@sjcrh/proteinpaint-rust 2.116.0 → 2.117.0

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Files changed (4) hide show
  1. package/Cargo.toml +2 -1
  2. package/package.json +2 -2
  3. package/src/readHDF5.rs +809 -240
  4. package/src/topGeneByExpressionVariance.rs +126 -126
package/src/topGeneByExpressionVariance.rs CHANGED
@@ -64,15 +64,15 @@ fn input_data_hdf5(
64
64
  let file = match File::open(filename) {
65
65
  Ok(f) => f,
66
66
  Err(err) => {
67
- eprintln!("Failed to open HDF5 file: {}", err);
68
- println!(
69
- "{}",
70
- serde_json::json!({
71
- "status": "error",
72
- "message": format!("Failed to open HDF5 file: {}", err),
73
- "file_path": filename
74
- })
75
- );
67
+ // eprintln!("Failed to open HDF5 file: {}", err);
68
+ // println!(
69
+ // "{}",
70
+ // serde_json::json!({
71
+ // "status": "error",
72
+ // "message": format!("Failed to open HDF5 file: {}", err),
73
+ // "file_path": filename
74
+ // })
75
+ // );
76
76
  return Err(hdf5::Error::Internal(format!(
77
77
  "Failed to open HDF5 file: {}",
78
78
  err
@@ -84,15 +84,15 @@ fn input_data_hdf5(
84
84
  let genes_dataset = match file.dataset("gene_symbols") {
85
85
  Ok(ds) => ds,
86
86
  Err(err) => {
87
- eprintln!("Failed to open gene_symbols dataset: {}", err);
88
- println!(
89
- "{}",
90
- serde_json::json!({
91
- "status": "error",
92
- "message": format!("Failed to open gene_symbols dataset: {}", err),
93
- "file_path": filename
94
- })
95
- );
87
+ // eprintln!("Failed to open gene_symbols dataset: {}", err);
88
+ // println!(
89
+ // "{}",
90
+ // serde_json::json!({
91
+ // "status": "error",
92
+ // "message": format!("Failed to open gene_symbols dataset: {}", err),
93
+ // "file_path": filename
94
+ // })
95
+ // );
96
96
  return Err(hdf5::Error::Internal(format!(
97
97
  "Failed to open gene_symbols dataset: {}",
98
98
  err
@@ -104,15 +104,15 @@ fn input_data_hdf5(
104
104
  let genes_varlen = match genes_dataset.read_1d::<VarLenAscii>() {
105
105
  Ok(g) => g,
106
106
  Err(err) => {
107
- eprintln!("Failed to read gene symbols: {}", err);
108
- println!(
109
- "{}",
110
- serde_json::json!({
111
- "status": "error",
112
- "message": format!("Failed to read gene symbols: {}", err),
113
- "file_path": filename
114
- })
115
- );
107
+ // eprintln!("Failed to read gene symbols: {}", err);
108
+ // println!(
109
+ // "{}",
110
+ // serde_json::json!({
111
+ // "status": "error",
112
+ // "message": format!("Failed to read gene symbols: {}", err),
113
+ // "file_path": filename
114
+ // })
115
+ // );
116
116
  return Err(hdf5::Error::Internal(format!(
117
117
  "Failed to read gene symbols: {}",
118
118
  err
@@ -129,7 +129,7 @@ fn input_data_hdf5(
129
129
  let samples_dataset = match file.dataset("samples") {
130
130
  Ok(ds) => ds,
131
131
  Err(err) => {
132
- eprintln!("Failed to open samples dataset: {}", err);
132
+ // eprintln!("Failed to open samples dataset: {}", err);
133
133
  println!(
134
134
  "{}",
135
135
  serde_json::json!({
@@ -149,7 +149,7 @@ fn input_data_hdf5(
149
149
  let samples_varlen = match samples_dataset.read_1d::<VarLenAscii>() {
150
150
  Ok(s) => s,
151
151
  Err(err) => {
152
- eprintln!("Failed to read sample names: {}", err);
152
+ // eprintln!("Failed to read sample names: {}", err);
153
153
  println!(
154
154
  "{}",
155
155
  serde_json::json!({
@@ -175,16 +175,16 @@ fn input_data_hdf5(
175
175
  if let Some(index) = all_samples.iter().position(|s| s == sample) {
176
176
  column_indices.push(index);
177
177
  } else {
178
- eprintln!("Sample {} not found in the dataset", sample);
179
- println!(
180
- "{}",
181
- serde_json::json!({
182
- "status": "error",
183
- "message": format!("Sample '{}' not found in the dataset", sample),
184
- "file_path": filename,
185
- "available_samples": all_samples
186
- })
187
- );
178
+ // eprintln!("Sample {} not found in the dataset", sample);
179
+ // println!(
180
+ // "{}",
181
+ // serde_json::json!({
182
+ // "status": "error",
183
+ // "message": format!("Sample '{}' not found in the dataset", sample),
184
+ // "file_path": filename,
185
+ // "available_samples": all_samples
186
+ // })
187
+ // );
188
188
  return Err(hdf5::Error::Internal(format!(
189
189
  "Sample '{}' not found in the dataset",
190
190
  sample
@@ -196,15 +196,15 @@ fn input_data_hdf5(
196
196
  let counts_dataset = match file.dataset("counts") {
197
197
  Ok(ds) => ds,
198
198
  Err(err) => {
199
- eprintln!("Failed to open counts dataset: {}", err);
200
- println!(
201
- "{}",
202
- serde_json::json!({
203
- "status": "error",
204
- "message": format!("Failed to open counts dataset: {}", err),
205
- "file_path": filename
206
- })
207
- );
199
+ // eprintln!("Failed to open counts dataset: {}", err);
200
+ // println!(
201
+ // "{}",
202
+ // serde_json::json!({
203
+ // "status": "error",
204
+ // "message": format!("Failed to open counts dataset: {}", err),
205
+ // "file_path": filename
206
+ // })
207
+ // );
208
208
  return Err(hdf5::Error::Internal(format!(
209
209
  "Failed to open counts dataset: {}",
210
210
  err
@@ -215,16 +215,16 @@ fn input_data_hdf5(
215
215
  // Get dataset dimensions for validation
216
216
  let dataset_shape = counts_dataset.shape();
217
217
  if dataset_shape.len() != 2 {
218
- eprintln!("Counts dataset does not have the expected 2D shape");
219
- println!(
220
- "{}",
221
- serde_json::json!({
222
- "status": "error",
223
- "message": "Expected a 2D dataset for counts",
224
- "file_path": filename,
225
- "actual_shape": dataset_shape
226
- })
227
- );
218
+ // eprintln!("Counts dataset does not have the expected 2D shape");
219
+ // println!(
220
+ // "{}",
221
+ // serde_json::json!({
222
+ // "status": "error",
223
+ // "message": "Expected a 2D dataset for counts",
224
+ // "file_path": filename,
225
+ // "actual_shape": dataset_shape
226
+ // })
227
+ // );
228
228
  return Err(hdf5::Error::Internal(
229
229
  "Expected a 2D dataset for counts".to_string(),
230
230
  ));
@@ -232,19 +232,19 @@ fn input_data_hdf5(
232
232
 
