids(file->id, H5F_OBJ_GROUP, size, groupList.get());
ss << "H5 has not closed all groups: " << H5Fget_obj_count(file->id, H5F_OBJ_GROUP) << " H5F_OBJ_GROUPs OPEN" << std::endl;
for (int i = 0; i < (int)size; i++) {
std::unique_ptr<char[]> buffer(new char[1024]);
H5Iget_name(groupList[i], buffer.get(), 1024);
ss << groupList[i] << " " << buffer.get() << std::endl;
}
}

if ((size = H5Fget_obj_count(file->id, H5F_OBJ_ATTR)) > 0) {
allClosed=false;
std::unique_ptr<hid_t[]> groupList(new hid_t[size]);
H5Fget_obj_ids(file->id, H5F_OBJ_ATTR, size, groupList.get());
ss << "H5 has not closed all attributes: " << H5Fget_obj_count(file->id, H5F_OBJ_ATTR) << " H5F_OBJ_ATTRs OPEN" << std::endl;
for (int i = 0; i < (int)size; i++) {
std::unique_ptr<char[]> buffer(new char[1024]);
H5Iget_name(groupList[i], buffer.get(), 1024);
ss << groupList[i] << " " << buffer.get() << std::endl;
}
}

if ((size = H5Fget_obj_count(file->id, H5F_OBJ_DATASET)) > 0) {
allClosed=false;
std::unique_ptr<hid_t[]> groupList(new hid_t[size]);
H5Fget_obj_ids(file->id, H5F_OBJ_DATASET, size, groupList.get());
ss << "H5 has not closed all datasets" << H5Fget_obj_count(file->id, H5F_OBJ_DATASET) << " H5F_OBJ_DATASETs OPEN" << std::endl;
for (int i = 0; i < (int)size; i++) {
std::unique_ptr<char[]> buffer(new char[1024]);
H5Iget_name(groupList[i], buffer.get(), 1024);
ss << groupList[i] << " " << buffer.get() << std::endl;
}
}

if ((size = H5Fget_obj_count(file->id, H5F_OBJ_DATATYPE)) > 0) {
allClosed=false;
std::unique_ptr<hid_t[]> groupList(new hid_t[size]);
H5Fget_obj_ids(file->id, H5F_OBJ_DATATYPE, size, groupList.get());
ss << "H5 has not closed all datatypes" << H5Fget_obj_count(file->id, H5F_OBJ_DATATYPE) << " H5F_OBJ_DATATYPEs OPEN" << std::endl;
for (int i = 0; i < (int)size; i++) {
std::unique_ptr<char[]> buffer(new char[1024]);
H5Iget_name(groupList[i], buffer.get(), 1024);
ss << groupList[i] << " " << buffer.get() << std::endl;
}
}
}
//if (H5Fget_obj_count(file->id, H5F_OBJ_FILE) == 1) {
// if ((size = H5Fget_obj_count(file->id, H5F_OBJ_GROUP)) > 0) {
// allClosed=false;
// std::unique_ptr<hid_t[]> groupList(new hid_t[size]);
// H5Fget_obj_ids(file->id, H5F_OBJ_GROUP, size, groupList.get());
// ss << "H5 has not closed all groups: " << H5Fget_obj_count(file->id, H5F_OBJ_GROUP) << " H5F_OBJ_GROUPs OPEN" << std::endl;
// for (int i = 0; i < (int)size; i++) {
// std::unique_ptr<char[]> buffer(new char[1024]);
// H5Iget_name(groupList[i], buffer.get(), 1024);
// ss << groupList[i] << " " << buffer.get() << std::endl;
// }
// }

// if ((size = H5Fget_obj_count(file->id, H5F_OBJ_ATTR)) > 0) {
// allClosed=false;
// std::unique_ptr<hid_t[]> groupList(new hid_t[size]);
// H5Fget_obj_ids(file->id, H5F_OBJ_ATTR, size, groupList.get());
// ss << "H5 has not closed all attributes: " << H5Fget_obj_count(file->id, H5F_OBJ_ATTR) << " H5F_OBJ_ATTRs OPEN" << std::endl;
// for (int i = 0; i < (int)size; i++) {
// std::unique_ptr<char[]> buffer(new char[1024]);
// H5Iget_name(groupList[i], buffer.get(), 1024);
// ss << groupList[i] << " " << buffer.get() << std::endl;
// }
// }

