SP-555 / BIS-366 : openbis.js - delete utilities.js files and use...

SP-555 / BIS-366 : openbis.js - delete utilities.js files and use openbis-action-deferrer.js - change js-test structure to support different versions of servers

SVN: 28962

js-test/servers/dsu/core-plugins/core-plugins.properties

+
+enabled-modules = downloader, illumina-ngs, laneStatistics, ngs-sample-overview-graph

js-test/servers/dsu/core-plugins/laneStatistics

+../../../../deep_sequencing_unit/source/core-plugins/laneStatistics
\ No newline at end of file

js-test/servers/dsu/datastore_server/data/store/deleteDatasetsAlreadyDeletedFromApplicationServerTaskLastSeen

+1060
\ No newline at end of file

js-test/servers/dsu/datastore_server/db/pathinfo_test_js_dsu.sql

+--
+-- PostgreSQL database dump
+--
+
+SET statement_timeout = 0;
+SET client_encoding = 'UTF8';
+SET standard_conforming_strings = on;
+SET check_function_bodies = false;
+SET client_min_messages = warning;
+
+--
+-- Name: plpgsql; Type: EXTENSION; Schema: -; Owner: -
+--
+
+CREATE EXTENSION IF NOT EXISTS plpgsql WITH SCHEMA pg_catalog;
+
+
+--
+-- Name: EXTENSION plpgsql; Type: COMMENT; Schema: -; Owner: -
+--
+
+COMMENT ON EXTENSION plpgsql IS 'PL/pgSQL procedural language';
+
+
+SET search_path = public, pg_catalog;
+
+--
+-- Name: boolean_char; Type: DOMAIN; Schema: public; Owner: -
+--
+
+CREATE DOMAIN boolean_char AS boolean DEFAULT false;
+
+
+--
+-- Name: code; Type: DOMAIN; Schema: public; Owner: -
+--
+
+CREATE DOMAIN code AS character varying(40);
+
+
+--
+-- Name: file_path; Type: DOMAIN; Schema: public; Owner: -
+--
+
+CREATE DOMAIN file_path AS character varying(1000);
+
+
+--
+-- Name: tech_id; Type: DOMAIN; Schema: public; Owner: -
+--
+
+CREATE DOMAIN tech_id AS bigint;
+
+
+--
+-- Name: time_stamp; Type: DOMAIN; Schema: public; Owner: -
+--
+
+CREATE DOMAIN time_stamp AS timestamp with time zone;
+
+
+SET default_tablespace = '';
+
+SET default_with_oids = false;
+
+--
+-- Name: data_set_files; Type: TABLE; Schema: public; Owner: -; Tablespace: 
+--
+
+CREATE TABLE data_set_files (
+    id bigint NOT NULL,
+    dase_id tech_id NOT NULL,
+    parent_id tech_id,
+    relative_path file_path NOT NULL,
+    file_name file_path NOT NULL,
+    size_in_bytes bigint NOT NULL,
+    checksum_crc32 integer,
+    is_directory boolean_char NOT NULL,
+    last_modified time_stamp DEFAULT now() NOT NULL
+);
+
+
+--
+-- Name: data_set_files_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE data_set_files_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
+
+
+--
+-- Name: data_set_files_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE data_set_files_id_seq OWNED BY data_set_files.id;
+
+
+--
+-- Name: data_set_files_id_seq; Type: SEQUENCE SET; Schema: public; Owner: -
+--
+
+SELECT pg_catalog.setval('data_set_files_id_seq', 1, false);
+
+
+--
+-- Name: data_sets; Type: TABLE; Schema: public; Owner: -; Tablespace: 
+--
+
+CREATE TABLE data_sets (
+    id bigint NOT NULL,
+    code code NOT NULL,
+    location file_path NOT NULL
+);
+
+
+--
+-- Name: data_sets_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE data_sets_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
+
+
+--
+-- Name: data_sets_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE data_sets_id_seq OWNED BY data_sets.id;
+
+
+--
+-- Name: data_sets_id_seq; Type: SEQUENCE SET; Schema: public; Owner: -
+--
+
+SELECT pg_catalog.setval('data_sets_id_seq', 1, false);
+
+
+--
+-- Name: database_version_logs; Type: TABLE; Schema: public; Owner: -; Tablespace: 
+--
+
+CREATE TABLE database_version_logs (
+    db_version character varying(4) NOT NULL,
+    module_name character varying(250),
+    run_status character varying(10),
+    run_status_timestamp timestamp without time zone,
+    module_code bytea,
+    run_exception bytea
+);
+
+
