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Cover all clickhouse tables with mysql import
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-88
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2 files changed

+208
-88
lines changed

‎dev/clickhouse/clickhouse_provisioning/c_import_mysql_data.sql

Lines changed: 107 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -6,3 +6,110 @@ select * from mysql(
66
'cbio',
77
'P@ssword1'
88
);
9+
10+
insert into cbioportal.sample_list
11+
select * from mysql(
12+
'127.0.0.1:3306',
13+
'cbioportal',
14+
'view_sample_list',
15+
'cbio',
16+
'P@ssword1'
17+
);
18+
19+
insert into cbioportal.structural_variant
20+
select * from mysql(
21+
'127.0.0.1:3306',
22+
'cbioportal',
23+
'view_structural_variant',
24+
'cbio',
25+
'P@ssword1'
26+
);
27+
28+
insert into cbioportal.sample
29+
select * from mysql(
30+
'127.0.0.1:3306',
31+
'cbioportal',
32+
'view_sample',
33+
'cbio',
34+
'P@ssword1'
35+
);
36+
37+
38+
insert into cbioportal.sample_clinical_attribute_numeric
39+
select * from mysql(
40+
'127.0.0.1:3306',
41+
'cbioportal',
42+
'view_sample_clinical_attribute_numeric',
43+
'cbio',
44+
'P@ssword1'
45+
);
46+
47+
48+
insert into cbioportal.sample_clinical_attribute_categorical
49+
select * from mysql(
50+
'127.0.0.1:3306',
51+
'cbioportal',
52+
'view_sample_clinical_attribute_categorical',
53+
'cbio',
54+
'P@ssword1'
55+
);
56+
57+
58+
insert into cbioportal.patient_clinical_attribute_numeric
59+
select * from mysql(
60+
'127.0.0.1:3306',
61+
'cbioportal',
62+
'view_patient_clinical_attribute_numeric',
63+
'cbio',
64+
'P@ssword1'
65+
);
66+
67+
68+
69+
insert into cbioportal.patient_clinical_attribute_categorical
70+
select * from mysql(
71+
'127.0.0.1:3306',
72+
'cbioportal',
73+
'view_patient_clinical_attribute_categorical',
74+
'cbio',
75+
'P@ssword1'
76+
);
77+
78+
79+
insert into cbioportal.genomic_event
80+
select * from mysql(
81+
'127.0.0.1:3306',
82+
'cbioportal',
83+
'view_genomic_event_mutation',
84+
'cbio',
85+
'P@ssword1'
86+
);
87+
88+
89+
insert into cbioportal.genomic_event
90+
select * from mysql(
91+
'127.0.0.1:3306',
92+
'cbioportal',
93+
'view_genomic_event_cna',
94+
'cbio',
95+
'P@ssword1'
96+
);
97+
98+
insert into cbioportal.genomic_event
99+
select * from mysql(
100+
'127.0.0.1:3306',
101+
'cbioportal',
102+
'view_genomic_event_sv_gene1',
103+
'cbio',
104+
'P@ssword1'
105+
);
106+
107+
108+
insert into cbioportal.genomic_event
109+
select * from mysql(
110+
'127.0.0.1:3306',
111+
'cbioportal',
112+
'view_genomic_event_sv_gene2',
113+
'cbio',
114+
'P@ssword1'
115+
);

‎dev/clickhouse/mysql_provisioning/cbio_database_views.sql

Lines changed: 101 additions & 88 deletions
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,10 @@ DROP VIEW IF EXISTS view_sample;
33
CREATE VIEW view_sample AS
44
SELECT
55
concat(cs.CANCER_STUDY_IDENTIFIER, '_', sample.STABLE_ID) as sample_unique_id,
6+
TO_BASE64(concat(cs.CANCER_STUDY_IDENTIFIER, '_', sample.STABLE_ID)) as sample_unique_id_base64,
67
sample.STABLE_ID as sample_stable_id,
78
concat(cs.CANCER_STUDY_IDENTIFIER, '_', p.STABLE_ID) as patient_unique_id,
9+
TO_BASE64(concat(cs.CANCER_STUDY_IDENTIFIER, '_', p.STABLE_ID)) as patient_unique_id_base64,
810
p.STABLE_ID as patient_stable_id,
911
cs.CANCER_STUDY_IDENTIFIER as cancer_study_identifier
1012
FROM sample
@@ -25,70 +27,81 @@ FROM sample_list as sl
2527
INNER JOIN cancer_study cs on sl.CANCER_STUDY_ID = cs.CANCER_STUDY_ID;
2628

2729
# genomic_event
28-
DROP TABLE IF EXISTS view_genomic_event;
30+
DROP VIEW IF EXISTS view_genomic_event;
31+
DROP VIEW IF EXISTS view_genomic_event_mutation;
2932
-- This view takes a long time to materialize. I store the data in a table to prevent repeated recalculations.