// if ((size = H5Fget_obj_count(file->id, H5F_OBJ_DATASET)) > 0) {
// allClosed=false;
// std::unique_ptr<hid_t[]> groupList(new hid_t[size]);
// H5Fget_obj_ids(file->id, H5F_OBJ_DATASET, size, groupList.get());
// ss << "H5 has not closed all datasets" << H5Fget_obj_count(file->id, H5F_OBJ_DATASET) << " H5F_OBJ_DATASETs OPEN" << std::endl;
// for (int i = 0; i < (int)size; i++) {
// std::unique_ptr<char[]> buffer(new char[1024]);
// H5Iget_name(groupList[i], buffer.get(), 1024);
// ss << groupList[i] << " " << buffer.get() << std::endl;
// }
// }

// if ((size = H5Fget_obj_count(file->id, H5F_OBJ_DATATYPE)) > 0) {
// allClosed=false;
// std::unique_ptr<hid_t[]> groupList(new hid_t[size]);
// H5Fget_obj_ids(file->id, H5F_OBJ_DATATYPE, size, groupList.get());
// ss << "H5 has not closed all datatypes" << H5Fget_obj_count(file->id, H5F_OBJ_DATATYPE) << " H5F_OBJ_DATATYPEs OPEN" << std::endl;
// for (int i = 0; i < (int)size; i++) {
// std::unique_ptr<char[]> buffer(new char[1024]);
// H5Iget_name(groupList[i], buffer.get(), 1024);
// ss << groupList[i] << " " << buffer.get() << std::endl;
// }
// }
//}

herr_t err = H5Fclose(file->id);
if (err < 0) {
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7 changes: 4 additions & 3 deletions src/h5_group.cc
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Expand Up @@ -574,6 +574,10 @@ namespace NodeHDF5 {
H5Pclose(group->gcpl_id);
herr_t err = H5Gclose(group->id);
if (err < 0) {
std::stringstream ss;
ss << "H5 close group failed: " << group->name << std::endl;
v8::Isolate::GetCurrent()->ThrowException(
v8::Exception::Error(String::NewFromUtf8(v8::Isolate::GetCurrent(), ss.str().c_str(), v8::NewStringType::kInternalized).ToLocalChecked()));
return;
}

Expand Down Expand Up @@ -606,9 +610,6 @@ namespace NodeHDF5 {
return instance.ToLocalChecked();
} else {
// return empty
std::stringstream ss;
ss << "Failed to read group. Group "<<(name)<< " doesn't exist.";
throw Exception(ss.str());
return tmp;
}
}
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4 changes: 2 additions & 2 deletions test/test_h5lt.js
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Expand Up @@ -969,7 +969,7 @@ var start = process.hrtime();
});
});

describe("create an xmol with frequency pulled from h5 ", function() {
describe("create a xmol with frequency pulled from h5 ", function() {
this.timeout(35000);
let file;
before(function(done) {
Expand Down Expand Up @@ -1037,7 +1037,7 @@ var start = process.hrtime();
xmolDocument+=elements[index]+' '+lastTrajectory[3*index]+' '+lastTrajectory[3*index+1]+' '+lastTrajectory[3*index+2]+' '+frequency[3*index]+' '+frequency[3*index+1]+' '+frequency[3*index+2]+'\n';
}
}
xmolDocument.length.should.equal(1435803);
xmolDocument.length.should.equal(1435989);
fs.writeFileSync('sodium-icosanoate.xmol', xmolDocument, { flag:'w'});
fs.writeFileSync('sodium-icosanoate.xml', xmlDocument, { flag:'w'});
groupGeometries.close();
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4 changes: 2 additions & 2 deletions test/test_hdf5.js
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Expand Up @@ -85,7 +85,7 @@ describe("testing c interface ", function() {
groupPmc.close();
}
catch(error) {
error.message.should.equal("Failed to read group. Group pmc doesn\'t exist.");
error.message.should.equal("Cannot read properties of undefined (reading 'id')");
}
var group;
try{
Expand All @@ -97,7 +97,7 @@ describe("testing c interface ", function() {
catch(error) {
group.close();
console.log(error.message);
error.message.should.equal("Failed to read group. Group polywog doesn\'t exist.");
error.message.should.equal("Cannot read properties of undefined (reading 'id')");
}
done();
});
Expand Down