+--
+-- Name: events; Type: TABLE; Schema: public; Owner: -; Tablespace: 
+--
+
+CREATE TABLE events (
+    last_seen_deletion_event_id tech_id NOT NULL
+);
+
+
+--
+-- Name: last_feeding_event; Type: TABLE; Schema: public; Owner: -; Tablespace: 
+--
+
+CREATE TABLE last_feeding_event (
+    registration_timestamp time_stamp NOT NULL
+);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE data_set_files ALTER COLUMN id SET DEFAULT nextval('data_set_files_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE data_sets ALTER COLUMN id SET DEFAULT nextval('data_sets_id_seq'::regclass);
+
+
+--
+-- Data for Name: data_set_files; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY data_set_files (id, dase_id, parent_id, relative_path, file_name, size_in_bytes, checksum_crc32, is_directory, last_modified) FROM stdin;
+\.
+
+
+--
+-- Data for Name: data_sets; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY data_sets (id, code, location) FROM stdin;
+\.
+
+
+--
+-- Data for Name: database_version_logs; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY database_version_logs (db_version, module_name, run_status, run_status_timestamp, module_code, run_exception) FROM stdin;
+005	../datastore_server/source/sql/postgresql/005/schema-005.sql	SUCCESS	2013-02-13 13:23:07.049	\\x0a2f2a202d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d202a2f0a2f2a20446f6d61696e73202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202a2f0a2f2a202d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d202a2f0a0a43524541544520444f4d41494e20544543485f494420415320424947494e543b0a0a43524541544520444f4d41494e20434f44452041532056415243484152283430293b0a0a43524541544520444f4d41494e2046494c455f5041544820415320564152434841522831303030293b0a0a43524541544520444f4d41494e20424f4f4c45414e5f4348415220415320424f4f4c45414e2044454641554c542046414c53453b0a0a43524541544520444f4d41494e2054494d455f5354414d502041532054494d455354414d5020574954482054494d45205a4f4e453b0a0a0a2f2a202d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d202a2f0a2f2a205461626c657320202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202a2f0a2f2a202d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d202a2f0a0a435245415445205441424c4520444154415f5345545320280a202049442042494753455249414c204e4f54204e554c4c2c0a2020434f444520434f4445204e4f54204e554c4c2c0a20204c4f434154494f4e2046494c455f50415448204e4f54204e554c4c2c0a0a20205052494d415259204b455920284944292c0a2020554e495155452028434f4445290a293b0a0a43524541544520494e44455820444154415f534554535f434f44455f494458204f4e20444154415f534554532028434f4445293b0a0a435245415445205441424c4520444154415f5345545f46494c455320280a202049442042494753455249414c204e4f54204e554c4c2c0a2020444153455f494420544543485f4944204e4f54204e554c4c2c0a2020504152454e545f494420544543485f49442c0a202052454c41544956455f504154482046494c455f50415448204e4f54204e554c4c2c0a202046494c455f4e414d452046494c455f50415448204e4f54204e554c4c2c0a202053495a455f494e5f425954455320424947494e54204e4f54204e554c4c2c0a2020434845434b53554d5f435243333220494e54454745522c0a202049535f4449524543544f525920424f4f4c45414e5f43484152204e4f54204e554c4c2c0a20204c4153545f4d4f4449464945442054494d455f5354414d50204e4f54204e554c4c2044454641554c54204e4f5728292c0a0a20205052494d415259204b455920284944292c0a2020434f4e53545241494e5420464b5f444154415f5345545f46494c45535f444154415f5345545320464f524549474e204b45592028444153455f494429205245464552454e43455320444154415f534554532028494429204f4e2044454c4554452043415343414445204f4e2055504441544520434153434144452c0a2020434f4e53545241494e5420464b5f444154415f5345545f46494c45535f444154415f5345545f46494c455320464f524549474e204b45592028504152454e545f494429205245464552454e43455320444154415f5345545f46494c45532028494429204f4e2044454c4554452043415343414445204f4e2055504441544520434153434144450a293b0a0a43524541544520494e44