From 4ae0934821b8374a190950924039a1f7573c82af Mon Sep 17 00:00:00 2001 From: Sajith Perera Date: Thu, 4 Oct 2012 10:48:07 +0100 Subject: [PATCH 1/7] new qc_run fixture data to test against --- t/fixtures/10-load-fixture-data.sql | 218 +++++++++++++++------------- 1 file changed, 119 insertions(+), 99 deletions(-) diff --git a/t/fixtures/10-load-fixture-data.sql b/t/fixtures/10-load-fixture-data.sql index d07dec361c..00eea9b131 100644 --- a/t/fixtures/10-load-fixture-data.sql +++ b/t/fixtures/10-load-fixture-data.sql @@ -106,28 +106,28 @@ SELECT pg_catalog.setval('projects_id_seq', 1, false); -- Name: qc_alignments_id_seq; Type: SEQUENCE SET; Schema: public; Owner: lims2_test_admin -- -SELECT pg_catalog.setval('qc_alignments_id_seq', 92, true); +SELECT pg_catalog.setval('qc_alignments_id_seq', 94, true); -- -- Name: qc_eng_seqs_id_seq; Type: SEQUENCE SET; Schema: public; Owner: lims2_test_admin -- -SELECT pg_catalog.setval('qc_eng_seqs_id_seq', 2219, true); +SELECT pg_catalog.setval('qc_eng_seqs_id_seq', 2221, true); -- -- Name: qc_run_seq_wells_id_seq; Type: SEQUENCE SET; Schema: public; Owner: lims2_test_admin -- -SELECT pg_catalog.setval('qc_run_seq_wells_id_seq', 69, true); +SELECT pg_catalog.setval('qc_run_seq_wells_id_seq', 72, true); -- -- Name: qc_template_wells_id_seq; Type: SEQUENCE SET; Schema: public; Owner: lims2_test_admin -- -SELECT pg_catalog.setval('qc_template_wells_id_seq', 3264, true); +SELECT pg_catalog.setval('qc_template_wells_id_seq', 3266, true); -- @@ -141,7 +141,7 @@ SELECT pg_catalog.setval('qc_templates_id_seq', 200, true); -- Name: qc_test_results_id_seq; Type: SEQUENCE SET; Schema: public; Owner: lims2_test_admin -- -SELECT pg_catalog.setval('qc_test_results_id_seq', 69, true); +SELECT pg_catalog.setval('qc_test_results_id_seq', 71, true); -- @@ -985,26 +985,6 @@ INSERT INTO backbones VALUES (1859, 'L4L3_pD223_DTA_spec', 'INVERTED R3 and R4 G -- Data for Name: cassettes; Type: TABLE DATA; Schema: public; Owner: lims2_test_admin -- -INSERT INTO cassettes VALUES (10447, 'pR6K_R1R2_ZP', 'Standard intermediate vector cassette', false, NULL, NULL, false); -INSERT INTO cassettes VALUES (10448, 'L1L2_hubi_P', '', true, NULL, NULL, false); -INSERT INTO cassettes VALUES (10449, 'L1L2_GOHANU', '', true, NULL, NULL, false); -INSERT INTO cassettes VALUES (10450, 'L1L2_Pgk_PM', 'PGK promoter driving mutant neo. Frame indendent IRES driven lacZ reporter', true, NULL, NULL, false); -INSERT INTO cassettes VALUES (10451, 'pL1L2_GT1_LF2A_nEGFPO_T2A_CreERT_puro', '', false, 'pL1L2_GT?_LF2A_nEGFPO_T2A_CreERT_puro', 1, false); -INSERT INTO cassettes VALUES (10452, 'pL1L2_GT0_T2A_H2BCherry_Puro_delRsrll_NO_DTA', '', true, 'pL1L2_GT?_T2A_H2BCherry_Puro_delRsrll_NO_DTA', NULL, false); -INSERT INTO cassettes VALUES (10453, 'pL1L2_GT0_T2A_iCre_KI_Puro', '', true, 'pL1L2_GT?_T2A_iCre_KI_Puro', NULL, false); -INSERT INTO cassettes VALUES (10454, 'pL1L2_GT1_LF2A_H2BCherry_Puro', '', true, 'pL1L2_GT?_LF2A_H2BCherry_Puro', 1, false); -INSERT INTO cassettes VALUES (10455, 'L1L2_Pgk_P', 'PGK promoter driving WT neo. Frame indendent IRES driven lacZ reporter', true, NULL, NULL, false); -INSERT INTO cassettes VALUES (10460, 'pL1L2_GT1_T2A_H2BCherry_Puro_delRsrll_NO_DTA', '', true, 'pL1L2_GT?_T2A_H2BCherry_Puro_delRsrll_NO_DTA', 1, false); -INSERT INTO cassettes VALUES (10466, 'L1L2_Del_BactPneo_FFL_TAG1A', '', true, NULL, NULL, false); -INSERT INTO cassettes VALUES (10467, 'V5_Flag_biotin', '', true, NULL, NULL, false); -INSERT INTO cassettes VALUES (10469, 'pL1L2_GT1_T2A_iCre_KI_Puro', '', true, 'pL1L2_GT?_T2A_iCre_KI_Puro', 1, false); -INSERT INTO cassettes VALUES (10472, 'B1B2_frame0_Norcomm', '', false, 'B1B2_frame?_Norcomm', NULL, false); -INSERT INTO cassettes VALUES (10473, 'pL1L2_GT2_T2A_H2BCherry_Puro_delRsrll_NO_DTA', '', true, 'pL1L2_GT?_T2A_H2BCherry_Puro_delRsrll_NO_DTA', 2, false); -INSERT INTO cassettes VALUES (10474, 'pL1L2_GT2_LF2A_H2BCherry_Puro', '', true, 'pL1L2_GT?_LF2A_H2BCherry_Puro', 1, false); -INSERT INTO cassettes VALUES (10417, 'Ty1_EGFP', '', true, NULL, NULL, false); -INSERT INTO cassettes VALUES (10419, 'L1L2_st0', 'Secretory Trap versions of EUCOMM vector with CD4 Tm domain for targeting secreted/TM loci', false, 'L1L2_st?', NULL, false); -INSERT INTO cassettes VALUES (10420, 'L1L2_NTARU-1', '', false, 'L1L2_NTARU-?', 1, false); -INSERT INTO cassettes VALUES (10423, 'L1L2_NTARU-0', '', false, 'L1L2_NTARU-?', NULL, false); INSERT INTO cassettes VALUES (10424, 'pL1L2_GT2_T2A_iCre_KI_Puro', '', true, 'pL1L2_GT?_T2A_iCre_KI_Puro', 2, false); INSERT INTO cassettes VALUES (10426, 'L1L2_GT0_T2A_H2BVenus_PGKPuro_delRsrII_NO_DTA', '', true, 'L1L2_GT?_T2A_H2BVenus_PGKPuro_delRsrII_NO_DTA', 2, false); INSERT INTO cassettes VALUES (10427, 'B1B2_frame2_Norcomm', '', false, 'B1B2_frame?_Norcomm', 2, false); @@ -1025,6 +1005,26 @@ INSERT INTO cassettes VALUES (10475, 'pL1L2_GTK_nEGFPO_T2A_CreERT_puro', '', fal INSERT INTO cassettes VALUES (10418, 'Ifitm2_intron_L1L2_GT2_LF2A_LacZ_BetactP_neo', '', true, 'Ifitm2_intron_L1L2_GT?_LF2A_LacZ_BetactP_neo', 2, true); INSERT INTO cassettes VALUES (10421, 'L1L2_GT0_LacZ_BSD', '', false, 'L1L2_GT?_LacZ_BSD', NULL, true); INSERT INTO cassettes VALUES (10422, 'L1L2_GT2_LF2A_LacZ_BetactP_neo', '', true, 'L1L2_GT?_LF2A_LacZ_BetactP_neo', 2, true); +INSERT INTO cassettes VALUES (10447, 'pR6K_R1R2_ZP', 'Standard intermediate vector cassette', false, NULL, NULL, false); +INSERT INTO cassettes VALUES (10448, 'L1L2_hubi_P', '', true, NULL, NULL, false); +INSERT INTO cassettes VALUES (10449, 'L1L2_GOHANU', '', true, NULL, NULL, false); +INSERT INTO cassettes VALUES (10450, 'L1L2_Pgk_PM', 'PGK promoter driving mutant neo. Frame indendent IRES driven lacZ reporter', true, NULL, NULL, false); +INSERT INTO cassettes VALUES (10451, 'pL1L2_GT1_LF2A_nEGFPO_T2A_CreERT_puro', '', false, 'pL1L2_GT?