30-
# CREATE TABLE view_genomic_event AS
31-
# SELECT
32-
# concat(cs.CANCER_STUDY_IDENTIFIER, '_', sample.STABLE_ID) as sample_unique_id,
33-
# gene.HUGO_GENE_SYMBOL as hugo_gene_symbol,
34-
# me.PROTEIN_CHANGE as variant,
35-
# gp.STABLE_ID as gene_panel_stable_id,
36-
# cs.CANCER_STUDY_IDENTIFIER as cancer_study_identifier,
37-
# g.STABLE_ID as genetic_profile_stable_id
38-
# FROM mutation
39-
# LEFT JOIN mutation_event as me ON mutation.MUTATION_EVENT_ID = me.MUTATION_EVENT_ID
40-
# LEFT JOIN sample_profile sp on mutation.SAMPLE_ID = sp.SAMPLE_ID and mutation.GENETIC_PROFILE_ID = sp.GENETIC_PROFILE_ID
41-
# LEFT JOIN gene_panel gp on sp.PANEL_ID = gp.INTERNAL_ID
42-
# LEFT JOIN genetic_profile g on sp.GENETIC_PROFILE_ID = g.GENETIC_PROFILE_ID
43-
# LEFT JOIN cancer_study cs on g.CANCER_STUDY_ID = cs.CANCER_STUDY_ID
44-
# LEFT JOIN sample on mutation.SAMPLE_ID = sample.INTERNAL_ID
45-
# LEFT JOIN gene ON mutation.ENTREZ_GENE_ID = gene.ENTREZ_GENE_ID;
46-
# INSERT INTO view_genomic_event
47-
# SELECT
48-
# concat(cs.CANCER_STUDY_IDENTIFIER, '_', sample.STABLE_ID) as sample_unique_id,
49-
# gene.HUGO_GENE_SYMBOL as hugo_gene_symbol,
50-
# convert(ce.ALTERATION, char) as variant,
51-
# gene_panel.STABLE_ID as gene_panel_stable_id,
52-
# cs.CANCER_STUDY_IDENTIFIER as cancer_study_identifier,
53-
# gp.STABLE_ID as genetic_profile_stable_id
54-
# FROM sample_cna_event
55-
# LEFT JOIN cna_event ce on sample_cna_event.CNA_EVENT_ID = ce.CNA_EVENT_ID
56-
# LEFT JOIN gene on ce.ENTREZ_GENE_ID = gene.ENTREZ_GENE_ID
57-
# LEFT JOIN genetic_profile gp on sample_cna_event.GENETIC_PROFILE_ID = gp.GENETIC_PROFILE_ID
58-
# LEFT JOIN sample_profile sp on gp.GENETIC_PROFILE_ID = sp.GENETIC_PROFILE_ID
59-
# LEFT JOIN cancer_study cs on gp.CANCER_STUDY_ID = cs.CANCER_STUDY_ID
60-
# LEFT JOIN sample on sample_cna_event.SAMPLE_ID = sample.INTERNAL_ID
61-
# LEFT JOIN gene_panel ON sp.PANEL_ID = gene_panel.INTERNAL_ID;
62-
# INSERT INTO view_genomic_event
63-
# SELECT
64-
# concat(cs.CANCER_STUDY_IDENTIFIER, '_', s.STABLE_ID) as sample_unique_id,
65-
# hugo_gene_symbol,
66-
# Event_Info as variant,
67-
# g.STABLE_ID as gene_panel_stable_id,
68-
# cs.CANCER_STUDY_IDENTIFIER as cancer_study_identifier,
69-
# gp.STABLE_ID as genetic_profile_stable_id
70-
# FROM structural_variant as sv
71-
# LEFT JOIN (SELECT ENTREZ_GENE_ID, HUGO_GENE_SYMBOL as hugo_gene_symbol FROM gene) gene1 on gene1.ENTREZ_GENE_ID = sv.SITE1_ENTREZ_GENE_ID
72-
# LEFT OUTER JOIN genetic_profile gp on gp.GENETIC_PROFILE_ID = sv.GENETIC_PROFILE_ID
73-
# LEFT JOIN sample s on sv.SAMPLE_ID = s.INTERNAL_ID
74-
# LEFT JOIN cancer_study cs on gp.CANCER_STUDY_ID = cs.CANCER_STUDY_ID
75-