455820444154415f5345545f46494c45535f444153455f49445f494458204f4e20444154415f5345545f46494c45532028444153455f4944293b0a43524541544520494e44455820444154415f5345545f46494c45535f444153455f49445f504152454e545f49445f494458204f4e20444154415f5345545f46494c45532028444153455f49442c20504152454e545f4944293b0a43524541544520494e44455820444154415f5345545f46494c45535f444153455f49445f52454c41544956455f504154485f494458204f4e20444154415f5345545f46494c45532028444153455f49442c2052454c41544956455f50415448293b0a43524541544520494e44455820444154415f5345545f46494c45535f444153455f49445f46494c455f4e414d455f494458204f4e20444154415f5345545f46494c45532028444153455f49442c2046494c455f4e414d45293b0a0a435245415445205441424c45204556454e545320280a20204c4153545f5345454e5f44454c4554494f4e5f4556454e545f494420544543485f4944204e4f54204e554c4c0a293b0a0a	\N
+006	../datastore_server/source/sql/postgresql/migration/migration-005-006.sql	SUCCESS	2013-03-20 13:20:21.176	\\x0a435245415445205441424c45204c4153545f46454544494e475f4556454e5420280a2020524547495354524154494f4e5f54494d455354414d502054494d455f5354414d50204e4f54204e554c4c0a293b0a	\N
+\.
+
+
+--
+-- Data for Name: events; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY events (last_seen_deletion_event_id) FROM stdin;
+\.
+
+
+--
+-- Data for Name: last_feeding_event; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY last_feeding_event (registration_timestamp) FROM stdin;
+\.
+
+
+--
+-- Name: data_set_files_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: 
+--
+
+ALTER TABLE ONLY data_set_files
+    ADD CONSTRAINT data_set_files_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: data_sets_code_key; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: 
+--
+
+ALTER TABLE ONLY data_sets
+    ADD CONSTRAINT data_sets_code_key UNIQUE (code);
+
+
+--
+-- Name: data_sets_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: 
+--
+
+ALTER TABLE ONLY data_sets
+    ADD CONSTRAINT data_sets_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: data_set_files_dase_id_file_name_idx; Type: INDEX; Schema: public; Owner: -; Tablespace: 
+--
+
+CREATE INDEX data_set_files_dase_id_file_name_idx ON data_set_files USING btree (dase_id, file_name);
+
+
+--
+-- Name: data_set_files_dase_id_idx; Type: INDEX; Schema: public; Owner: -; Tablespace: 
+--
+
+CREATE INDEX data_set_files_dase_id_idx ON data_set_files USING btree (dase_id);
+
+
+--
+-- Name: data_set_files_dase_id_parent_id_idx; Type: INDEX; Schema: public; Owner: -; Tablespace: 
+--
+
+CREATE INDEX data_set_files_dase_id_parent_id_idx ON data_set_files USING btree (dase_id, parent_id);
+
+
+--
+-- Name: data_set_files_dase_id_relative_path_idx; Type: INDEX; Schema: public; Owner: -; Tablespace: 
+--
+
+CREATE INDEX data_set_files_dase_id_relative_path_idx ON data_set_files USING btree (dase_id, relative_path);
+
+
+--
+-- Name: data_sets_code_idx; Type: INDEX; Schema: public; Owner: -; Tablespace: 
+--
+
+CREATE INDEX data_sets_code_idx ON data_sets USING btree (code);
+
+
+--
+-- Name: fk_data_set_files_data_set_files; Type: FK CONSTRAINT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY data_set_files
+    ADD CONSTRAINT fk_data_set_files_data_set_files FOREIGN KEY (parent_id) REFERENCES data_set_files(id) ON UPDATE CASCADE ON DELETE CASCADE;
+
+
+--
+-- Name: fk_data_set_files_data_sets; Type: FK CONSTRAINT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY data_set_files
+    ADD CONSTRAINT fk_data_set_files_data_sets FOREIGN KEY (dase_id) REFERENCES data_sets(id) ON UPDATE CASCADE ON DELETE CASCADE;
+
+
+--
+-- Name: public; Type: ACL; Schema: -; Owner: -
+--
+
+REVOKE ALL ON SCHEMA public FROM PUBLIC;
+REVOKE ALL ON SCHEMA public FROM postgres;
+GRANT ALL ON SCHEMA public TO postgres;
+GRANT ALL ON SCHEMA public TO PUBLIC;
+
+
+--
+-- PostgreSQL database dump complete
+--
+