_LF2A_nEGFPO_T2A_CreERT_puro', 1, false); +INSERT INTO cassettes VALUES (10452, 'pL1L2_GT0_T2A_H2BCherry_Puro_delRsrll_NO_DTA', '', true, 'pL1L2_GT?_T2A_H2BCherry_Puro_delRsrll_NO_DTA', NULL, false); +INSERT INTO cassettes VALUES (10453, 'pL1L2_GT0_T2A_iCre_KI_Puro', '', true, 'pL1L2_GT?_T2A_iCre_KI_Puro', NULL, false); +INSERT INTO cassettes VALUES (10454, 'pL1L2_GT1_LF2A_H2BCherry_Puro', '', true, 'pL1L2_GT?_LF2A_H2BCherry_Puro', 1, false); +INSERT INTO cassettes VALUES (10455, 'L1L2_Pgk_P', 'PGK promoter driving WT neo. Frame indendent IRES driven lacZ reporter', true, NULL, NULL, false); +INSERT INTO cassettes VALUES (10460, 'pL1L2_GT1_T2A_H2BCherry_Puro_delRsrll_NO_DTA', '', true, 'pL1L2_GT?_T2A_H2BCherry_Puro_delRsrll_NO_DTA', 1, false); +INSERT INTO cassettes VALUES (10466, 'L1L2_Del_BactPneo_FFL_TAG1A', '', true, NULL, NULL, false); +INSERT INTO cassettes VALUES (10467, 'V5_Flag_biotin', '', true, NULL, NULL, false); +INSERT INTO cassettes VALUES (10469, 'pL1L2_GT1_T2A_iCre_KI_Puro', '', true, 'pL1L2_GT?_T2A_iCre_KI_Puro', 1, false); +INSERT INTO cassettes VALUES (10472, 'B1B2_frame0_Norcomm', '', false, 'B1B2_frame?_Norcomm', NULL, false); +INSERT INTO cassettes VALUES (10473, 'pL1L2_GT2_T2A_H2BCherry_Puro_delRsrll_NO_DTA', '', true, 'pL1L2_GT?_T2A_H2BCherry_Puro_delRsrll_NO_DTA', 2, false); +INSERT INTO cassettes VALUES (10474, 'pL1L2_GT2_LF2A_H2BCherry_Puro', '', true, 'pL1L2_GT?_LF2A_H2BCherry_Puro', 1, false); +INSERT INTO cassettes VALUES (10417, 'Ty1_EGFP', '', true, NULL, NULL, false); +INSERT INTO cassettes VALUES (10419, 'L1L2_st0', 'Secretory Trap versions of EUCOMM vector with CD4 Tm domain for targeting secreted/TM loci', false, 'L1L2_st?', NULL, false); +INSERT INTO cassettes VALUES (10420, 'L1L2_NTARU-1', '', false, 'L1L2_NTARU-?', 1, false); +INSERT INTO cassettes VALUES (10423, 'L1L2_NTARU-0', '', false, 'L1L2_NTARU-?', NULL, false); INSERT INTO cassettes VALUES (10425, 'Ifitm2_intron_L1L2_GT1_LF2A_LacZ_BetactP_neo', '', true, 'Ifitm2_intron_L1L2_GT?_LF2A_LacZ_BetactP_neo', 1, true); INSERT INTO cassettes VALUES (10428, 'Ifitm2_intron_R1_ZeoPheS_R2', '', false, NULL, NULL, true); INSERT INTO cassettes VALUES (10435, 'L1L2_GT0_LF2A_LacZ_BetactP_neo', '', true, 'L1L2_GT?_LF2A_LacZ_BetactP_neo', NULL, true); @@ -4607,6 +4607,16 @@ INSERT INTO plates VALUES (988, 'SEP_POOL0001', '', 'SEP_POOL', 985, '2012-09-14 -- Data for Name: plate_comments; Type: TABLE DATA; Schema: public; Owner: lims2_test_admin -- +INSERT INTO plate_comments VALUES (44, 955, 'New promoterless gateway', 751, '2008-02-08 00:00:00'); +INSERT INTO plate_comments VALUES (45, 955, 'Production Gateway finished', 751, '2007-11-21 00:00:00'); +INSERT INTO plate_comments VALUES (46, 955, 'PCS_A and PGS_A stored', 751, '2007-11-21 00:00:00'); +INSERT INTO plate_comments VALUES (47, 955, 'at the CRE step, handed for QC 3rd week of January', 958, '2008-01-10 00:00:00'); +INSERT INTO plate_comments VALUES (48, 955, 'recombineering will be repeated 1st week of Dec', 958, '2007-11-29 00:00:00'); +INSERT INTO plate_comments VALUES (49, 955, 'PC 100% positive combining te two plates A+B and C+D', 877, '2010-01-29 00:00:00'); +INSERT INTO plate_comments VALUES (50, 956, '89 pass PCQC', 751, '2009-05-05 00:00:00'); +INSERT INTO plate_comments VALUES (51, 960, 'all wells passed recombineering (there were some fails in the C+D)', 958, '2009-02-04 00:00:00'); +INSERT INTO plate_comments VALUES (52, 965, 'This plate has been arrayed in the wrong order A01=H12 etc', 751, '2010-07-29 00:00:00'); +INSERT INTO plate_comments VALUES (53, 966, 'Production Gateway finished', 751, '2007-11-20 00:00:00'); INSERT INTO plate_comments VALUES (54, 966, 'Second Recomb attempt in analysis', 751, '2008-01-11 00:00:00'); INSERT INTO plate_comments VALUES (55, 966, 'plate 100% OK combining different PC plates', 877, '2010-01-29 00:00:00'); INSERT INTO plate_comments VALUES (56, 972, 'PCS_A and PGS_A stored', 751, '2007-11-21 00:00:00'); @@ -4647,16 +4657,6 @@ INSERT INTO plate_comments VALUES (40, 942, '61 pass (3P), 6 pass (2P), 2 pass ( INSERT INTO plate_comments VALUES (41, 947, 'Gateway in process', 751, '2007-11-21 00:00:00'); INSERT INTO plate_comments VALUES (42, 947, '2nd set PC anlysis in process', 751, '2007-11-20 00:00:00'); INSERT INTO plate_comments VALUES (43, 947, 'Production Gateway finished', 751, '2007-11-26 00:00:00'); -INSERT INTO plate_comments VALUES (44, 955, 'New promoterless gateway', 751, '2008-02-08 00:00:00'); -INSERT INTO plate_comments VALUES (45, 955, 'Production Gateway finished', 751, '2007-11-21 00:00:00'); -INSERT INTO plate_comments VALUES (46, 955, 'PCS_A and PGS_A stored', 751, '2007-11-21 00:00:00'); -INSERT INTO plate_comments VALUES (47, 955, 'at the CRE step, handed for QC 3rd week of January', 958, '2008-01-10 00:00:00'); -INSERT INTO plate_comments VALUES (48, 955, 'recombineering will be repeated 1st week of Dec', 958, '2007-11-29 00:00:00'); -INSERT INTO plate_comments VALUES (49, 955, 'PC 100% positive combining te two plates A+B and C+D', 877, '2010-01-29 00:00:00'); -INSERT INTO plate_comments VALUES (50, 956, '89 pass PCQC', 751, '2009-05-05 00:00:00'); -INSERT INTO plate_comments VALUES (51, 960, 'all wells passed recombineering (there were some fails in the C+D)', 958, '2009-02-04 00:00:00'); -INSERT INTO plate_comments VALUES (52, 965, 'This plate has been arrayed in the wrong order A01=H12 etc', 751, '2010-07-29 00:00:00'); -INSERT INTO plate_comments VALUES (53, 966, 