233
233
  // Check dimensions match expected values
234
234
  if dataset_shape[0] != num_genes {
235
- eprintln!(
236
- "Counts dataset first dimension ({}) doesn't match number of genes ({})",
237
- dataset_shape[0], num_genes
238
- );
239
- println!(
240
- "{}",
241
- serde_json::json!({
242
- "status": "error",
243
- "message": format!("Counts dataset first dimension ({}) doesn't match number of genes ({})",
244
- dataset_shape[0], num_genes),
245
- "file_path": filename
246
- })
247
- );
235
+ // eprintln!(
236
+ // "Counts dataset first dimension ({}) doesn't match number of genes ({})",
237
+ // dataset_shape[0], num_genes
238
+ // );
239
+ // println!(
240
+ // "{}",
241
+ // serde_json::json!({
242
+ // "status": "error",
243
+ // "message": format!("Counts dataset first dimension ({}) doesn't match number of genes ({})",
244
+ // dataset_shape[0], num_genes),
245
+ // "file_path": filename
246
+ // })
247
+ // );
248
248
  return Err(hdf5::Error::Internal(format!(
249
249
  "Counts dataset first dimension ({}) doesn't match number of genes ({})",
250
250
  dataset_shape[0], num_genes
@@ -252,20 +252,20 @@ fn input_data_hdf5(
252
252
  }
253
253
 
