Merge pull request #1067 from Ferrisx4/7.x-3.x

Fix for #1064 - Chado Upgrade 1.2-1.3 SQL

README.md

@@ -52,7 +52,7 @@ are available in Tripal v3.
   * Drupal contributed modules: 
     * [Views](http://drupal.org/project/views)
     * [Entity API](http://drupal.org/project/entity)
-* PostgreSQL
+* PostgreSQL 9.3 or higher (9.5 required for Chado 1.2 to 1.3 upgrade)
 * PHP 5.5+
 * UNIX/Linux
 

docs/user_guide/install_tripal/server_setup.rst

@@ -6,7 +6,7 @@ Before installation of Tripal, a web server must be configured and ready, and Tr
 1. A UNIX-based server (e.g. Ubuntu Linux or CentOS are the most popularly used).
 2. Web server software. The `Apache web server <https://httpd.apache.org/>`_ is most commonly used.
 3. `PHP <http://php.net/>`_ version 5.6 or higher (the most recent version is recommended).
-4. `PostgreSQL <https://www.postgresql.org/>`_ 9.3 or higher
+4. `PostgreSQL <https://www.postgresql.org/>`_ 9.3 or higher (9.5 required for Chado 1.2 to 1.3 upgrade)
 5. `Drush <http://www.drush.org/en/master/>`_ 7 or higher
 6. `Drupal <https://www.drupal.org/>`_ 7.
 

tripal_chado/chado_schema/default_schema-1.2-1.3-diff.sql

@@ -3010,12 +3010,12 @@ NOT have the specified term.';
 -- Name: analysis_cvterm_analysis_cvterm_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE analysis_cvterm_analysis_cvterm_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS analysis_cvterm_analysis_cvterm_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 
 --
@@ -3057,12 +3057,12 @@ accessions should set this field to false';
 -- Name: analysis_dbxref_analysis_dbxref_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE analysis_dbxref_analysis_dbxref_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS analysis_dbxref_analysis_dbxref_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 
 --
@@ -3095,12 +3095,12 @@ COMMENT ON TABLE analysis_pub IS 'Provenance. Linking table between analyses and
 -- Name: analysis_pub_analysis_pub_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE analysis_pub_analysis_pub_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS analysis_pub_analysis_pub_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 
 