'Production Gateway finished', 751, '2007-11-20 00:00:00'); -- @@ -9557,30 +9557,39 @@ INSERT INTO sponsors VALUES ('Human', 'Homozygous - Human'); -- Data for Name: qc_eng_seqs; Type: TABLE DATA; Schema: public; Owner: lims2_test_admin -- +INSERT INTO qc_eng_seqs VALUES (2220, 'conditional_vector_seq', '{"backbone":{"name":"L3L4_pD223_DTA_T_spec"},"chromosome":"15","d_insertion":{"name":"LoxP"},"design_id":"372441","display_id":"372441#L1L2_Bact_P#L3L4_pD223_DTA_T_spec","five_arm_end":"38155533","five_arm_start":"38149485","recombinase":[],"strand":"1","target_region_end":"38156625","target_region_start":"38155546","three_arm_end":"38159537","three_arm_start":"38156657","u_insertion":{"name":"L1L2_Bact_P"}}'); +INSERT INTO qc_eng_seqs VALUES (2221, 'conditional_vector_seq', '{"backbone":{"name":"L3L4_pD223_DTA_T_spec"},"chromosome":"3","d_insertion":{"name":"LoxP"},"design_id":"372441","display_id":"372441#L1L2_Bact_P#L3L4_pD223_DTA_T_spec","five_arm_end":"38155533","five_arm_start":"38149485","recombinase":[],"strand":"1","target_region_end":"38156625","target_region_start":"38155546","three_arm_end":"38159537","three_arm_start":"38156657","u_insertion":{"name":"L1L2_Bact_P"}}'); -- -- Data for Name: qc_seq_projects; Type: TABLE DATA; Schema: public; Owner: lims2_test_admin -- +INSERT INTO qc_seq_projects VALUES ('PCS05036_A', 'Mouse'); -- -- Data for Name: qc_seq_reads; Type: TABLE DATA; Schema: public; Owner: lims2_test_admin -- +INSERT INTO qc_seq_reads VALUES ('PCS05036_A_1g12.p1kLR', 'bases 110 to 454 (QL to QR)', 'LR', 'CTCTATAAAAATGTNGNATAGTGAAACATGCTTATAAATACTGGGAATGTTTATCTTTGAGTAGAATAATATCTTGAATTTGTGTTTTTCTTCCTTGTCTTTTCCAGCCTTTCAAGGCAGTCTTGTTAGTTCTGATTTGGAGACAAACTTAAGAACTAGATGTGATGGCACATGCCTCTCATCCGAGACCCAGCAAGCACAGGAAGATTACAAGTTTGAGGCCAGTTTGGCTAGAGAGTAAAATTCAGTCTTTAAAGTGAAAATATTTCAACAAAATAATACATACTTCCATAACTGTGAAAGGTTTAATATCAAAACAGAAAAATATTAGATATCAAAATGATT', 345, 'PCS05036_A'); +INSERT INTO qc_seq_reads VALUES ('PCS05036_A_1b02.p1kLR', 'bases 46 to 469 (QL to QR)', 'LR', 'TCTCACCCAGCCCTTCCATTTCCCTCCTCCCATCATGGGATGTCTCCAGNTTTGCTACACAGACCCAGGATGTACCCTTTGGGCTGGAATACCCATGGGCAGCTTACTGTGTTTGTTCTGGAATCCTGCAGTGTAAACTTCCATGCCCTGGAAAAAATGAAAAAACAGAGTACTCTGAAGTAATCCAACATTCCAACGATTCTTAAGTTCAGATAAGCCTCGGCAGTCCCGGAAAGGCTTCTGTGTAGAGAGGGACGGCTAGGCCCTAATCGCAGCACTTAGGAGGTATATACAGGAGGACTCCCATGAGCGTAGATAGATAGCTGCATAAACAATCCTCCCTTTCTCTTCACTTGATGGCTGCAGAAGGCAATCCAGATTTGTTTCCTCATCTTTCCTCAGAGGTCTCTGTTCCCATGGATTG', 424, 'PCS05036_A'); -- -- Data for Name: qc_alignments; Type: TABLE DATA; Schema: public; Owner: lims2_test_admin -- +INSERT INTO qc_alignments VALUES (93, 'PCS05036_A_1b02.p1kLR', 2221, 'LR', 0, 521, 1, 11191, 10670, -1, 2605, true, 'synthetic loxP region,Critical Region', 'cigar: PCS05036_A_1a01.p1kcLR 0 521 + 372239#pR6K_R1R2_ZP#R3R4_pBR_amp 11191 10670 - 2605 M 521', 'M 521'); +INSERT INTO qc_alignments VALUES (94, 'PCS05036_A_1g12.p1kLR', 2220, 'LR', 0, 569, 1, 11049, 10480, -1, 2836, true, 'synthetic loxP region,Critical Region', 'cigar: PCS05036_A_1a03.p1kcLR 0 569 + 372471#pR6K_R1R2_ZP#R3R4_pBR_amp 11049 10480 - 2836 M 569', 'M 569'); -- -- Data for Name: qc_alignment_regions; Type: TABLE DATA; Schema: public; Owner: lims2_test_admin -- +INSERT INTO qc_alignment_regions VALUES (93, 'target-region-rev-72-80', 1064, 518, 'AAGCCTTTTGGTGGGAATGGGATGTGGAAGGTGCGGCAGAGGGGTAATAAGATGGCGATGCTGCCAAGGACACTGTGGAAGGTGGCACCTCTTAGCAACACTTAGGCAATAAAGGCCCCATAGTGGAGCAAATGCTTAGCATGCACAATCCTCTGGGCTCGTGCACACACGCACATGGGCACATGTGCACACACACACACACACCAAGAGCCCATTATTACATCATTTTCTAAAGTAAAAATGAGAATTGTCTTGTAAAATTCCAACACTAATGGATCCATAAGGTTTACAGAATTATAAACAGACAGACCAACCCCCAGAGTGACAGACCAAACCCCCAGAGTGTCATTTAGGAGACATGTGACACAGGCTCTACCCTGTTCTCCGGCAACAGGATATGGCTTTGGGCTCACCTTGAACTTCCACGTATATGGGATCAGATACAATCTCTCTATTGTTCACCTTCATCTTACAGAAGTACGACCCATTGTCTGAGCGCTGCACACTGGCTATGCTTC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------', 'AAGCCTTTTGGTGGGAATGGGATGTGGAAGGTGCGGCAGAGGGGTAATAAGATGGCGATGCTGCCAAGGACACTGTGGAAGGTGGCACCTCTTAGCAACACTTAGGCAATAAAGGCCCCATAGTGGAGCAAATGCTTAGCATGCACAATCCTCTGGGCTCGTGCACACACGCACATGGGCACATGTGCACACACACACACACACCAAGAGCCCATTATTACATCATTTTCTAAAGTAAAAATGAGAATTGTCTTGTAAAATTCCAACACTAATGGATCCATAAGGTTTACAGAATTATAAACAGACAGACCAACCCCCAGAGTGACAGACCAAACCCCCAGAGTGTCATTTAGGAGACATGTGACACAGGCTCTACCCTGTTCTCCGGCAACAGGATATGGCTTTGGGCTCACCTTGAACTTCCACGTATATGGGATCAGATACAATCTCTCTATTGTTCACCTTCATCTTACAGAAGTACGACCCATTGTCTGAGCGCTGCACACTGGCTATGCTTCAAAGAGAACACAAAAAGAAATTTGCAGTGACTATCTTTTGAGTCCCCATTATAGAAATAGAAGATCCTTCAACACACTTATCATGTGGTTAACTTTTTGTGTCAACATGGCCAGGCTGTAGTACTTGGTGGTCTACATGCTGCTGTAAGAATATGTTCCAAATGCTGTGAACATTTAACTTGGCAACCTTTGAGTAAAGCAGTTGACCCTCCCCAGCATGCGTGGGTCTCCTCTAATCAGCTGCAGACTGAGGTCCCCTGAGGAAGGTCAGCAGCAGTCTGCCAGGGTCTCCAACCAACACCCGGCTGGCCTCAGATTCGTTAATGTTTACTATAGTATGAATTCACTGACCCTTTCCCTCTCTTTCTCTAGTGTGTGCTCGAGAGTACATACGCATGCGGGGGCGCGCGCGCGCGCGCGCACACACACACACACACACACACACACACACGGTTGCTCTTGCACTCACATCTCTTGCTTTCATCCATCTTTGAATCTCTAATACACGTACTATCAGGTGTCTTGCTTACCATGGCGGCTTCTAAA', '|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ', true); +INSERT INTO qc_alignment_regions VALUES (94, 'target-region-rev-72-80', 992, 560, 'TCTGTGACAGGAACCTACTATTATCACTCACGACGGGGCAAAACATGTTAAATTCCTGTGCAAACTGATTATCCCCGGATGAGTCAACACTGTCATGAAGAACTTCCAAAAGGGATGCCTCTGCATCCCATAGGCGACTGTGACAAATTCCGTCTAGAAGCCATTTAGGGATGCTTAAAAAGAGAGAGAAAAAAGACAGTAGCAAATTTCCCCTTAACTTTTAAATAACACCCTCAAAAAGGAAACATCTACTCCTATGCTGACTTTGCCTTCCTTTTCCTGCGTCAGTTAACCCTGAGAGTTCAAATATAAACAAACGCAATTCCCAATGGTACATCTGAACCAGAAGAAATCTGGAATTAATTGCCAAGTATTTTGGGTCCTATTGCAGCTGTTACAAGTGTTTGATTTGGCGAGGGAAGAGAAAAGGCGTTGCATACCAATTTCATGAGCCACAGTGAAGGCTGCATGGAGGCCATCATCTTCAATCACTGCACAGCTGCGCTCCGGAGAACATATGGTCCCAACGTCTGCCATTTCCAGGGTGTCACATGAATGATG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------', 