# LEFT JOIN sample_profile sp on gp.GENETIC_PROFILE_ID = sp.GENETIC_PROFILE_ID
76-
# LEFT JOIN gene_panel g on sp.PANEL_ID = g.INTERNAL_ID;
77-
# INSERT INTO view_genomic_event
78-
# SELECT
79-
# concat(cs.CANCER_STUDY_IDENTIFIER, '_', s.STABLE_ID) as sample_unique_id,
80-
# hugo_gene_symbol,
81-
# Event_Info as variant,
82-
# g.STABLE_ID as gene_panel_stable_id,
83-
# cs.CANCER_STUDY_IDENTIFIER as cancer_study_identifier,
84-
# gp.STABLE_ID as genetic_profile_stable_id
85-
# FROM structural_variant as sv
86-
# LEFT JOIN (SELECT ENTREZ_GENE_ID, HUGO_GENE_SYMBOL as hugo_gene_symbol FROM gene) gene2 on gene2.ENTREZ_GENE_ID = sv.SITE2_ENTREZ_GENE_ID
87-
# LEFT OUTER JOIN genetic_profile gp on gp.GENETIC_PROFILE_ID = sv.GENETIC_PROFILE_ID
88-
# LEFT JOIN sample s on sv.SAMPLE_ID = s.INTERNAL_ID
89-
# LEFT JOIN cancer_study cs on gp.CANCER_STUDY_ID = cs.CANCER_STUDY_ID
90-
# LEFT JOIN sample_profile sp on gp.GENETIC_PROFILE_ID = sp.GENETIC_PROFILE_ID
91-
# LEFT JOIN gene_panel g on sp.PANEL_ID = g.INTERNAL_ID;
33+
CREATE VIEW view_genomic_event_mutation AS
34+
SELECT
35+
concat(cs.CANCER_STUDY_IDENTIFIER, '_', sample.STABLE_ID) as sample_unique_id,
36+
gene.HUGO_GENE_SYMBOL as hugo_gene_symbol,
37+
me.PROTEIN_CHANGE as variant,
38+
'mutation',
39+
gp.STABLE_ID as gene_panel_stable_id,
40+
cs.CANCER_STUDY_IDENTIFIER as cancer_study_identifier,
41+
g.STABLE_ID as genetic_profile_stable_id
42+
FROM mutation
43+
LEFT JOIN mutation_event as me ON mutation.MUTATION_EVENT_ID = me.MUTATION_EVENT_ID
44+
LEFT JOIN sample_profile sp on mutation.SAMPLE_ID = sp.SAMPLE_ID and mutation.GENETIC_PROFILE_ID = sp.GENETIC_PROFILE_ID
45+
LEFT JOIN gene_panel gp on sp.PANEL_ID = gp.INTERNAL_ID
46+
LEFT JOIN genetic_profile g on sp.GENETIC_PROFILE_ID = g.GENETIC_PROFILE_ID
47+
LEFT JOIN cancer_study cs on g.CANCER_STUDY_ID = cs.CANCER_STUDY_ID
48+
LEFT JOIN sample on mutation.SAMPLE_ID = sample.INTERNAL_ID
49+
LEFT JOIN gene ON mutation.ENTREZ_GENE_ID = gene.ENTREZ_GENE_ID;
50+
51+
DROP VIEW IF EXISTS view_genomic_event_cna;
52+
CREATE VIEW view_genomic_event_cna AS
53+
SELECT
54+
concat(cs.CANCER_STUDY_IDENTIFIER, '_', sample.STABLE_ID) as sample_unique_id,
55+
gene.HUGO_GENE_SYMBOL as hugo_gene_symbol,
56+
convert(ce.ALTERATION, char) as variant,
57+
'cna',
58+
gene_panel.STABLE_ID as gene_panel_stable_id,
59+
cs.CANCER_STUDY_IDENTIFIER as cancer_study_identifier,
60+
gp.STABLE_ID as genetic_profile_stable_id
61+
FROM sample_cna_event
62+
INNER JOIN cna_event ce on sample_cna_event.CNA_EVENT_ID = ce.CNA_EVENT_ID
63+
INNER JOIN gene on ce.ENTREZ_GENE_ID = gene.ENTREZ_GENE_ID
64+