254
254
  if dataset_shape[1] != all_samples.len() {
255
- eprintln!(
256
- "Counts dataset second dimension ({}) doesn't match number of samples ({})",
257
- dataset_shape[1],
258
- all_samples.len()
259
- );
260
- println!(
261
- "{}",
262
- serde_json::json!({
263
- "status": "error",
264
- "message": format!("Counts dataset second dimension ({}) doesn't match number of samples ({})",
265
- dataset_shape[1], all_samples.len()),
266
- "file_path": filename
267
- })
268
- );
255
+ // eprintln!(
256
+ // "Counts dataset second dimension ({}) doesn't match number of samples ({})",
257
+ // dataset_shape[1],
258
+ // all_samples.len()
259
+ // );
260
+ // println!(
261
+ // "{}",
262
+ // serde_json::json!({
263
+ // "status": "error",
264
+ // "message": format!("Counts dataset second dimension ({}) doesn't match number of samples ({})",
265
+ // dataset_shape[1], all_samples.len()),
266
+ // "file_path": filename
267
+ // })
268
+ // );
269
269
  return Err(hdf5::Error::Internal(format!(
270
270
  "Counts dataset second dimension ({}) doesn't match number of samples ({})",
271
271
  dataset_shape[1],
@@ -277,15 +277,15 @@ fn input_data_hdf5(
277
277
  let all_counts = match counts_dataset.read::<f64, Dim<[usize; 2]>>() {
278
278
  Ok(data) => data,
279
279
  Err(err) => {
280
- eprintln!("Failed to read expression data: {}", err);
281
- println!(
282
- "{}",
283
- serde_json::json!({
284
- "status": "error",
285
- "message": format!("Failed to read expression data: {}", err),
286
- "file_path": filename
287
- })
288
- );
280
+ // eprintln!("Failed to read expression data: {}", err);
281
+ // println!(
282
+ // "{}",
283
+ // serde_json::json!({
284
+ // "status": "error",
285
+ // "message": format!("Failed to read expression data: {}", err),
286
+ // "file_path": filename
287
+ // })
288
+ // );
289
289
  return Err(hdf5::Error::Internal(format!(
290
290
  "Failed to read expression data: {}",
291
291
  err
@@ -536,28 +536,28 @@ fn cpm(
536
536
  }
537
537
 
