Add more data types to incremental data upload folder

tests/system_tests_import_data.py

@@ -107,6 +107,16 @@ def test_incremental_load(self, run_java, locate_jar):
             '--meta', f'{data_directory}/meta_clinical_samples.txt', '--loadMode', 'bulkload', '--data', f'{data_directory}/data_clinical_samples.txt', '--noprogress')
         mutation_call = call(*common_part, 'org.mskcc.cbio.portal.scripts.ImportProfileData', '--overwrite-existing',
             '--meta', f'{data_directory}/meta_mutations_extended.txt', '--loadMode', 'bulkload', '--update-info', 'False', '--data', f'{data_directory}/data_mutations_extended.maf', '--noprogress')
+        cna_discrete_call = call(*common_part, 'org.mskcc.cbio.portal.scripts.ImportProfileData', '--overwrite-existing',
+            '--meta', f'{data_directory}/meta_cna_discrete.txt', '--loadMode', 'bulkload', '--update-info', 'False', '--data', f'{data_directory}/data_cna_discrete.txt', '--noprogress')
+        cna_log2_call = call(*common_part, 'org.mskcc.cbio.portal.scripts.ImportProfileData', '--overwrite-existing',
+            '--meta', f'{data_directory}/meta_cna_log2.txt', '--loadMode', 'bulkload', '--update-info', 'False', '--data', f'{data_directory}/data_cna_log2.txt', '--noprogress')
+        expression_median_call = call(*common_part, 'org.mskcc.cbio.portal.scripts.ImportProfileData', '--overwrite-existing',
+            '--meta', f'{data_directory}/meta_expression_median.txt', '--loadMode', 'bulkload', '--update-info', 'False', '--data', f'{data_directory}/data_expression_median.txt', '--noprogress')
+        methylation_hm27_call = call(*common_part, 'org.mskcc.cbio.portal.scripts.ImportProfileData', '--overwrite-existing',
+            '--meta', f'{data_directory}/meta_methylation_hm27.txt', '--loadMode', 'bulkload', '--update-info', 'False', '--data', f'{data_directory}/data_methylation_hm27.txt', '--noprogress')
+        treatment_ic50_call = call(*common_part, 'org.mskcc.cbio.portal.scripts.ImportProfileData', '--overwrite-existing',
+            '--meta', f'{data_directory}/meta_treatment_ic50.txt', '--loadMode', 'bulkload', '--update-info', 'False', '--data', f'{data_directory}/data_treatment_ic50.txt', '--noprogress')
         case_list_call = call(*common_part, 'org.mskcc.cbio.portal.scripts.UpdateCaseListsSampleIds',
             '--meta', f'{data_directory}/meta_clinical_samples.txt', '--case-lists', f'{data_directory}/case_lists')
 
@@ -115,6 +125,11 @@ def test_incremental_load(self, run_java, locate_jar):
             clinical_patient_call,
             clinical_sample_call,
             mutation_call,
+            cna_discrete_call,
+            cna_log2_call,
+            expression_median_call,
+            methylation_hm27_call,
+            treatment_ic50_call,
             case_list_call,
         ])
 

tests/test_data/study_es_0_inc/data_cna_discrete.txt

@@ -0,0 +1,10 @@
+Hugo_Symbol	Entrez_Gene_Id	TCGA-A1-A0SB-01	TCGA-A1-A0SB-03	TCGA-BH-NEW
+ACAP3	116983	0	0	-1
+	375790	-1	-1	0
+ATAD3A	55210	0	0	-2
+ATAD3B	83858	-2	-1	0
+ATAD3C	219293	0	0	0
+#AURKAIP1	54998
+ERCC5	2073	0	-1	-2
+ACP3	55	0	0	0
+TP53		-1	0	-2

tests/test_data/study_es_0_inc/data_cna_log2.txt

@@ -0,0 +1,10 @@
+Hugo_Symbol	Entrez_Gene_Id	TCGA-A1-A0SB-01	TCGA-A1-A0SB-03	TCGA-BH-NEW
+ACAP3	116983	0.751	0.533	0.114
+	375790	0.062	0.071	0.948
+ATAD3A	55210	0.487	0.695	0.364
+ATAD3B	83858	0.150	0.492	0.300
+ATAD3C	219293	0.995	0.170	0.654
+#AURKAIP1	54998
+ERCC5	2073	0.816	0.514	0.165
+ACP3	55	0.252	0.713	0.513
+TP53		0.360	0.538	0.891

tests/test_data/study_es_0_inc/data_expression_median.txt

@@ -0,0 +1,10 @@
+Hugo_Symbol	Entrez_Gene_Id	TCGA-A1-A0SB-01	TCGA-A1-A0SB-03	TCGA-BH-NEW
+ACAP3	116983	0.096	0.826	0.032
+	375790	0.309	0.399	0.680
+ATAD3A	55210	0.569	0.189	0.266
+ATAD3B	83858	0.829	0.473	0.611
+ATAD3C	219293	0.307	0.445	0.045
+#AURKAIP1	54998
+ERCC5	2073	0.171	0.766	0.590
+ACP3	55	0.422	0.870	0.745
+TP53		0.179	0.694	0.808