INNER JOIN genetic_profile gp on sample_cna_event.GENETIC_PROFILE_ID = gp.GENETIC_PROFILE_ID
65+
INNER JOIN sample on sample_cna_event.SAMPLE_ID = sample.INTERNAL_ID
66+
INNER JOIN sample_profile sp on gp.GENETIC_PROFILE_ID = sp.GENETIC_PROFILE_ID AND sp.SAMPLE_ID = sample.INTERNAL_ID
67+
INNER JOIN cancer_study cs on gp.CANCER_STUDY_ID = cs.CANCER_STUDY_ID
68+
INNER JOIN gene_panel ON sp.PANEL_ID = gene_panel.INTERNAL_ID;
69+
70+
DROP VIEW IF EXISTS view_genomic_event_sv_gene1;
71+
CREATE VIEW view_genomic_event_sv_gene1 AS
72+
SELECT
73+
concat(cs.CANCER_STUDY_IDENTIFIER, '_', s.STABLE_ID) as sample_unique_id,
74+
hugo_gene_symbol,
75+
Event_Info as variant,
76+
'sv',
77+
g.STABLE_ID as gene_panel_stable_id,
78+
cs.CANCER_STUDY_IDENTIFIER as cancer_study_identifier,
79+
gp.STABLE_ID as genetic_profile_stable_id
80+
FROM structural_variant as sv
81+
INNER JOIN (SELECT ENTREZ_GENE_ID, HUGO_GENE_SYMBOL as hugo_gene_symbol FROM gene) gene1 on gene1.ENTREZ_GENE_ID = sv.SITE1_ENTREZ_GENE_ID
82+
INNER JOIN genetic_profile gp on gp.GENETIC_PROFILE_ID = sv.GENETIC_PROFILE_ID
83+
INNER JOIN sample s on sv.SAMPLE_ID = s.INTERNAL_ID
84+
INNER JOIN cancer_study cs on gp.CANCER_STUDY_ID = cs.CANCER_STUDY_ID
85+
INNER JOIN sample_profile sp on sp.SAMPLE_ID = sv.SAMPLE_ID and sp.GENETIC_PROFILE_ID = sv.GENETIC_PROFILE_ID
86+
INNER JOIN gene_panel g on sp.PANEL_ID = g.INTERNAL_ID;
87+
88+
DROP VIEW IF EXISTS view_genomic_event_sv_gene2;
89+
CREATE VIEW view_genomic_event_sv_gene2 AS
90+
SELECT
91+
concat(cs.CANCER_STUDY_IDENTIFIER, '_', s.STABLE_ID) as sample_unique_id,
92+
hugo_gene_symbol,
93+
Event_Info as variant,
94+
'sv',
95+
g.STABLE_ID as gene_panel_stable_id,
96+
cs.CANCER_STUDY_IDENTIFIER as cancer_study_identifier,
97+
gp.STABLE_ID as genetic_profile_stable_id
98+
FROM structural_variant as sv
99+
INNER JOIN (SELECT ENTREZ_GENE_ID, HUGO_GENE_SYMBOL as hugo_gene_symbol FROM gene) gene2 on gene2.ENTREZ_GENE_ID = sv.SITE2_ENTREZ_GENE_ID
100+
INNER JOIN genetic_profile gp on gp.GENETIC_PROFILE_ID = sv.GENETIC_PROFILE_ID
101+
INNER JOIN sample s on sv.SAMPLE_ID = s.INTERNAL_ID
102+
INNER JOIN cancer_study cs on gp.CANCER_STUDY_ID = cs.CANCER_STUDY_ID
103+
INNER JOIN sample_profile sp on sp.SAMPLE_ID = sv.SAMPLE_ID and sp.GENETIC_PROFILE_ID = sv.GENETIC_PROFILE_ID
104+
INNER JOIN gene_panel g on sp.PANEL_ID = g.INTERNAL_ID;
92105

93106
-- structural variant
94107
DROP VIEW IF EXISTS view_structural_variant;
@@ -101,25 +114,25 @@ SELECT
101114
cs.CANCER_STUDY_IDENTIFIER as cancer_study_identifier,
102115
gp.STABLE_ID as genetic_profile_stable_id
103116
FROM structural_variant as sv
104-