@@ -3171,12 +3171,12 @@ important where rank is used to order these; starts from zero.';
 -- Name: analysis_relationship_analysis_relationship_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE analysis_relationship_analysis_relationship_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS analysis_relationship_analysis_relationship_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 
 --
@@ -3492,12 +3492,12 @@ relational schema, and is completely extensible.';
 -- Name: contactprop_contactprop_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE contactprop_contactprop_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS contactprop_contactprop_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 
 --
@@ -3589,12 +3589,12 @@ the combination of db_id, rank, and type_id. Multivalued property-value pairs mu
 -- Name: dbprop_dbprop_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE dbprop_dbprop_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS dbprop_dbprop_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: dbprop_dbprop_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -3747,12 +3747,12 @@ person or organization responsible for discovery or that can provide more inform
 -- Name: feature_contact_feature_contact_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE feature_contact_feature_contact_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS feature_contact_feature_contact_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: feature_contact_feature_contact_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -3920,12 +3920,12 @@ that can provide more information on a particular featuremap.';
 -- Name: featuremap_contact_featuremap_contact_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE featuremap_contact_featuremap_contact_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS featuremap_contact_featuremap_contact_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: featuremap_contact_featuremap_contact_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -3949,12 +3949,12 @@ CREATE TABLE IF NOT EXISTS featuremap_dbxref (
 -- Name: featuremap_dbxref_featuremap_dbxref_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE featuremap_dbxref_featuremap_dbxref_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS featuremap_dbxref_featuremap_dbxref_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: featuremap_dbxref_featuremap_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -3984,12 +3984,12 @@ COMMENT ON TABLE featuremap_organism IS 'Links a featuremap to the organism(s) w
 -- Name: featuremap_organism_featuremap_organism_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE featuremap_organism_featuremap_organism_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS featuremap_organism_featuremap_organism_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: featuremap_organism_featuremap_organism_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -4031,12 +4031,12 @@ relational schema, and is completely extensible.';
 -- Name: featuremapprop_featuremapprop_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE featuremapprop_featuremapprop_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS featuremapprop_featuremapprop_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 
 --
@@ -4081,12 +4081,12 @@ COMMENT ON TABLE featureposprop IS 'Property or attribute of a featurepos record
 -- Name: featureposprop_featureposprop_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE featureposprop_featureposprop_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS featureposprop_featureposprop_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: featureposprop_featureposprop_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -4171,12 +4171,12 @@ COMMENT ON TABLE library_contact IS 'Links contact(s) with a library.  Used to i
 -- Name: library_contact_library_contact_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE library_contact_library_contact_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS library_contact_library_contact_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: library_contact_library_contact_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -4231,12 +4231,12 @@ COMMENT ON TABLE library_expression IS 'Links a library to expression statements
 -- Name: library_expression_library_expression_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE library_expression_library_expression_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS library_expression_library_expression_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: library_expression_library_expression_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -4268,12 +4268,12 @@ COMMENT ON TABLE library_expressionprop IS 'Attributes of a library_expression r
 -- Name: library_expressionprop_library_expressionprop_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE library_expressionprop_library_expressionprop_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS library_expressionprop_library_expressionprop_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: library_expressionprop_library_expressionprop_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -4313,12 +4313,12 @@ COMMENT ON TABLE library_featureprop IS 'Attributes of a library_feature relatio
 -- Name: library_featureprop_library_featureprop_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE library_featureprop_library_featureprop_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS library_featureprop_library_featureprop_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: library_featureprop_library_featureprop_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -4364,12 +4364,12 @@ COMMENT ON TABLE library_relationship IS 'Relationships between libraries.';
 -- Name: library_relationship_library_relationship_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE library_relationship_library_relationship_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS library_relationship_library_relationship_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 
 --
@@ -4400,12 +4400,12 @@ COMMENT ON TABLE library_relationship_pub IS 'Provenance of library_relationship
 -- Name: library_relationship_pub_library_relationship_pub_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE library_relationship_pub_library_relationship_pub_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS library_relationship_pub_library_relationship_pub_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: library_relationship_pub_library_relationship_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -4518,12 +4518,12 @@ COMMENT ON TABLE nd_experiment_analysis IS 'An analysis that is used in an exper
 -- Name: nd_experiment_analysis_nd_experiment_analysis_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE nd_experiment_analysis_nd_experiment_analysis_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS nd_experiment_analysis_nd_experiment_analysis_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: nd_experiment_analysis_nd_experiment_analysis_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -4774,12 +4774,12 @@ the default 0 value should be used';
 -- Name: organism_cvterm_organism_cvterm_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE organism_cvterm_organism_cvterm_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS organism_cvterm_organism_cvterm_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: organism_cvterm_organism_cvterm_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -4843,12 +4843,12 @@ the default 0 value should be used';
 -- Name: organism_cvtermprop_organism_cvtermprop_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE organism_cvtermprop_organism_cvtermprop_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS organism_cvtermprop_organism_cvtermprop_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: organism_cvtermprop_organism_cvtermprop_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -4893,12 +4893,12 @@ COMMENT ON TABLE organism_pub IS 'Attribution for organism.';
 -- Name: organism_pub_organism_pub_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE organism_pub_organism_pub_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS organism_pub_organism_pub_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: organism_pub_organism_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -4933,12 +4933,12 @@ relatinoships should be housed in the phylogeny tables.';
 -- Name: organism_relationship_organism_relationship_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE organism_relationship_organism_relationship_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS organism_relationship_organism_relationship_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: organism_relationship_organism_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -4978,12 +4978,12 @@ COMMENT ON TABLE organismprop_pub IS 'Attribution for organismprop.';
 -- Name: organismprop_pub_organismprop_pub_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE organismprop_pub_organismprop_pub_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS organismprop_pub_organismprop_pub_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: organismprop_pub_organismprop_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -5077,12 +5077,12 @@ COMMENT ON TABLE phenotypeprop IS 'A phenotype can have any number of slot-value
 -- Name: phenotypeprop_phenotypeprop_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE phenotypeprop_phenotypeprop_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS phenotypeprop_phenotypeprop_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: phenotypeprop_phenotypeprop_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -5233,12 +5233,12 @@ default 0 value should be used';
 -- Name: phylotreeprop_phylotreeprop_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE phylotreeprop_phylotreeprop_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS phylotreeprop_phylotreeprop_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 
 --
@@ -5287,12 +5287,12 @@ The rank column can be used to specify a simple ordering in which analyses were
 -- Name: project_analysis_project_analysis_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE project_analysis_project_analysis_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS project_analysis_project_analysis_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 
 --
@@ -5347,12 +5347,12 @@ COMMENT ON COLUMN project_dbxref.is_current IS 'The is_current boolean indicates
 -- Name: project_dbxref_project_dbxref_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE project_dbxref_project_dbxref_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS project_dbxref_project_dbxref_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: project_dbxref_project_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -5383,12 +5383,12 @@ COMMENT ON TABLE project_feature IS 'This table is intended associate records in
 -- Name: project_feature_project_feature_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE project_feature_project_feature_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS project_feature_project_feature_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: project_feature_project_feature_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -5453,12 +5453,12 @@ COMMENT ON TABLE project_stock IS 'This table is intended associate records in t
 -- Name: project_stock_project_stock_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE project_stock_project_stock_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS project_stock_project_stock_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 --
 -- Name: projectprop; Type: TABLE; Schema: public; Owner: chado; Tablespace: 
 --
@@ -5537,12 +5537,12 @@ COMMENT ON TABLE pubauthor_contact IS 'An author on a publication may have a cor
 -- Name: pubauthor_contact_pubauthor_contact_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE pubauthor_contact_pubauthor_contact_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS pubauthor_contact_pubauthor_contact_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: pubauthor_contact_pubauthor_contact_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -5660,12 +5660,12 @@ COMMENT ON TABLE stock_feature IS 'Links a stock to a feature.';
 -- Name: stock_feature_stock_feature_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE stock_feature_stock_feature_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS stock_feature_stock_feature_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: stock_feature_stock_feature_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: chado
@@ -5697,12 +5697,12 @@ COMMENT ON TABLE stock_featuremap IS 'Links a featuremap to a stock.';
 -- Name: stock_featuremap_stock_featuremap_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE stock_featuremap_stock_featuremap_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS stock_featuremap_stock_featuremap_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: stock_genotype; Type: TABLE; Schema: public; Owner: chado; Tablespace: 
@@ -5735,12 +5735,12 @@ COMMENT ON TABLE stock_library IS 'Links a stock with a library.';
 -- Name: stock_library_stock_library_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE stock_library_stock_library_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS stock_library_stock_library_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: stock_pub; Type: TABLE; Schema: public; Owner: chado; Tablespace: 
@@ -5815,12 +5815,12 @@ db_id record';
 -- Name: stockcollection_db_stockcollection_db_id_seq; Type: SEQUENCE; Schema: public; Owner: chado
 --
 