538
538
  fn main() {
539
- // eprintln!("Starting gene variance calculation...");
539
+ // println!("Starting gene variance calculation...");
540
540
  let mut input = String::new();
541
541
  match io::stdin().read_line(&mut input) {
542
542
  // Accepting the piped input from nodejs (or command line from testing)
543
543
  Ok(_bytes_read) => {
544
- // eprintln!("Read {} bytes from stdin", _bytes_read);
545
- //println!("{} bytes read", bytes_read);
546
- //println!("{}", input);
544
+ // eprintln!("Read {} bytes from stdin", bytes_read);
545
+ // println!("{} bytes read", bytes_read);
546
+ // println!("{}", input);
547
547
  let input_json = json::parse(&input);
548
548
  match input_json {
549
549
  Ok(json_string) => {
550
- // eprintln!("Successfully parsed JSON input");
550
+ // println!("Successfully parsed JSON input");
551
551
  // let now = Instant::now();
552
552
  let samples_string_result = &json_string["samples"].to_owned();
553
553
  let samples_string;
554
554
  match samples_string_result.as_str() {
555
555
  Some(x) => {
556
556
  samples_string = x.to_string();
557
- // eprintln!("Samples: {}", samples_string);
557
+ // println!("Samples: {}", samples_string);
558
558
  }
559
559
  None => {
560
- eprintln!("ERROR: Samples not provided in JSON");
560
+ // eprintln!("ERROR: Samples not provided in JSON");
561
561
  println!(
562
562
  "{}",
563
563
  serde_json::json!({
@@ -583,14 +583,14 @@ fn main() {
583
583
  // );
584
584
  }
585
585
  None => {
586
- eprintln!("ERROR: File name missing in JSON");
587
- println!(
588
- "{}",
589
- serde_json::json!({
590
- "status": "error",
591
- "message": "File name is missing"
592
- })
593
- );
586
+ // eprintln!("ERROR: File name missing in JSON");
587
+ // println!(
588
+ // "{}",
589
+ // serde_json::json!({
590
+ // "status": "error",
591
+ // "message": "File name is missing"
592
+ // })
593
+ // );
594
594
  return;
595
595
  }
596
596
  }
@@ -613,14 +613,14 @@ fn main() {
613
613
  // eprintln!("Rank type: {}", rank_type);
614
614
  if rank_type != "var" && rank_type != "iqr" {
615
615
  // Check if any unknown method has been provided
616
- eprintln!("ERROR: Unknown rank method: {}", rank_type);
617
- println!(
618
- "{}",
619
- serde_json::json!({
620
- "status": "error",
621
- "message": format!("Unknown rank method: {}. Must be 'var' or 'iqr'", rank_type)
622
- })
623
- );
616
+ // eprintln!("ERROR: Unknown rank method: {}", rank_type);
617
+ // println!(
618
+ // "{}",
619
+ // serde_json::json!({
620
+ // "status": "error",
621
+ // "message": format!("Unknown rank method: {}. Must be 'var' or 'iqr'", rank_type)
622
+ // })
623
+ // );
624
624
  return;
625
625
  }
626
626
  let filter_extreme_values_result = &json_string["filter_extreme_values"];
@@ -629,7 +629,7 @@ fn main() {
629
629
  match filter_extreme_values_result.as_bool() {
630
630
  Some(x) => {
631
631
  filter_extreme_values = x;
632
- eprintln!("Filter extreme values: {}", filter_extreme_values);
632
+ // eprintln!("Filter extreme values: {}", filter_extreme_values);
633
633
  }
634
634
  None => {
635
635
  filter_extreme_values = true; // If filter_extreme_values field is missing, set it to true by default
@@ -648,7 +648,7 @@ fn main() {
648
648
  // eprintln!("Number of genes requested: {}", num_genes);
649
649
  }
650
650
  None => {
651
- eprintln!("ERROR: Number of genes to be given is missing");
651
+ // eprintln!("ERROR: Number of genes to be given is missing");
652
652
  println!(
653
653
  "{}",
654
654
  serde_json::json!({
@@ -668,7 +668,7 @@ fn main() {
668
668
  // eprintln!("Min count: {}", x);
669
669
  }
670
670
  None => {
671
- eprintln!("Min count not specified, will use default");
671
+ // eprintln!("Min count not specified, will use default");
672
672
  }
673
673
  }
674
674
 
@@ -680,7 +680,7 @@ fn main() {
680
680
  // eprintln!("Min total count: {}", x);
681
681
  }
682
682
  None => {
683
- eprintln!("Min total count not specified, will use default");
683
+ // eprintln!("Min total count not specified, will use default");
684
684
  }
685
685
  }
686
686
 
@@ -780,11 +780,11 @@ fn main() {
780
780
 
781
781
  // Check if we have enough genes for the requested output
782
782
  if gene_infos.len() < num_genes {
783
- eprintln!(
784
- "WARNING: Only {} genes found, but {} were requested",
785
- gene_infos.len(),
786
- num_genes
787
- );
783
+ // eprintln!(
784
+ // "WARNING: Only {} genes found, but {} were requested",
785
+ // gene_infos.len(),
786
+ // num_genes
787
+ // );
788
788
  }
789
789
 
790
790
  let actual_num_genes = std::cmp::min(num_genes, gene_infos.len());