From 16a0a982d8e26b86e5fd36eca45931b39a3fa87e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?= <ak4@sanger.ac.uk> Date: Thu, 30 Jul 2009 13:47:05 +0000 Subject: [PATCH] SQL comments need a space after '--'. --- sql/patch_55_56_c.sql | 60 +++++++++++++++++++++---------------------- 1 file changed, 30 insertions(+), 30 deletions(-) diff --git a/sql/patch_55_56_c.sql b/sql/patch_55_56_c.sql index 1a37dd04e1..078e2a5172 100644 --- a/sql/patch_55_56_c.sql +++ b/sql/patch_55_56_c.sql @@ -6,8 +6,8 @@ # Drop oligo tables and remove association xref schema data ---Delete all AFFY object_xrefs ---Do this on external_db_ids and dbname, to be safer i.e. we do not want to corrupt and custom data +-- Delete all AFFY object_xrefs +-- Do this on external_db_ids and dbname, to be safer i.e. we do not want to corrupt and custom data DELETE ox from external_db edb, xref x, object_xref ox where edb.external_db_id>=3000 and edb.external_db_id<3200 and edb.db_name like 'AFFY\_%' and edb.external_db_id=x.external_db_id and x.xref_id=ox.xref_id; @@ -19,12 +19,12 @@ DELETE x from external_db edb, xref x where edb.external_db_id>=3000 and edb.ext DELETE from external_db where external_db_id>=3000 and external_db_id<3200 and db_name like 'AFFY\_%'; ---Species specific xrefs, to do this safely have to do these on a per db basis due to specific names ---aedes_aegypti_core_55_1d ---oligo_array_id parent_array_id probe_setsize name type external_db_id ---3 NULL 1 ARRAY_ND_TIGRTC_9_6K_v1 OLIGO 3207 ---2 NULL 1 ARRAY_LIV_AEGDETOX_0_25K_v1 OLIGO 3206 ---4 NULL 1 ARRAY_UCR_GillMgMT_0_2K_v2 OLIGO 3208 +-- Species specific xrefs, to do this safely have to do these on a per db basis due to specific names +-- aedes_aegypti_core_55_1d +-- oligo_array_id parent_array_id probe_setsize name type external_db_id +-- 3 NULL 1 ARRAY_ND_TIGRTC_9_6K_v1 OLIGO 3207 +-- 2 NULL 1 ARRAY_LIV_AEGDETOX_0_25K_v1 OLIGO 3206 +-- 4 NULL 1 ARRAY_UCR_GillMgMT_0_2K_v2 OLIGO 3208 DELETE ox from external_db edb, xref x, object_xref ox where edb.external_db_id=3207 and edb.db_name='ARRAY_ND_TIGRTC_9_6K_v1' and edb.external_db_id=x.external_db_id and x.xref_id=ox.xref_id; DELETE ox from external_db edb, xref x, object_xref ox where edb.external_db_id=3206 and edb.db_name='ARRAY_LIV_AEGDETOX_0_25K_v1' and edb.external_db_id=x.external_db_id and x.xref_id=ox.xref_id; @@ -45,13 +45,13 @@ DELETE from external_db where external_db_id=3206 and db_name='ARRAY_LIV_AEGDET DELETE from external_db where external_db_id=3209 and db_name='ARRAY_UCR_GillMgMT_0_2K_v2'; ---anopheles_gambiae_core_55_3k ---oligo_array_id parent_array_id probe_setsize name type external_db_id ---3 NULL 1 LIV_GAMDETOX_0.25k_v1 OLIGO 3204 ---4 NULL 1 LIV_GAMDETOX_0.25k_v2 OLIGO 3210 ---5 NULL 1 EMBL_MMC1_20k_v1 OLIGO 3201 ---6 NULL 1 EMBL_MMC2_12k_v1 OLIGO 3202 ---7 NULL 1 JHSPH_AG_GAMBER_15k_v1 OLIGO 3209 +-- anopheles_gambiae_core_55_3k +-- oligo_array_id parent_array_id probe_setsize name type external_db_id +-- 3 NULL 1 LIV_GAMDETOX_0.25k_v1 OLIGO 3204 +-- 4 NULL 1 LIV_GAMDETOX_0.25k_v2 OLIGO 3210 +-- 5 NULL 1 EMBL_MMC1_20k_v1 OLIGO 3201 +-- 6 NULL 1 EMBL_MMC2_12k_v1 OLIGO 3202 +-- 7 NULL 1 JHSPH_AG_GAMBER_15k_v1 OLIGO 3209 DELETE