----CREATE SEQUENCE stockcollection_db_stockcollection_db_id_seq
----    START WITH 1
----    INCREMENT BY 1
----    NO MINVALUE
----    NO MAXVALUE
----    CACHE 1;
+CREATE SEQUENCE IF NOT EXISTS stockcollection_db_stockcollection_db_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
 
 --
 -- Name: stockcollection_stock; Type: TABLE; Schema: public; Owner: chado; Tablespace: 

tripal_chado/includes/tripal_chado.install.inc

@@ -58,7 +58,7 @@ function tripal_chado_load_form($form, $form_state) {
         'stockcollection_db',
       ]);
       $items = [
-        'PostgreSQL version 9.1 is required to perform this upgrade. If your Tripal
+        'PostgreSQL version 9.5 is required to perform this upgrade. If your Tripal
          site uses an older version please upgrade before proceeding.',
         'A major change between Chado v1.2 and v1.3 is that primary and foreign
          keys were upgraded from integers to big integers. If your site has custom
@@ -501,54 +501,6 @@ function tripal_chado_upgrade_chado_1_2_to_1_3_pre_alter() {
 
     }
   }
-  // Now create the sequences if they don't already exist.
-  $sequences = [
-    'analysis_cvterm_analysis_cvterm_id_seq',
-    'analysis_dbxref_analysis_dbxref_id_seq',
-    'analysis_pub_analysis_pub_id_seq',
-    'analysis_relationship_analysis_relationship_id_seq',
-    'contactprop_contactprop_id_seq',
-    'dbprop_dbprop_id_seq',
-    'feature_contact_feature_contact_id_seq',
-    'featuremap_contact_featuremap_contact_id_seq',
-    'featuremap_dbxref_featuremap_dbxref_id_seq',
-    'featuremap_organism_featuremap_organism_id_seq',
-    'featuremapprop_featuremapprop_id_seq',
-    'featureposprop_featureposprop_id_seq',
-    'library_contact_library_contact_id_seq',
-    'library_expression_library_expression_id_seq',
-    'library_expressionprop_library_expressionprop_id_seq',
-    'library_featureprop_library_featureprop_id_seq',
-    'library_relationship_library_relationship_id_seq',
-    'library_relationship_pub_library_relationship_pub_id_seq',
-    'nd_experiment_analysis_nd_experiment_analysis_id_seq',
-    'organism_cvterm_organism_cvterm_id_seq',
-    'organism_cvtermprop_organism_cvtermprop_id_seq',
-    'organism_pub_organism_pub_id_seq',
-    'organism_relationship_organism_relationship_id_seq',
-    'organismprop_pub_organismprop_pub_id_seq',
-    'phenotypeprop_phenotypeprop_id_seq',
-    'phylotreeprop_phylotreeprop_id_seq',
-    'project_analysis_project_analysis_id_seq',
-    'project_dbxref_project_dbxref_id_seq',
-    'project_feature_project_feature_id_seq',
-    'project_stock_project_stock_id_seq',
-    'pubauthor_contact_pubauthor_contact_id_seq',
-    'stock_feature_stock_feature_id_seq',
-    'stock_featuremap_stock_featuremap_id_seq',
-    'stock_library_stock_library_id_seq',
-    'stockcollection_db_stockcollection_db_id_seq',
-  ];
-  foreach ($sequences as $sequence) {
-
-    // Now add in the sequences if they don't already exist. There is no
-    // PostgreSQL 'CREATE SEQUENCE IF NOT EXIST' so we're forced to do it here
-    // and these create statements were removed from the diff upgrade file.
-    if (!chado_sequence_exists($sequence)) {
-      $sql = "CREATE SEQUENCE {" . $sequence . "} START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1";
-      chado_query($sql);
-    }
-  }
 }
 
 /**