tests/test_data/study_es_0_inc/data_methylation_hm27.txt

@@ -0,0 +1,10 @@
+Hugo_Symbol	Entrez_Gene_Id	TCGA-A1-A0SB-01	TCGA-A1-A0SB-03	TCGA-BH-NEW
+ACAP3	116983	0.022	0.681	0.790
+	375790	0.435	0.340	0.321
+ATAD3A	55210	0.229	0.946	0.439
+ATAD3B	83858	0.885	0.707	0.664
+ATAD3C	219293	0.660	0.315	0.694
+#AURKAIP1	54998
+ERCC5	2073	0.436	0.749	0.345
+ACP3	55	0.622	0.396	0.029
+TP53		0.563	0.686	0.607

tests/test_data/study_es_0_inc/data_treatment_ic50.txt

@@ -0,0 +1,11 @@
+ENTITY_STABLE_ID	NAME	DESCRIPTION	URL	TCGA-A1-A0SB-01	TCGA-A1-A0SB-03	TCGA-BH-NEW
+17-AAG	Name of 17-AAG	Desc of 17-AAG	Url of 17-AAG	0.315	0.329701692	0.053038094
+AEW541	Name of AEW541	Desc of AEW541	Url of AEW541	>8	2.353	2.68212986
+AZD0530	Name of AZD0530	Desc of AZD0530	Url of AZD0530	0.234	>8	4.597949505
+AZD6244	Name of AZD6244	Desc of AZD6244	Url of AZD6244	>8	>8	>8
+Erlotinib	Name of Erlotinib	Desc of Erlotinib	Url of Erlotinib	>8	>8	>8
+Irinotecan	Name of Irinotecan	Desc of Irinotecan	Url of Irinotecan	NA	0.083	NA
+L-685458	Name of L-685458	Desc of L-685458	Url of L-685458	>8	>8	3.267752409
+#Lapatinib	Name of Lapatinib	Desc of Lapatinib	Url of Lapatinib
+LBW242	Name of LBW242	Desc of LBW242	Url of LBW242	NA	>8	>8
+Nilotinib	Name of Nilotinib	Desc of Nilotinib	Url of Nilotinib	>8	>8	NA

tests/test_data/study_es_0_inc/meta_cna_discrete.txt

@@ -0,0 +1,10 @@
+cancer_study_identifier: study_es_0
+genetic_alteration_type: COPY_NUMBER_ALTERATION
+datatype: DISCRETE
+stable_id: gistic
+show_profile_in_analysis_tab: true
+profile_description: Putative copy-number from GISTIC 2.0. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification.
+profile_name: Putative copy-number alterations from GISTIC
+data_filename: data_cna_discrete.txt
+pd_annotations_filename: data_cna_pd_annotations.txt
+namespaces: CustomNamespace

tests/test_data/study_es_0_inc/meta_cna_log2.txt

@@ -0,0 +1,8 @@
+cancer_study_identifier: study_es_0
+genetic_alteration_type: COPY_NUMBER_ALTERATION
+datatype: LOG2-VALUE
+stable_id: log2CNA
+show_profile_in_analysis_tab: false
+profile_description: Log2 copy-number values for each gene (from Affymetrix SNP6).
+profile_name: Log2 copy-number values
+data_filename: data_cna_log2.txt

tests/test_data/study_es_0_inc/meta_expression_median.txt

@@ -0,0 +1,8 @@
+cancer_study_identifier: study_es_0
+genetic_alteration_type: MRNA_EXPRESSION
+datatype: CONTINUOUS
+stable_id: mrna
+profile_description: Expression levels (Agilent microarray).
+show_profile_in_analysis_tab: false
+profile_name: mRNA expression (microarray)
+data_filename: data_expression_median.txt

tests/test_data/study_es_0_inc/meta_methylation_hm27.txt

@@ -0,0 +1,8 @@
+cancer_study_identifier: study_es_0
+genetic_alteration_type: METHYLATION
+datatype: CONTINUOUS
+stable_id: methylation_hm27
+profile_description: Methylation beta-values (HM27 platform). For genes with multiple methylation probes, the probe least correlated with expression is selected.
+show_profile_in_analysis_tab: false
+profile_name: Methylation (HM27)
+data_filename: data_methylation_hm27.txt

tests/test_data/study_es_0_inc/meta_treatment_ic50.txt

@@ -0,0 +1,12 @@
+cancer_study_identifier: study_es_0
+genetic_alteration_type: GENERIC_ASSAY
+generic_assay_type: TREATMENT_RESPONSE
+datatype: LIMIT-VALUE
+stable_id: treatment_ic50
+profile_name: IC50 values of compounds on cellular phenotype readout
+profile_description: IC50 (compound concentration resulting in half maximal inhibition) of compounds on cellular phenotype readout of cultured mutant cell lines.
+data_filename: data_treatment_ic50.txt
+show_profile_in_analysis_tab: true
+pivot_threshold_value: 0.1
+value_sort_order: ASC
+generic_entity_meta_properties: NAME,DESCRIPTION,URL