[Nelsonlab-cmts] libnelson/java gecCel.java,1.2,1.3

[<all...@su...>]

Update of /cvsroot/libnelson/java
In directory sumo.genetics.ucla.edu:/tmp/cvs-serv24819

Modified Files:
	gecCel.java 
Log Message:
add run, user, experiment ids


Index: gecCel.java
===================================================================
RCS file: /cvsroot/libnelson/java/gecCel.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** gecCel.java	17 Feb 2006 01:45:32 -0000	1.2
--- gecCel.java	27 Feb 2006 07:58:07 -0000	1.3
***************
*** 17,22 ****
  public class gecCel {
    public static void main(String[] argv) {
!     String SEL_EXP_RUN = "SELECT sample.sample_id, chip.chip_id, chip.file_id || '.file' file_id FROM gen_experiment_chips sample, gen_chip_files chip, gen_file_types type WHERE type.file_type_id = chip.file_type_id AND sample.chip_id = chip.chip_id AND type.file_extension = 'cel'";
! 
  //    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";
  //    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 = ?";
  
***************
*** 33,41 ****
        System.out.println("<files>");
        while(rs1.next()) {
!         int chip_id   = rs1.getInt("CHIP_ID");
!         String file_id   = rs1.getString("FILE_ID");
!         int sample_id = rs1.getInt("SAMPLE_ID");
  
!         System.out.println("  <file file_id=\"" + file_id + "\" chip_id=\"" + chip_id + "\" sample_id=\"" + sample_id + "\">"); 
  
          stmt2 = conn.prepareStatement(
--- 32,50 ----
        System.out.println("<files>");
        while(rs1.next()) {
!         int chip_id    = rs1.getInt("CHIP_ID");
!         int sample_id  = rs1.getInt("SAMPLE_ID");
!         int run_id     = rs1.getInt("RUN_ID");
!         int exp_id     = rs1.getInt("EXPERIMENT_ID");
!         int user_id    = rs1.getInt("USER_ID");
!         String file_id = rs1.getString("FILE_ID");
  
!         System.out.println("  <file run_id=\""        + run_id        + "\" " +
!                                    "file_id=\""       + file_id       + "\" " +
!                                    "chip_id=\""       + chip_id       + "\" " +
!                                    "sample_id=\""     + sample_id     + "\" " +
!                                    "user_id=\""       + user_id       + "\" " +
!                                    "run_id=\""        + run_id        + "\" " +
!                                    "experiment_id=\"" + exp_id        + "\" " +
!                              ">"); 
  
          stmt2 = conn.prepareStatement(