sql table creation added to docker + WIP1 of changes for comex_shared DB...

sql table creation added to docker + WIP1 of changes for comex_shared DB ('luid' = new local id + team_lab more important than org now)

doc/table_specifications.md

@@ -28,21 +28,21 @@ CREATE TABLE scholars (
     home_url             varchar(120),   -- homepage
     pic_url              varchar(120),   -- an alternative to pic_file blob
     pic_file             mediumblob,
-    record_status        varchar(10),
+    record_status        varchar(25),
 
     INDEX luid_index_sch (luid),
     INDEX duid_index_sch (doors_uid),
-    INDEX affs_index_sch (affiliation_id)
+    INDEX affs_index_sch (affiliation_id),
     INDEX country_index_sch (country),
-    INDEX status_index_sch (record_status)
+    INDEX rstatus_index_sch (record_status)
 ) ;
 
 -- affiliations: institutions and labs
 CREATE TABLE affiliations(
     affid               int(15) not null auto_increment,
-    org                 varchar(120) not null,
-    org_type            varchar(50) not null,
-    team_lab            varchar(120),
+    org                 varchar(120),
+    org_type            varchar(50),
+    team_lab            varchar(120) not null,
     org_city            varchar(50),
     INDEX affid_index_affs (affid),
     PRIMARY KEY (affid),

services/db.py

@@ -40,9 +40,9 @@ USER_COLS = [
       ]
 
 ORG_COLS = [
-         ("org",                    True,       120),
-         ("org_type",               True,        50),
-         ("team_lab",              False,       120),
+         ("org",                   False,       120),
+         ("org_type",              False,        50),
+         ("team_lab",               True,       120),
          ("org_city",              False,        50)
     ]
 

setup/dockers/comex2_mysql_server/Dockerfile

+#  mysql server for comex 2
+# --------------------------
+
+FROM mysql
+
+# init script for our db comex_shared (mysql container will run it iff data volume is empty)
+ADD init_comex_shared.sql /docker-entrypoint-initdb.d/

setup/dockers/comex2_mysql_server/init_comex_shared.sql

+/******************************
+** File: init_comex_shared.sql
+** Desc: Creates comex tables
+         => docker-entrypoint-initdb.d
+** Date: 2017-01-19
+*******************************/
+
+CREATE DATABASE comex_shared CHARACTER SET utf8 COLLATE utf8_general_ci ;
+USE comex_shared ;
+CREATE TABLE scholars (
+    -- local uid necessary for users who still have no doors_uid
+    luid                 int(15) not null auto_increment unique primary key,
+    -- doors uid common to all lab's services
+    doors_uid            char(36) not null unique,
+    last_modified_date   char(24) not null,
+    email                varchar(255) not null unique,
+    country              varchar(60) not null,
+    first_name           varchar(30) not null,
+    middle_name          varchar(30),
+    last_name            varchar(50) not null,
+    initials             varchar(7) not null,
+    affiliation_id       int(15) not null,
+    position             varchar(30),            -- eg Director
+    hon_title            varchar(30),            -- eg Doctor
+    interests_text       varchar(1200),
+    gender               char(1),
+    job_looking_date     char(24),       -- null if not looking for a job
+    home_url             varchar(120),   -- homepage
+    pic_url              varchar(120),   -- an alternative to pic_file blob
+    pic_file             mediumblob,
+    record_status        varchar(25),
+
+    INDEX luid_index_sch (luid),
+    INDEX duid_index_sch (doors_uid),
+    INDEX affs_index_sch (affiliation_id),
+    INDEX country_index_sch (country),
+    INDEX rstatus_index_sch (record_status)
+) ;
+
+-- affiliations: institutions and labs
+CREATE TABLE affiliations(
+    affid               int(15) not null auto_increment,
+    org                 varchar(120),
+    org_type            varchar(50),
+    team_lab            varchar(120) not null,
+    org_city            varchar(50),
+    INDEX affid_index_affs (affid),
+    PRIMARY KEY (affid),
+    UNIQUE KEY full_affiliation (org, team_lab, org_city, org_type)
+    -- NB org_type should be entailed by other 3 in business logic
+);
+
+ALTER TABLE scholars ADD FOREIGN KEY (affiliation_id) REFERENCES affiliations(affid) ;
+
+-- keyword/subject terms
+CREATE TABLE keywords(
+    kwid                int(15) not null auto_increment,
+    kwstr               char(50) not null unique,   -- eg 'complex networks'
+    INDEX kwid_index_kws (kwid),
+    INDEX kwstr_index_kws (kwstr),
+    PRIMARY KEY (kwid)
+);
+
+-- relationship scholars <n=n> keywords
+CREATE TABLE sch_kw(
+    uid            int(15) not null,
+    kwid           int(15) not null,
+    INDEX uid_index_schkw (uid),
+    INDEX kwid_index_schkw (kwid),
+    PRIMARY KEY (uid, kwid),
+    FOREIGN KEY (uid)  REFERENCES scholars(luid) ON DELETE CASCADE,
+    FOREIGN KEY (kwid) REFERENCES keywords(kwid)
+);
+
+-- hashtag/workgroup terms
+CREATE TABLE hashtags(
+    htid                int(15) not null auto_increment,
+    htstr               char(50) not null unique,   -- eg '#dataviz'
+    INDEX htid_index_hts (htid),
+    INDEX htstr_index_hts (htstr),
+    PRIMARY KEY (htid)
+);
+
+-- relationship scholars <n=n> hashtags
+CREATE TABLE sch_ht(
+    uid            int(15) not null,
+    htid           int(15) not null,
+    INDEX uid_index_schht (uid),
+    INDEX htid_index_schht (htid),
+    PRIMARY KEY (uid, htid),
+    FOREIGN KEY (uid)  REFERENCES scholars(luid) ON DELETE CASCADE,
+    FOREIGN KEY (htid) REFERENCES hashtags(htid)
+);
+
+-- linked identities (various users' ids on soc. media and research networks)
+-- TODO use this :)
+CREATE TABLE linked_ids(
+    linkid              int(15) not null auto_increment,
+    uid                 int(15) not null,
+    ext_id_type         char(50) not null,   -- eg 'orcid','LinkedIn','Twitter'
+    ext_id              char(50) not null,   -- eg "0000-0002-1825-0097"
+    INDEX uid_index_eids (uid),
+    PRIMARY KEY (linkid),
+    FOREIGN KEY (uid) REFERENCES scholars(luid) ON DELETE CASCADE
+);

setup/dockers/docker-compose.yml

     version: '2'
     services:
 
-      comex_db_test:
-        image: mysql
+      comex_db:
+        image: comex2_mysql_server:latest
+        build: ./comex2_mysql_server
         environment:
          - MYSQL_ROOT_PASSWORD=very-safe-pass
         volumes:
@@ -28,7 +29,7 @@
          # we expose the entire contained nginx
          - "8080:80"
         links:
-         - comex_db_test
+         - comex_db
         volumes:
          # /!\ this uses outside conf to replace :contained conf
          - ../../config:/comex2/config
@@ -38,6 +39,6 @@
             # override values from parametres_comex.ini
             # for a double reason:
             #   - both apps have ENV vals preempt INI vals
-            #   - if we're here (in docker-compose) then by definition the mysql must be coming from comex_db_test container
-            - SQL_HOST=comex_db_test
+            #   - if we're here (in docker-compose) then by definition the mysql must be coming from comex_db container
+            - SQL_HOST=comex_db
             - SQL_PORT=3306