@sjcrh/proteinpaint-server 2.86.1 → 2.87.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (49) hide show
  1. package/dataset/termdb.test.js +0 -11
  2. package/package.json +6 -10
  3. package/routes/_template_.js +1 -1
  4. package/routes/brainImaging.js +1 -1
  5. package/routes/burden.js +1 -1
  6. package/routes/dataset.js +1 -1
  7. package/routes/dsdata.js +1 -1
  8. package/routes/dzimages.js +1 -1
  9. package/routes/gdc.maf.js +2 -2
  10. package/routes/gdc.mafBuild.js +2 -2
  11. package/routes/gdc.topMutatedGenes.js +1 -1
  12. package/routes/genelookup.js +1 -1
  13. package/routes/genesetEnrichment.js +5 -3
  14. package/routes/genesetOverrepresentation.js +1 -1
  15. package/routes/healthcheck.js +1 -1
  16. package/routes/hicdata.js +1 -1
  17. package/routes/hicgenome.js +1 -1
  18. package/routes/hicstat.js +1 -1
  19. package/routes/isoformlst.js +1 -1
  20. package/routes/ntseq.js +1 -1
  21. package/routes/pdomain.js +1 -1
  22. package/routes/sampledzimages.js +1 -1
  23. package/routes/samplewsimages.js +1 -1
  24. package/routes/snp.js +1 -1
  25. package/routes/termdb.DE.js +1 -1
  26. package/routes/termdb.boxplot.js +34 -25
  27. package/routes/termdb.categories.js +1 -1
  28. package/routes/termdb.cluster.js +1 -1
  29. package/routes/termdb.cohort.summary.js +2 -2
  30. package/routes/termdb.cohorts.js +3 -1
  31. package/routes/termdb.config.js +5 -5
  32. package/routes/termdb.descrstats.js +1 -1
  33. package/routes/termdb.numericcategories.js +1 -1
  34. package/routes/termdb.percentile.js +1 -1
  35. package/routes/termdb.rootterm.js +1 -1
  36. package/routes/termdb.sampleImages.js +1 -1
  37. package/routes/termdb.singleSampleMutation.js +1 -1
  38. package/routes/termdb.singlecellDEgenes.js +1 -1
  39. package/routes/termdb.singlecellData.js +1 -1
  40. package/routes/termdb.singlecellSamples.js +5 -5
  41. package/routes/termdb.termchildren.js +1 -1
  42. package/routes/termdb.termsbyids.js +1 -1
  43. package/routes/termdb.topTermsByType.js +1 -1
  44. package/routes/termdb.topVariablyExpressedGenes.js +1 -1
  45. package/routes/termdb.violin.js +1 -1
  46. package/routes/tileserver.js +1 -1
  47. package/routes/wsimages.js +1 -1
  48. package/src/app.js +364 -298
  49. package/utils/gsea.py +13 -3
package/utils/gsea.py CHANGED
@@ -10,7 +10,7 @@ import numpy as np
10
10
  import pandas as pd
11
11
 
12
12
  def extract_symbols(x):
13
- return x['symbol']
13
+ return x['symbol']
14
14
 
15
15
  def extract_plot_data(signature, geneset, library, result, center=True):
16
16
  signature = signature.copy()
@@ -48,6 +48,7 @@ try:
48
48
  genes=json_object['genes']
49
49
  fold_change=json_object['fold_change']
50
50
  table_name=json_object['geneset_group']
51
+ filter_non_coding_genes=json_object['filter_non_coding_genes']
51
52
  df = {'Genes': genes, 'fold_change': fold_change}
52
53
  signature=pd.DataFrame(df)
53
54
  db=json_object['db']
@@ -59,10 +60,19 @@ try:
59
60
 
60
61
  # SQL query to select all data from the table
61
62
  query = f"select id from terms where parent_id='" + table_name + "'"
62
-
63
63
  # Execute the SQL query
64
64
  cursor.execute(query)
65
-
65
+ if filter_non_coding_genes == True:
66
+ # SQL query to code all the protein coding genes
67
+ coding_genes_query = f"select * from codingGenes"
68
+ genedb = json_object['genedb']
69
+ gene_conn = sqlite3.connect(genedb)
70
+ gene_cursor = gene_conn.cursor()
71
+ gene_cursor.execute(coding_genes_query)
72
+ coding_genes_list=gene_cursor.fetchall()
73
+ coding_genes_list=list(map(lambda x: x[0],coding_genes_list))
74
+ signature=signature[signature['Genes'].isin(coding_genes_list)]
75
+
66
76
  # Fetch all rows from the executed SQL query
67
77
  rows = cursor.fetchall()
68
78