Merge pull request #70 from cBioPortal/jamesqo-patch-1

Fix false negatives for validator for GDC data
cBioPortal · Dec 13, 2024 · 64176ae · 64176ae
2 parents fb81dc6 + 293e183
commit 64176ae
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diff --git a/scripts/importer/allowed_data_types.txt b/scripts/importer/allowed_data_types.txt
@@ -36,6 +36,7 @@ MRNA_EXPRESSION	CONTINUOUS	mrna_seq_tpm
 MRNA_EXPRESSION	Z-SCORE	mrna_seq_tpm_Zscores
 MRNA_EXPRESSION	Z-SCORE	mrna_seq_cpm_Zscores
 MRNA_EXPRESSION	Z-SCORE	rna_seq_mrna_capture_Zscores
+MRNA_EXPRESSION	CONTINUOUS	mrna_seq_fpkm
 MRNA_EXPRESSION	CONTINUOUS	mrna_seq_fpkm_capture
 MRNA_EXPRESSION	Z-SCORE	mrna_seq_fpkm_capture_Zscores
 MRNA_EXPRESSION	CONTINUOUS	mrna_seq_fpkm_polya
@@ -53,6 +54,7 @@ MRNA_EXPRESSION	Z-SCORE	mrna_seq_fpkm_capture_all_sample_Zscores
 MRNA_EXPRESSION	Z-SCORE	mrna_seq_fpkm_polya_all_sample_Zscores
 MRNA_EXPRESSION	Z-SCORE	mrna_seq_fpkm_Zscores
 MRNA_EXPRESSION	Z-SCORE	mrna_seq_fpkm_all_sample_Zscores
+MRNA_EXPRESSION	Z-SCORE	mrna_seq_read_counts_Zscores
 METHYLATION	CONTINUOUS	methylation_hm27
 METHYLATION	CONTINUOUS	methylation_hm450
 METHYLATION	CONTINUOUS	methylation_epic

diff --git a/tests/test_data/study_wr_clin/result_report.html b/tests/test_data/study_wr_clin/result_report.html
@@ -192,7 +192,7 @@ <h4 class="panel-title">meta_expression_median.txt</h4>
                 <td><span class="glyphicon glyphicon-remove" aria-hidden="true"></span><span class="sr-only">Error</span></td>
                 <td>&ndash;</td>
                 <td>&ndash;</td>
-                <td>Invalid stable id for genetic_alteration_type &#39;MRNA_EXPRESSION&#39;, data_type &#39;Z-SCORE&#39;; expected one of [mrna_U133_Zscores, rna_seq_mrna_median_Zscores, mrna_median_Zscores, rna_seq_v2_mrna_median_Zscores, rna_seq_v2_mrna_median_normals_Zscores, mirna_median_Zscores, mrna_merged_median_Zscores, mrna_zbynorm, mrna_seq_tpm_Zscores, mrna_seq_cpm_Zscores, rna_seq_mrna_capture_Zscores, mrna_seq_fpkm_capture_Zscores, mrna_seq_fpkm_polya_Zscores, mrna_U133_all_sample_Zscores, mrna_all_sample_Zscores, rna_seq_mrna_median_all_sample_Zscores, mrna_median_all_sample_Zscores, rna_seq_v2_mrna_median_all_sample_Zscores, rna_seq_v2_mrna_median_all_sample_ref_normal_Zscores, mrna_seq_cpm_all_sample_Zscores, mrna_seq_tpm_all_sample_Zscores, rna_seq_mrna_capture_all_sample_Zscores, mrna_seq_fpkm_capture_all_sample_Zscores, mrna_seq_fpkm_polya_all_sample_Zscores, mrna_seq_fpkm_Zscores, mrna_seq_fpkm_all_sample_Zscores]</td>
+                <td>Invalid stable id for genetic_alteration_type &#39;MRNA_EXPRESSION&#39;, data_type &#39;Z-SCORE&#39;; expected one of [mrna_U133_Zscores, rna_seq_mrna_median_Zscores, mrna_median_Zscores, rna_seq_v2_mrna_median_Zscores, rna_seq_v2_mrna_median_normals_Zscores, mirna_median_Zscores, mrna_merged_median_Zscores, mrna_zbynorm, mrna_seq_tpm_Zscores, mrna_seq_cpm_Zscores, rna_seq_mrna_capture_Zscores, mrna_seq_fpkm_capture_Zscores, mrna_seq_fpkm_polya_Zscores, mrna_U133_all_sample_Zscores, mrna_all_sample_Zscores, rna_seq_mrna_median_all_sample_Zscores, mrna_median_all_sample_Zscores, rna_seq_v2_mrna_median_all_sample_Zscores, rna_seq_v2_mrna_median_all_sample_ref_normal_Zscores, mrna_seq_cpm_all_sample_Zscores, mrna_seq_tpm_all_sample_Zscores, rna_seq_mrna_capture_all_sample_Zscores, mrna_seq_fpkm_capture_all_sample_Zscores, mrna_seq_fpkm_polya_all_sample_Zscores, mrna_seq_fpkm_Zscores, mrna_seq_fpkm_all_sample_Zscores, mrna_seq_read_counts_Zscores]</td>
                 <td>mrna</td>
                 <td></td>
               </tr>