'TCTGTGACAGGAACCTACTATTATCACTCACGACGGGGCAAAACATGTTAAATTCCTGTGCAAACTGATTATCCCCGGATGAGTCAACACTGTCATGAAGAACTTCCAAAAGGGATGCCTCTGCATCCCATAGGCGACTGTGACAAATTCCGTCTAGAAGCCATTTAGGGATGCTTAAAAAGAGAGAGAAAAAAGACAGTAGCAAATTTCCCCTTAACTTTTAAATAACACCCTCAAAAAGGAAACATCTACTCCTATGCTGACTTTGCCTTCCTTTTCCTGCGTCAGTTAACCCTGAGAGTTCAAATATAAACAAACGCAATTCCCAATGGTACATCTGAACCAGAAGAAATCTGGAATTAATTGCCAAGTATTTTGGGTCCTATTGCAGCTGTTACAAGTGTTTGATTTGGCGAGGGAAGAGAAAAGGCGTTGCATACCAATTTCATGAGCCACAGTGAAGGCTGCATGGAGGCCATCATCTTCAATCACTGCACAGCTGCGCTCCGGAGAACATATGGTCCCAACGTCTGCCATTCCCAGGGTGTCACATGAATGATGCCCACATAAATCCTGCCCGGGAGAAAGAAAGAAATCATTAAAATCAATTTACATCCAGAAGGAGCCACCATGGACAGCCACTTGTTCACCCCAAATGGCAAGACTGAGATATGTTTATGGTGTCACCTGCTCAGCGCTGGAGGCCTTCCAAAGACAAATTCAAAGCAGGAACTCTTCTGAGCTACTTTGTAACCCAGAAGCACAGAAGGATAAAGACATTCAATGACATTTTAAAAGAAGCCACGGTTATAGCCTGTTCATTACACTCCAAGCTCTACAGCCCGAACAAAGATTAAGTGCCTACACAAATGTCAAAGGTTACATGTGTTCAATACAGAAGTGCCTAATATTCTGAGCTAAATTCAGACTGAACTTCTTGGAAGAGAGGTCTAATAATTTGTTTTCTGTTAGAGTCAAACTACAATCACACT', '|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| ', true); -- @@ -9595,36 +9604,47 @@ INSERT INTO qc_templates VALUES (200, 'T001', '2012-07-25 14:01:33.89531', 'Mous -- INSERT INTO qc_runs VALUES ('3C41F49A-B6D6-11E1-8038-C8C8F7D1DA10', '2012-07-26 13:23:42.011512', 1, 'test', 200, '0.001', false); +INSERT INTO qc_runs VALUES ('534EE22E-3DBF-22E4-5EF2-1234F5CB64C7', '2012-10-03 11:13:52.960754', 1, 'eucomm-cre', 200, '0.002', true); -- -- Data for Name: qc_run_seq_project; Type: TABLE DATA; Schema: public; Owner: lims2_test_admin -- +INSERT INTO qc_run_seq_project VALUES ('534EE22E-3DBF-22E4-5EF2-1234F5CB64C7', 'PCS05036_A'); -- -- Data for Name: qc_run_seq_wells; Type: TABLE DATA; Schema: public; Owner: lims2_test_admin -- +INSERT INTO qc_run_seq_wells VALUES (70, '534EE22E-3DBF-22E4-5EF2-1234F5CB64C7', 'PCS05036_A_1', 'B02'); +INSERT INTO qc_run_seq_wells VALUES (71, '534EE22E-3DBF-22E4-5EF2-1234F5CB64C7', 'PCS05036_A_1', 'G12'); +INSERT INTO qc_run_seq_wells VALUES (72, '534EE22E-3DBF-22E4-5EF2-1234F5CB64C7', 'PCS05036_A_1', 'A01'); -- -- Data for Name: qc_run_seq_well_qc_seq_read; Type: TABLE DATA; Schema: public; Owner: lims2_test_admin -- +INSERT INTO qc_run_seq_well_qc_seq_read VALUES (70, 'PCS05036_A_1b02.p1kLR'); +INSERT INTO qc_run_seq_well_qc_seq_read VALUES (71, 'PCS05036_A_1g12.p1kLR'); -- -- Data for Name: qc_template_wells; Type: TABLE DATA; Schema: public; Owner: lims2_test_admin -- +INSERT INTO qc_template_wells VALUES (3265, 200, 'A01', 2220); +INSERT INTO qc_template_wells VALUES (3266, 200, 'A02', 2221); -- -- Data for Name: qc_test_results; Type: TABLE DATA; Schema: public; Owner: lims2_test_admin -- +INSERT INTO qc_test_results VALUES (70, '534EE22E-3DBF-22E4-5EF2-1234F5CB64C7', 2221, 2605, false, 70); +INSERT INTO qc_test_results VALUES (71, '534EE22E-3DBF-22E4-5EF2-1234F5CB64C7', 2220, 2836, true, 71); -- @@ -10123,6 +10143,70 @@ INSERT INTO well_dna_status VALUES (1516, true, '', '2012-06-25 00:00:00', 985); -- Data for Name: well_qc_sequencing_result; Type: TABLE DATA; Schema: public; Owner: lims2_test_admin -- +INSERT INTO well_qc_sequencing_result VALUES (977, 'LR,LRR,R3F,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027949', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (978, '', false, false, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2253911', '2010-04-08 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (981, 'LR,LRR,R3F,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=127585', '2008-06-11 00:00:00', 1058); +INSERT INTO well_qc_sequencing_result VALUES (982, 'LR,LRR,R4R,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027837', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (983, 'L1,LR,R2R,R3', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254077', '2010-04-08 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (986, 'LR,PGO,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=1734163', '2010-02-01 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (987, 'LR,LRR,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027687', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (988, 'FCHK,L1,LR,R2R,R3,R4', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2253897', '2010-04-08 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (991, '', false, false, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=1355254', '2009-10-22 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (992, 'LRR', false, false, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027858', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (993, 'LRR', false, false, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027858', '2010-03-22 00:00:00', 722); +INSERT INTO well_qc_sequencing_result VALUES (996, 'LR,LRR,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=54905', '2008-06-11 00:00:00', 1058); +INSERT INTO well_qc_sequencing_result VALUES (997, 'LR,LRR,R3F,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027769', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (998, 'FCHK,R2R,R3', false, false, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254240', '2010-04-08 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1001, 'LR,PGO,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=1727678', '2010-02-01 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1002, 'Z1,Z2', false, false, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027659', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (1003, 'L1,NF,R2R,R3,R4', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2188402', '2010-03-25 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1006, 