LEFT JOIN (SELECT ENTREZ_GENE_ID, HUGO_GENE_SYMBOL FROM gene) gene1 on gene1.ENTREZ_GENE_ID = sv.SITE1_ENTREZ_GENE_ID
105-
LEFT JOIN (SELECT ENTREZ_GENE_ID, HUGO_GENE_SYMBOL FROM gene) gene2 on gene2.ENTREZ_GENE_ID = sv.SITE2_ENTREZ_GENE_ID
106-
LEFT OUTER JOIN genetic_profile gp on gp.GENETIC_PROFILE_ID = sv.GENETIC_PROFILE_ID
107-
LEFT JOIN sample s on sv.SAMPLE_ID = s.INTERNAL_ID
108-
LEFT JOIN cancer_study cs on gp.CANCER_STUDY_ID = cs.CANCER_STUDY_ID
109-
LEFT JOIN sample_profile sp on gp.GENETIC_PROFILE_ID = sp.GENETIC_PROFILE_ID
110-
LEFT JOIN gene_panel g on sp.PANEL_ID = g.INTERNAL_ID;
117+
INNER JOIN (SELECT ENTREZ_GENE_ID, HUGO_GENE_SYMBOL FROM gene) gene1 on gene1.ENTREZ_GENE_ID = sv.SITE1_ENTREZ_GENE_ID
118+
INNER JOIN (SELECT ENTREZ_GENE_ID, HUGO_GENE_SYMBOL FROM gene) gene2 on gene2.ENTREZ_GENE_ID = sv.SITE2_ENTREZ_GENE_ID
119+
INNER JOIN genetic_profile gp on gp.GENETIC_PROFILE_ID = sv.GENETIC_PROFILE_ID
120+
INNER JOIN sample s on sv.SAMPLE_ID = s.INTERNAL_ID
121+
INNER JOIN cancer_study cs on gp.CANCER_STUDY_ID = cs.CANCER_STUDY_ID
122+
INNER JOIN sample_profile sp on gp.GENETIC_PROFILE_ID = sp.GENETIC_PROFILE_ID AND sp.SAMPLE_ID = sv.SAMPLE_ID
123+
INNER JOIN gene_panel g on sp.PANEL_ID = g.INTERNAL_ID;
111124

112125
-- sample_clinical_attribute_numeric
113126
DROP VIEW IF EXISTS view_sample_clinical_attribute_numeric;
114127
CREATE VIEW view_sample_clinical_attribute_numeric AS
115128
SELECT
116-
concat(cs.CANCER_STUDY_IDENTIFIER, '_', s.STABLE_ID) as sample_unique_id,
117-
concat(cs.CANCER_STUDY_IDENTIFIER, '_', p.STABLE_ID) as patient_unique_id,
129+
concat(cancer_study.CANCER_STUDY_IDENTIFIER, '_', s.STABLE_ID) as sample_unique_id,
130+
concat(cancer_study.CANCER_STUDY_IDENTIFIER, '_', p.STABLE_ID) as patient_unique_id,
118131
ATTR_ID as attribute_name,
119132
ATTR_VALUE as attribute_value,
120-
cs.CANCER_STUDY_IDENTIFIER as cancer_study_identifier
121-
FROM cancer_study cs
122-
INNER JOIN patient p on cs.CANCER_STUDY_ID = p.CANCER_STUDY_ID
133+
cancer_study.CANCER_STUDY_IDENTIFIER as cancer_study_identifier
134+
FROM cancer_study
135+
INNER JOIN patient p on cancer_study.CANCER_STUDY_ID = p.CANCER_STUDY_ID
123136
INNER JOIN sample s on p.INTERNAL_ID = s.PATIENT_ID
124137
INNER JOIN clinical_sample cs on s.INTERNAL_ID = cs.INTERNAL_ID
125138
WHERE ATTR_VALUE REGEXP '^[0-9.]+$';
@@ -128,13 +141,13 @@ WHERE ATTR_VALUE REGEXP '^[0-9.]+$';
128141
DROP VIEW IF EXISTS view_sample_clinical_attribute_categorical;
129142
CREATE VIEW view_sample_clinical_attribute_categorical AS
130143
SELECT
131-
concat(cs.CANCER_STUDY_IDENTIFIER, '_', s.STABLE_ID) as sample_unique_id,
132-
