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From: <all...@su...> - 2006-02-28 19:49:05
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Update of /cvsroot/libnelson/java In directory sumo.genetics.ucla.edu:/tmp/cvs-serv26404 Modified Files: gecCel.java Log Message: get new samples first Index: gecCel.java =================================================================== RCS file: /cvsroot/libnelson/java/gecCel.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** gecCel.java 28 Feb 2006 19:37:25 -0000 1.4 --- gecCel.java 28 Feb 2006 19:48:56 -0000 1.5 *************** *** 17,21 **** public class gecCel { public static void main(String[] argv) { ! String SEL_EXP_RUN = "SELECT u.acs_user_id user_id, experiment.experiment_id, run.run_id, sample.sample_id, chip.chip_id, chip.file_id || '.file' file_id FROM sb_users u, gen_experiments experiment, gen_experiment_runs run, gen_experiment_chips sample, gen_chip_files chip, gen_file_types type WHERE run.run_id = sample.run_id AND type.file_type_id = chip.file_type_id AND sample.chip_id = chip.chip_id AND type.file_extension = 'cel' AND experiment.experiment_id = run.experiment_id AND experiment.survey_taker_id = u.user_id"; // String SEL_ANNOT = "SELECT d.sample_id, x.accession FROM gen_annotation_exp_sample_data d, gen_annotation_cvterm c, gen_annotation_dbxref x WHERE d.cell_type_level_id = c.cvterm_id AND c.dbxref_id = x.dbxref_id AND sample_id = ? UNION SELECT d.sample_id, 'null:' || c.name FROM gen_annotation_exp_sample_data d, gen_annotation_cvterm c WHERE d.dev_stage_level_id = c.cvterm_id AND sample_id = ? UNION SELECT d.sample_id, 'null:' || c.name FROM gen_annotation_exp_sample_data d, gen_annotation_cvterm c WHERE d.cell_growth_level_id = c.cvterm_id AND sample_id = ? UNION SELECT d.sample_id, x.accession FROM gen_annotation_exp_sample_ds d, gen_annotation_cvterm c, gen_annotation_dbxref x WHERE d.disease_state_level_id = c.cvterm_id AND c.dbxref_id = x.dbxref_id AND d.sample_id = ? UNION SELECT d.sample_id, x.accession FROM gen_annotation_exp_sample_ed d, gen_annotation_cvterm c, gen_annotation_dbxref x WHERE d.experiment_design_level_id = c.cvterm_id AND c.dbxref_id = x.dbxref! _id AND d.sample_id = ? UNION SELECT d.sample_id, x.accession FROM gen_annotation_exp_sample_pt d, gen_annotation_cvterm c, gen_annotation_dbxref x WHERE d.phenotype_level_id = c.cvterm_id AND c.dbxref_id = x.dbxref_id AND d.sample_id = ? UNION SELECT d.sample_id, x.accession FROM gen_annotation_exp_sample_data d, gen_annotation_cvterm c, gen_annotation_dbxref x WHERE d.rna_level_id = c.cvterm_id AND c.dbxref_id = x.dbxref_id AND sample_id = ?"; --- 17,21 ---- public class gecCel { public static void main(String[] argv) { ! String SEL_EXP_RUN = "SELECT u.acs_user_id user_id, experiment.experiment_id, run.run_id, sample.sample_id, chip.chip_id, chip.file_id || '.file' file_id FROM sb_users u, gen_experiments experiment, gen_experiment_runs run, gen_experiment_chips sample, gen_chip_files chip, gen_file_types type WHERE run.run_id = sample.run_id AND type.file_type_id = chip.file_type_id AND sample.chip_id = chip.chip_id AND type.file_extension = 'cel' AND experiment.experiment_id = run.experiment_id AND experiment.survey_taker_id = u.user_id ORDER BY sample_id DESC"; // String SEL_ANNOT = "SELECT d.sample_id, x.accession FROM gen_annotation_exp_sample_data d, gen_annotation_cvterm c, gen_annotation_dbxref x WHERE d.cell_type_level_id = c.cvterm_id AND c.dbxref_id = x.dbxref_id AND sample_id = ? UNION SELECT d.sample_id, 'null:' || c.name FROM gen_annotation_exp_sample_data d, gen_annotation_cvterm c WHERE d.dev_stage_level_id = c.cvterm_id AND sample_id = ? UNION SELECT d.sample_id, 'null:' || c.name FROM gen_annotation_exp_sample_data d, gen_annotation_cvterm c WHERE d.cell_growth_level_id = c.cvterm_id AND sample_id = ? UNION SELECT d.sample_id, x.accession FROM gen_annotation_exp_sample_ds d, gen_annotation_cvterm c, gen_annotation_dbxref x WHERE d.disease_state_level_id = c.cvterm_id AND c.dbxref_id = x.dbxref_id AND d.sample_id = ? UNION SELECT d.sample_id, x.accession FROM gen_annotation_exp_sample_ed d, gen_annotation_cvterm c, gen_annotation_dbxref x WHERE d.experiment_design_level_id = c.cvterm_id AND c.dbxref_id = x.dbxref! _id AND d.sample_id = ? UNION SELECT d.sample_id, x.accession FROM gen_annotation_exp_sample_pt d, gen_annotation_cvterm c, gen_annotation_dbxref x WHERE d.phenotype_level_id = c.cvterm_id AND c.dbxref_id = x.dbxref_id AND d.sample_id = ? UNION SELECT d.sample_id, x.accession FROM gen_annotation_exp_sample_data d, gen_annotation_cvterm c, gen_annotation_dbxref x WHERE d.rna_level_id = c.cvterm_id AND c.dbxref_id = x.dbxref_id AND sample_id = ?"; |