'LR,LRR,R3F,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=7271', '2008-06-11 00:00:00', 1058); +INSERT INTO well_qc_sequencing_result VALUES (1007, 'LR,LRR,R4R,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2028001', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (1008, 'FCHK,L1,LR,R2R,R3', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254328', '2010-04-08 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1011, 'LR,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=1375329', '2009-11-05 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1012, 'R3F,Z1,Z2', false, false, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2028016', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (1013, '', false, false, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254012', '2010-04-08 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1016, 'LR,LRR,R3F,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=362901', '2008-07-28 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1017, '', false, false, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027673', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (1018, '', false, false, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027673', '2010-03-22 00:00:00', 722); +INSERT INTO well_qc_sequencing_result VALUES (1021, '', false, false, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=1378660', '2009-11-05 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1022, 'LR,LRR,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027928', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (1023, 'L1,LR,R2R,R3,R4', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254180', '2010-04-08 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1026, 'LR,LRR,R3F,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=7507', '2008-06-11 00:00:00', 1058); +INSERT INTO well_qc_sequencing_result VALUES (1027, 'LR,LRR,R3F,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027921', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (1028, 'FCHK,L1,LR,R2R,R3,R4', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2253862', '2010-04-08 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1031, 'LR,PGO,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=1795332', '2010-02-15 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1032, 'LR,LRR,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027755', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (1033, 'L1,LR,R2R,R3,R4', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254379', '2010-04-08 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1036, '', false, false, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=1411324', '2010-02-15 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1037, 'LR,LRR,R3F,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2028229', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (1038, 'L1,LR,R2R,R3,R4', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254028', '2010-04-08 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1041, 'LR,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=1352499', '2009-10-22 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1042, 'LR,LRR,R3F,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2028075', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (1043, 'FCHK,L1,LR,R2R,R3,R4', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254113', '2010-04-08 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1046, 'LR,PGO,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=1790832', '2010-02-15 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1047, 'LR,LRR,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027726', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (1048, 'L1,LR,R3,R4', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254416', '2010-04-08 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1052, 'LR,LRR,R3F,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2028152', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (1053, '', false, false, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254451', '2010-04-08 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1056, 'LR,LRR,R3F,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=7879', '2008-06-11 00:00:00', 1058); +INSERT INTO well_qc_sequencing_result VALUES (1057, 'LR,LRR,R3F,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027851', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (1058, '', false, false, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254169', '2010-04-08 00:00:00', 751); 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+INSERT INTO well_qc_sequencing_result VALUES (1072, 'LR,LRR,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027963', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (1073, 'FCHK,L1,LR,R2R,R3,R4', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254092', '2010-04-08 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1076, 'LR,LRR,R3F,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=7436', '2008-06-11 00:00:00', 1058); +INSERT INTO well_qc_sequencing_result VALUES (1077, 'LR,LRR,R3F,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027638', '2010-03-15 00:00:00', 953); +INSERT INTO well_qc_sequencing_result VALUES (1078, 'FCHK,L1,LR,R2R,R3,R4', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254277', '2010-04-08 00:00:00', 751); +INSERT INTO well_qc_sequencing_result VALUES (1081, 'LR,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=1815036', '2010-12-09 00:00:00', 1058); 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-INSERT INTO well_qc_sequencing_result VALUES (1073, 'FCHK,L1,LR,R2R,R3,R4', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254092', '2010-04-08 00:00:00', 751); -INSERT INTO well_qc_sequencing_result VALUES (1076, 'LR,LRR,R3F,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=7436', '2008-06-11 00:00:00', 1058); -INSERT INTO well_qc_sequencing_result VALUES (1077, 'LR,LRR,R3F,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027638', '2010-03-15 00:00:00', 953); -INSERT INTO well_qc_sequencing_result VALUES (1078, 'FCHK,L1,LR,R2R,R3,R4', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254277', '2010-04-08 00:00:00', 751); -INSERT INTO well_qc_sequencing_result VALUES (1081, 'LR,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=1815036', '2010-12-09 00:00:00', 1058); -INSERT INTO well_qc_sequencing_result VALUES (1082, 'LR,LRR,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027680', '2010-03-15 00:00:00', 953); -INSERT INTO well_qc_sequencing_result VALUES (1083, 'FCHK,L1,LR,R2R,R3,R4', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254284', '2010-04-08 00:00:00', 751); -INSERT INTO well_qc_sequencing_result VALUES (1086, 'LR', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=1374309', '2009-11-05 00:00:00', 751); INSERT INTO well_qc_sequencing_result VALUES (1087, 'LR,LRR,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2028043', '2010-03-15 00:00:00', 953); INSERT INTO well_qc_sequencing_result VALUES (1088, 'L1,LR,R2R,R3,R4', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2254225', '2010-04-08 00:00:00', 751); INSERT INTO well_qc_sequencing_result VALUES (1092, 'LR,LRR,R3F,R4R,Z1,Z2', false, true, 'http://www.sanger.ac.uk/htgt/qc/qctest_result_view?qctest_result_id=2027908', '2010-03-15 00:00:00', 953); From e8b1ed9db2284cab522a964c40801f92c93e51de Mon Sep 17 00:00:00 2001 From: Sajith Perera Date: Fri, 5 Oct 2012 11:29:04 +0100 Subject: [PATCH 2/7] bugfix, check file format exists --- lib/LIMS2/Model/Util/QCResults.pm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/lib/LIMS2/Model/Util/QCResults.pm b/lib/LIMS2/Model/Util/QCResults.pm index 02fd9b0f0e..83b00ebd04 100644 --- a/lib/LIMS2/Model/Util/QCResults.pm +++ b/lib/LIMS2/Model/Util/QCResults.pm @@ -20,6 +20,7 @@ use Sub::Exporter -setup => { use Log::Log4perl qw( :easy ); use Const::Fast; use Bio::SeqIO; +use IO::String; use List::Util qw(sum); use List::MoreUtils qw(uniq); use LIMS2::Exception::Validation; @@ -202,7 +203,7 @@ sub _validated_download_seq_params { $format =~ s/^\s+//; $format =~ s/\s+$//; $format = lc($format); - if ( $SUFFIX_FOR{$format} ) { + if ( exists $SUFFIX_FOR{$format} ) { $params{format} = $format; } } From b0678b7932cad133fcefed88fb588b9b7cbc4c6f Mon Sep 17 00:00:00 2001 From: Sajith Perera Date: Fri, 5 Oct 2012 11:48:23 +0100 Subject: [PATCH 3/7] add tests for retrieval of qc run results --- t/50-model-plugin-qc.t | 82 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 82 insertions(+) diff --git a/t/50-model-plugin-qc.t b/t/50-model-plugin-qc.t index a75d76cc98..cdf92f5c62 100755 --- a/t/50-model-plugin-qc.t +++ b/t/50-model-plugin-qc.t @@ -158,4 +158,86 @@ throws_ok { model->delete_qc_template( { id => $id } ) } qr/Template \d+ has been used in one or more QC runs, so cannot be deleted/; +note( "Testing Qc Run Retrieval" ); + +{ + ok my ($qc_runs_data) = model->retrieve_qc_runs( { species => 'Mouse' } ), + 'Can retrieve all qc runs'; + is scalar( @{$qc_runs_data} ), 2, '.. we have 2 qc runs'; + + ok my ($qc_runs_profile_data) + = model->retrieve_qc_runs( { species => 'Mouse', profile => 'eucomm-post-cre' } ), + 'Can retrieve all qc runs with specific profile'; + is scalar( @{$qc_runs_profile_data} ), 1, '.. we have no qc runs with specfied profile'; + + ok my $qc_run = model->retrieve_qc_run( { id => '687EE35E-9DBF-11E1-8EF3-9484F3CB94C8' } ) + , 'can retrieve single Qc Run'; +} + +note ( 'Qc Run Seq Well Retrieval' ); + +{ + ok my $qc_seq_well = model->retrieve_qc_run_seq_well( + { qc_run_id => '687EE35E-9DBF-11E1-8EF3-9484F3CB94C8', + plate_name => 'PCS04026_A_1', + well_name => 'B02' + } + ), 'can retrieve qc run seq well'; + + isa_ok $qc_seq_well, 'LIMS2::Model::Schema::Result::QcRunSeqWell'; + + is $qc_seq_well->qc_run_id, '687EE35E-9DBF-11E1-8EF3-9484F3CB94C8', '..seq well belongs to correct Qc Run'; +} + +note ( 'Qc Run Results Retrieval' ); + +{ + lives_ok { + model->qc_run_results( { qc_run_id => '687EE35E-9DBF-11E1-8EF3-9484F3CB94C8' } ), + } 'can retrieve Qc Run results'; + + lives_ok { + model->qc_run_summary_results( { qc_run_id => '687EE35E-9DBF-11E1-8EF3-9484F3CB94C8' } ) + } 'can retrieve Qc Run summary results'; + + lives_ok { + model->qc_run_seq_well_results( + { qc_run_id => '687EE35E-9DBF-11E1-8EF3-9484F3CB94C8', + plate_name => 'PCS04026_A_1', + well_name => 'B02' + } + ) + } 'can retrieve qc run seq well results'; + + lives_ok { + model->qc_alignment_result( { qc_alignment_id => 93 } ) + } 'can get qc alignment result'; + + lives_ok { + model->qc_seq_read_sequences( + { qc_run_id => '687EE35E-9DBF-11E1-8EF3-9484F3CB94C8', + plate_name => 'PCS04026_A_1', + well_name => 'B02', + format => 'fasta', + } + ) + } 'can retrieve qc seq read sequences'; + + lives_ok { + model->qc_eng_seq_sequence( + { format => 'fasta', + qc_test_result_id => 70, + } + ) + } 'can retrieve qc eng seq sequence'; + +} + +note ( "Testing List Profiles" ); + +{ + ok my $profiles = model->list_profiles(), 'list_profiles ok'; + is_deeply $profiles, [ 'eucomm-cre', 'eucomm-post-cre', 'test' ], '.. profile list is correct'; +} + done_testing(); From f1099a3406588d8389df68192d2cc0a340d03225 Mon Sep 17 00:00:00 2001 From: Sajith Perera Date: Tue, 9 Oct 2012 08:39:19 +0100 Subject: [PATCH 4/7] add tests for QcResults Util module --- t/40-model-util-qcresults.t | 214 ++++++++++++++++++++++++++++++++++++ 1 file changed, 214 insertions(+) create mode 100644 t/40-model-util-qcresults.t diff --git a/t/40-model-util-qcresults.t b/t/40-model-util-qcresults.t new file mode 100644 index 0000000000..40832a0647 --- /dev/null +++ b/t/40-model-util-qcresults.t @@ -0,0 +1,214 @@ +#!