ox from external_db edb, xref x, object_xref ox where edb.external_db_id=3204 and edb.db_name='ARRAY_LIV_GAMDETOX_0.25k_v1' and edb.external_db_id=x.external_db_id and x.xref_id=ox.xref_id; @@ -74,12 +74,12 @@ DELETE from external_db where external_db_id=3202 and db_name='ARRAY_EMBL_MMC2_ DELETE from external_db where external_db_id=3200 and db_name='ARRAY_JHSPH_AG_GAMBER_15k_v1'; ---danio ---oligo_array_id parent_array_id probe_setsize name type external_db_id ---2 NULL 1 AGILENT_G2518A OLIGO 3251 ---3 NULL 1 AGILENT_G2519F OLIGO 3252 ---4 NULL 1 LEIDEN2 OLIGO 3260 ---5 NULL 1 LEIDEN3 OLIGO 3261 +-- danio +-- oligo_array_id parent_array_id probe_setsize name type external_db_id +-- 2 NULL 1 AGILENT_G2518A OLIGO 3251 +-- 3 NULL 1 AGILENT_G2519F OLIGO 3252 +-- 4 NULL 1 LEIDEN2 OLIGO 3260 +-- 5 NULL 1 LEIDEN3 OLIGO 3261 DELETE ox from external_db edb, xref x, object_xref ox where edb.external_db_id=3251 and edb.db_name='AGILENT_G2518A' and edb.external_db_id=x.external_db_id and x.xref_id=ox.xref_id; DELETE ox from external_db edb, xref x, object_xref ox where edb.external_db_id=3252 and edb.db_name='AGILENT_G2519F' and edb.external_db_id=x.external_db_id and x.xref_id=ox.xref_id; @@ -96,7 +96,7 @@ DELETE from external_db where external_db_id=3252 and db_name='AGILENT_G2519F'; DELETE from external_db where external_db_id=3260 and db_name='ARRAY_ZFISH_LEIDEN2'; DELETE from external_db where external_db_id=3261 and db_name='ARRAY_ZFISH_LEIDEN3'; ---platypus +-- platypus -- platypus_exon? Is done as affy for oligos, but no for xrefs. -- Platypus_exon 3299 DELETE ox from external_db edb, xref x, object_xref ox where edb.external_db_id=3299 and edb.db_name='Platypus_exon' and edb.external_db_id=x.external_db_id and x.xref_id=ox.xref_id; @@ -104,12 +104,12 @@ DELETE x from external_db edb, xref x where edb.external_db_id=3299 and edb.db_n DELETE from external_db where external_db_id=3299 and db_name='Platypus_exon'; ---Also have: ---VB_array 3200 ---ARRAY_JHU_GAM3_0_21k_v1 3203 ---ARRAY_JHU_AEG1_0_20k_v1 3205 ---ARRAY_LIV_AEGDETOX_0_25k_v2 3211 ---Seeking confirmation from Dan Lawson wrt removing these +-- Also have: +-- VB_array 3200 +-- ARRAY_JHU_GAM3_0_21k_v1 3203 +-- ARRAY_JHU_AEG1_0_20k_v1 3205 +-- ARRAY_LIV_AEGDETOX_0_25k_v2 3211 +-- Seeking confirmation from Dan Lawson wrt removing these DELETE ox from external_db edb, xref x, object_xref ox where edb.external_db_id=3203 and edb.db_name='ARRAY_JHU_GAM3_0_21k_v1' and edb.external_db_id=x.external_db_id and x.xref_id=ox.xref_id; DELETE ox from external_db edb, xref x, object_xref ox where edb.external_db_id=3205 and edb.db_name='ARRAY_JHU_AEG1_0_20k_v1' and edb.external_db_id=x.external_db_id and x.xref_id=ox.xref_id; @@ -165,11 +165,11 @@ DELETE from external_db where external_db_id=6000 and db_name='Codelink'; ---Delete unmapped_reasons +-- Delete unmapped_reasons DELETE ur from unmapped_reason ur, unmapped_object uo where uo.type='probe2transcript' and uo.unmapped_reason_id=ur.unmapped_reason_id; ---Delete unmapped_objects, separately just in case of orhpans +-- Delete unmapped_objects, separately just in case of orhpans DELETE from unmapped_object where type='probe2transcript'; -- GitLab