concat(cs.CANCER_STUDY_IDENTIFIER, '_', p.STABLE_ID) as patient_unique_id,
144+
concat(cancer_study.CANCER_STUDY_IDENTIFIER, '_', s.STABLE_ID) as sample_unique_id,
145+
concat(cancer_study.CANCER_STUDY_IDENTIFIER, '_', p.STABLE_ID) as patient_unique_id,
133146
ATTR_ID as attribute_name,
134147
ATTR_VALUE as attribute_value,
135-
cs.CANCER_STUDY_IDENTIFIER as cancer_study_identifier
136-
FROM cancer_study cs
137-
INNER JOIN patient p on cs.CANCER_STUDY_ID = p.CANCER_STUDY_ID
148+
cancer_study.CANCER_STUDY_IDENTIFIER as cancer_study_identifier
149+
FROM cancer_study
150+
INNER JOIN patient p on cancer_study.CANCER_STUDY_ID = p.CANCER_STUDY_ID
138151
INNER JOIN sample s on p.INTERNAL_ID = s.PATIENT_ID
139152
INNER JOIN clinical_sample cs on s.INTERNAL_ID = cs.INTERNAL_ID
140153
WHERE ATTR_VALUE NOT REGEXP '^[0-9.]+$';
@@ -143,25 +156,25 @@ WHERE ATTR_VALUE NOT REGEXP '^[0-9.]+$';
143156
DROP VIEW IF EXISTS view_patient_clinical_attribute_numeric;
144157
CREATE VIEW view_patient_clinical_attribute_numeric AS
145158
SELECT
146-
concat(cs.CANCER_STUDY_IDENTIFIER, '_', p.STABLE_ID) as patient_unique_id,
159+
concat(cancer_study.CANCER_STUDY_IDENTIFIER, '_', p.STABLE_ID) as patient_unique_id,
147160
ATTR_ID as attribute_name,
148161
ATTR_VALUE as attribute_value,
149-
cs.CANCER_STUDY_IDENTIFIER as cancer_study_identifier
150-
FROM cancer_study cs
151-
INNER JOIN patient p on cs.CANCER_STUDY_ID = p.CANCER_STUDY_ID
162+
cancer_study.CANCER_STUDY_IDENTIFIER as cancer_study_identifier
163+
FROM cancer_study
164+
INNER JOIN patient p on cancer_study.CANCER_STUDY_ID = p.CANCER_STUDY_ID
152165
INNER JOIN clinical_patient cp on p.INTERNAL_ID = cp.INTERNAL_ID
153166
WHERE ATTR_VALUE REGEXP '^[0-9.]+$';
154167

155168
-- patient_clinical_attribute_categorical
156169
DROP VIEW IF EXISTS view_patient_clinical_attribute_categorical;
157170
CREATE VIEW view_patient_clinical_attribute_categorical AS
158171
SELECT
159-
concat(cs.CANCER_STUDY_IDENTIFIER, '_', p.STABLE_ID) as patient_unique_id,
172+
concat(cancer_study.CANCER_STUDY_IDENTIFIER, '_', p.STABLE_ID) as patient_unique_id,
160173
ATTR_ID as attribute_name,
161174
ATTR_VALUE as attribute_value,
162-
cs.CANCER_STUDY_IDENTIFIER as cancer_study_identifier
163-
FROM cancer_study cs
164-
INNER JOIN patient p on cs.CANCER_STUDY_ID = p.CANCER_STUDY_ID
175+
cancer_study.CANCER_STUDY_IDENTIFIER as cancer_study_identifier
176+
FROM cancer_study
177+
INNER JOIN patient p on cancer_study.CANCER_STUDY_ID = p.CANCER_STUDY_ID
165178
INNER JOIN clinical_patient cp on p.INTERNAL_ID = cp.INTERNAL_ID
166179
WHERE ATTR_VALUE NOT REGEXP '^[0-9.]+$';
167180

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