/usr/bin/env perl + +use strict; +use warnings FATAL => 'all'; + +BEGIN { + use Log::Log4perl qw( :easy ); + Log::Log4perl->easy_init($FATAL); +} + +use LIMS2::Test; +use Test::Most; +use Try::Tiny; +use IO::File; + +BEGIN { + use_ok( + 'LIMS2::Model::Util::QCResults', qw( + retrieve_qc_run_results + retrieve_qc_run_summary_results + retrieve_qc_run_seq_well_results + retrieve_qc_alignment_results + retrieve_qc_seq_read_sequences + retrieve_qc_eng_seq_sequence + build_qc_runs_search_params + ) + ); +} + +note('Test retrieve_qc_run_results'); +{ + ok my $qc_run = model->retrieve_qc_run( { id => '534EE22E-3DBF-22E4-5EF2-1234F5CB64C7' } ), + 'retrieve qc run'; + + ok my $qc_run_results = retrieve_qc_run_results($qc_run), 'retrieve qc run results'; + + for my $result ( @{$qc_run_results} ) { + is $result->{LR_pass}, 1, 'result has correct LR pass value' if exists $result->{LR_pass}; + is $result->{design_id}, 372441, 'result has correct design_id' + if exists $result->{design_id}; + is $result->{plate_name}, 'PCS05036_A_1', 'result has correct plate name'; + } + +} + +note('Test retrieve_qc_run_summary_results'); +{ + ok my $qc_run = model->retrieve_qc_run( { id => '534EE22E-3DBF-22E4-5EF2-1234F5CB64C7' } ), + 'retrieve qc run'; + + ok my $qc_run_summary_results = retrieve_qc_run_summary_results($qc_run), + 'retrieve qc run summary results'; + my $result = $qc_run_summary_results->[0]; + + is $result->{design_id}, 372441, '.. correct design_id'; + is $result->{valid_primers}, 'LR', '.. correct valid primer'; + is $result->{pass}, 1, '..correct pass level'; + +} + +note('Test retrieve_qc_run_seq_well_results'); +{ + ok my $seq_well = model->retrieve_qc_run_seq_well( + { qc_run_id => '534EE22E-3DBF-22E4-5EF2-1234F5CB64C7', + plate_name => 'PCS05036_A_1', + well_name => 'B02', + } + ), + 'retrieve qc run seq well'; + + ok my ( $seq_reads, $qc_seq_well_results ) = retrieve_qc_run_seq_well_results($seq_well), + 'can retrieve qc run seq well results'; + + for my $seq_read ( @{$seq_reads} ) { + isa_ok $seq_read, 'LIMS2::Model::Schema::Result::QcSeqRead'; + } + + my $result = $qc_seq_well_results->[0]; + is $result->{design_id}, 372441, '.. correct design id'; + is $result->{score}, 2605, '.. correct score'; + is $result->{pass}, 0, '.. correct pass value'; + + ok my $seq_well2 = model->retrieve_qc_run_seq_well( + { qc_run_id => '534EE22E-3DBF-22E4-5EF2-1234F5CB64C7', + plate_name => 'PCS05036_A_1', + well_name => 'A01', + } + ), + 'retrieve qc run seq well'; + + throws_ok { + retrieve_qc_run_seq_well_results($seq_well2); + } + 'LIMS2::Exception::Validation', 'throws error if seq well has no seq reads'; + +} + +note('Test retrieve_qc_alignment_results'); +{ + ok my $qc_alignment = model->retrieve( 'QcAlignment' => { 'me.id' => 93 } ), + 'retrieve qc alignment'; + + ok my $result = retrieve_qc_alignment_results( model->eng_seq_builder, $qc_alignment ), + 'can retrieve qc alignment results'; + + is $result->{target}, '372441#L1L2_Bact_P#L3L4_pD223_DTA_T_spec', '.. correct target'; + is $result->{query}, 'PCS05036_A_1b02.p1kLR', '.. correct query'; + +} + +note('Test retrieve_qc_seq_read_sequences'); +{ + ok my $seq_well = model->retrieve_qc_run_seq_well( + { qc_run_id => '534EE22E-3DBF-22E4-5EF2-1234F5CB64C7', + plate_name => 'PCS05036_A_1', + well_name => 'B02', + } + ), + 'retrieve qc run seq well'; + + ok my ( $filename, $seq ) = retrieve_qc_seq_read_sequences( $seq_well, 'fasta' ), + 'can retrieve qc seq read sequences'; + + is $filename, 'seq_reads_PCS05036_A_1B02.fasta', '.. correct filename'; + like $seq, qr/>PCS05036_A_1b02\.p1kLR/, '..seq looks correct'; + + ok my ( $other_filename, $other_seq ) = retrieve_qc_seq_read_sequences( $seq_well, 'blah' ), + 'retrieve qc seq read sequences with invalid format'; + + is $other_filename, 'seq_reads_PCS05036_A_1B02.gbk', '.. defaults to genbank file'; + + ok my $seq_well2 = model->retrieve_qc_run_seq_well( + { qc_run_id => '534EE22E-3DBF-22E4-5EF2-1234F5CB64C7', + plate_name => 'PCS05036_A_1', + well_name => 'A01', + } + ), + 'retrieve qc run seq well'; + + throws_ok { + retrieve_qc_seq_read_sequences($seq_well2); + } + 'LIMS2::Exception::Validation', 'throws error if seq well has no seq reads'; +} + +note('Test retrieve_qc_eng_seq_sequence'); +{ + ok my $qc_test_result = model->retrieve( 'QcTestResult' => { id => 70 } ), + 'can retrive qc test result'; + + ok my ( $filename, $seq ) + = retrieve_qc_eng_seq_sequence( model->eng_seq_builder, $qc_test_result, 'fasta' ), + 'can retrieve qc eng seq sequence'; + + is $filename, '372441#L1L2_Bact_P#L3L4_pD223_DTA_T_spec.fasta', '.. correct filename'; + like $seq, qr/>372441#L1L2_Bact_P#L3L4_pD223_DTA_T_spec/, '..seq looks correct'; + + ok my ( $other_filename, $other_seq ) + = retrieve_qc_eng_seq_sequence( model->eng_seq_builder, $qc_test_result ), + 'retrieve qc seq read sequences with no format'; + + is $other_filename, '372441#L1L2_Bact_P#L3L4_pD223_DTA_T_spec.gbk', + '.. defaults to genbank file'; +} + +note('Test build_qc_runs_search_params'); +{ + + ok my $params_show_all + = build_qc_runs_search_params( { show_all => 1, species_id => 'Mouse' } ), + 'can build qc runs search params'; + + is_deeply $params_show_all, + { 'me.upload_complete' => 't', 'qc_seq_project.species_id' => 'Mouse' }, + '.. search params correct with show_all option set'; + + ok my $params_seq_project + = build_qc_runs_search_params( { sequencing_project => 1, species_id => 'Mouse' } ), + 'can build qc runs search params'; + + is_deeply $params_seq_project, + { + 'me.upload_complete' => 't', + 'qc_seq_project.species_id' => 'Mouse', + 'qc_run_seq_projects.qc_seq_project_id' => 1 + }, + '.. search params correct with sequencing project specified'; + + ok my $params_template + = build_qc_runs_search_params( { template_plate => 'test', species_id => 'Mouse' } ), + 'can build qc runs search params'; + + is_deeply $params_template, + { + 'me.upload_complete' => 't', + 'qc_seq_project.species_id' => 'Mouse', + 'qc_template.name' => 'test' + }, + '.. search params correct with template plate specified'; + + ok my $params_profile + = build_qc_runs_search_params( { profile => 'foo', species_id => 'Mouse' } ), + 'can build qc runs search params'; + + is_deeply $params_profile, + { + 'me.upload_complete' => 't', + 'qc_seq_project.species_id' => 'Mouse', + 'me.profile' => 'foo' + }, + '.. search params correct with profile specified'; +} + +done_testing(); From c1f74f3b78f02c7a0740a79552b5837984f8ab1b Mon Sep 17 00:00:00 2001 From: Sajith Perera Date: Thu, 11 Oct 2012 09:11:38 +0100 Subject: [PATCH 5/7] REST authentication no longer done using http basic auth, pass in username and password through request params --- lib/LIMS2/WebApp/Controller/API.pm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/lib/LIMS2/WebApp/Controller/API.pm b/lib/LIMS2/WebApp/Controller/API.pm index acf0dd0841..dee6dfc5f7 100644 --- a/lib/LIMS2/WebApp/Controller/API.pm +++ b/lib/LIMS2/WebApp/Controller/API.pm @@ -27,7 +27,11 @@ sub auto : Private { # further authentication, and provides an HTTP basic auth fallback # for programmatic access unless ( $c->user_exists ) { - $c->authenticate( { realm => 'LIMS2 API' }, 'basic' ); + my $username = delete $c->req->parameters->{ 'username' }; + my $password = delete $c->req->parameters->{ 'password' }; + return 1 unless ( $username && $password ); + + $c->authenticate( { name => lc($username), password => $password, active => 1 } ); } if ( ! $c->session->{selected_species} ) { From 42e9cb2ef30fda972fbb3d4f8529d119eca10296 Mon Sep 17 00:00:00 2001 From: Sajith Perera Date: Thu, 11 Oct 2012 10:45:40 +0100 Subject: [PATCH 6/7] get authenticated mech through login form, not thorugh HTTP Basic Auth --- lib/LIMS2/Test.pm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/lib/LIMS2/Test.pm b/lib/LIMS2/Test.pm index 5717d1fd5e..4900515157 100644 --- a/lib/LIMS2/Test.pm +++ b/lib/LIMS2/Test.pm @@ -47,7 +47,15 @@ sub unauthenticated_mech { sub mech { my $mech = unauthenticated_mech(); - $mech->credentials( $TEST_USER, $TEST_PASSWD ); + + $mech->get( '/login' ); + + $mech->submit_form( + form_name => 'login_form', + fields => { username => $TEST_USER, password => $TEST_PASSWD }, + button => 'login' + ); + return $mech; } From 85981eab5abe5b932097292b657fbf69f1e98243 Mon Sep 17 00:00:00 2001 From: Sajith Perera Date: Thu, 11 Oct 2012 11:23:08 +0100 Subject: [PATCH 7/7] use pre authenticated mech for tests --- t/80-change_password.t | 9 +-------- t/80-dna_status_upload.t | 9 +-------- t/80-plate_upload.t | 9 +-------- t/80-plate_view.t | 9 +-------- 4 files changed, 4 insertions(+), 32 deletions(-) diff --git a/t/80-change_password.t b/t/80-change_password.t index d01ddb9f37..ad84c9811a 100644 --- a/t/80-change_password.t +++ b/t/80-change_password.t @@ -6,14 +6,7 @@ use warnings FATAL => 'all'; use LIMS2::Test; use Test::Most; -my $mech = unauthenticated_mech(); - -$mech->get_ok( '/login' ); -ok $mech->submit_form( - form_name => 'login_form', - fields => { username => 'test_user@example.org', password => 'ahdooS1e' }, - button => 'login' -), 'Login with correct username and password'; +my $mech = mech(); { note( "Don't specify new password" ); diff --git a/t/80-dna_status_upload.t b/t/80-dna_status_upload.t index 7474c5765f..d996c11e3b 100755 --- a/t/80-dna_status_upload.t +++ b/t/80-dna_status_upload.t @@ -7,14 +7,7 @@ use LIMS2::Test; use Test::Most; use File::Temp ':seekable'; -my $mech = unauthenticated_mech(); - -$mech->get_ok( '/login' ); -ok $mech->submit_form( - form_name => 'login_form', - fields => { username => 'test_user@example.org', password => 'ahdooS1e' }, - button => 'login' -), 'Login with correct username and password'; +my $mech = mech(); { note( "No well data file set" ); diff --git a/t/80-plate_upload.t b/t/80-plate_upload.t index 6080cf44c4..d963494598 100644 --- a/t/80-plate_upload.t +++ b/t/80-plate_upload.t @@ -7,14 +7,7 @@ use LIMS2::Test; use Test::Most; use File::Temp ':seekable'; -my $mech = unauthenticated_mech(); - -$mech->get_ok( '/login' ); -ok $mech->submit_form( - form_name => 'login_form', - fields => { username => 'test_user@example.org', password => 'ahdooS1e' }, - button => 'login' -), 'Login with correct username and password'; +my $mech = mech(); { note( "set undef process type" ); diff --git a/t/80-plate_view.t b/t/80-plate_view.t index 4dfbe3b21a..d0df0d16e1 100644 --- a/t/80-plate_view.t +++ b/t/80-plate_view.t @@ -6,14 +6,7 @@ use warnings FATAL => 'all'; use LIMS2::Test; use Test::Most; -my $mech = unauthenticated_mech(); - -$mech->get_ok( '/login' ); -ok $mech->submit_form( - form_name => 'login_form', - fields => { username => 'test_user@example.org', password => 'ahdooS1e' }, - button => 'login' -), 'Login with correct username and password'; +my $mech = mech(); my $plate_without_children = model->retrieve_plate( { name => 'FFP0001' } ); my $plate_with_children = model->retrieve_plate( { name => 'PCS00097_A' } );