js-test/servers/dsu/datastore_server/etc/log.xml

+<?xml version="1.0" encoding="UTF-8" ?>
+<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
+
+<log4j:configuration xmlns:log4j='http://jakarta.apache.org/log4j/'>
+
+  <appender name="STDOUT" class="org.apache.log4j.ConsoleAppender">
+     <layout class="org.apache.log4j.PatternLayout">
+       <param name="ConversionPattern" value="%d %-5p [%t] %c - %m%n"/>
+     </layout>
+  </appender>
+
+  <appender name="NULL" class="org.apache.log4j.varia.NullAppender" />
+
+  <root>
+     <priority value ="info" />
+     <appender-ref ref="STDOUT" />
+  </root>
+
+</log4j:configuration>

js-test/servers/dsu/datastore_server/etc/service.properties

+# Unique code of this Data Store Server. Not more than 40 characters.
+data-store-server-code = DSS1
+
+# host name of the machine on which the datastore server is running
+host-address = http://localhost
+
+# parent directory of the store directory and all the dropboxes
+root-dir = data
+
+# The root directory of the data store
+storeroot-dir = ${root-dir}/store
+
+incoming-root-dir = ${root-dir}
+
+# Cache for data set files from other Data Store Servers
+cache-workspace-folder ${root-dir}/dss-cache
+
+# The directory where the command queue file is located; defaults to storeroot-dir 
+commandqueue-dir =
+
+# Port
+port = 20001
+use-ssl = false
+
+# Session timeout in minutes
+session-timeout = 720
+
+# Path to the keystore
+keystore.path = etc/openBIS.keystore
+# Password of the keystore
+keystore.password = changeit
+# Key password of the keystore
+keystore.key-password = changeit
+
+# The check interval (in seconds)
+check-interval = 5
+
+quiet-period = 10
+
+
+# The time-out for clean up work in the shutdown sequence (in seconds).
+# Note that that the maximal time for the shutdown sequence to complete can be as large 
+# as twice this time.
+# Remark: On a network file system, it is not recommended to turn this value to something 
+# lower than 180.
+shutdown-timeout = 180
+
+# The minimum time (in seconds) of availability of the data stream since moment when user requested
+# for the data stream url. If not specified default value (20 seconds) will be used.
+# minimum-time-to-keep-streams-in-sec = 20
+
+#�If free disk space goes below value defined here, a notification email will be sent.
+# Value must be specified in kilobytes (1048576 = 1024 * 1024 = 1GB). If no high water mark is
+# specified or if value is negative, the system will not be watching. There are 2 different kinds
+# of highwater mark supported: the one that is checking the space on the store, and one that is
+# checking the amount of free space for recovery state (on the local filesystem). 
+highwater-mark = -1
+recovery-highwater-mark = -1
+
+# If a data set is successfully registered it sends out an email to the registrator. 
+# If this property is not specified, no email is sent to the registrator. This property
+# does not affect the mails which are sent, when the data set could not be registered.
+notify-successful-registration = false
+
+# The URL of the openBIS server
+server-url = ${host-address}:20000
+
+# The username to use when contacting the openBIS server
+username = etlserver_bsse
+
+# The password for the etlserver user who contacts the openBIS server
+password=e1AWO4f0ro
+
+# The base URL for Web client access to the data store server.
+download-url = ${host-address}:${port}
+
+# SMTP properties (must start with 'mail' to be considered).
+# The current configuration saves the emails in the file system in the root directory 
+mail.smtp.host = file://${root-dir}
+# mail.smtp.host = localhost
+# mail.from = openbis-dss@localhost
+# mail.smtp.user = 
+# mail.smtp.password = 
+
+
+# Data sources
+data-sources = path-info-db 
+
+# Data source for pathinfo database
+path-info-db.version-holder-class = ch.systemsx.cisd.openbis.dss.generic.shared.PathInfoDatabaseVersionHolder
+path-info-db.databaseEngineCode = postgresql
+path-info-db.basicDatabaseName = pathinfo
+# The host and optionally port. Default is 'localhost'.
+# path-info-db.urlHostPart =
+path-info-db.databaseKind = test_js_dsu
+path-info-db.scriptFolder = datastore_server/sql
+
+# ---------------------------------------------------------------------------
+# maintenance plugins configuration
+# ---------------------------------------------------------------------------
+
+# Comma separated names of maintenance plugins. Each plugin should have configuration properties prefixed with its name.
+maintenance-plugins = post-registration, path-info-deletion
+
+# Maintenance task for post registration of all paths of a freshly registered data set to be fed into pathinfo database  
+post-registration.class = ch.systemsx.cisd.etlserver.postregistration.PostRegistrationMaintenanceTask
+post-registration.interval = 30
+post-registration.cleanup-tasks-folder = ${root-dir}/post-registration/cleanup-tasks
+post-registration.last-seen-data-set-file = ${root-dir}/post-registration/last-seen-data-set.txt
+post-registration.post-registration-tasks = pathinfo-feeding
+post-registration.pathinfo-feeding.class = ch.systemsx.cisd.etlserver.path.PathInfoDatabaseFeedingTask
+post-registration.pathinfo-feeding.compute-checksum = true
+
+# Maintenance task for deleting entries from pathinfo database after deletion of a data set
+path-info-deletion.class = ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask
+path-info-deletion.interval = 120
+path-info-deletion.data-source = path-info-db
+path-info-deletion.data-set-table-name = data_sets
+path-info-deletion.data-set-perm-id = CODE
+
+# ---------------------------------------------------------------------------
+# processing plugins configuration
+# ---------------------------------------------------------------------------
+
+# Comma separated names of processing plugins. Each plugin should have configuration properties prefixed with its name.
+processing-plugins = path-info-db-consistency-check
+
+# Processing task that checks the consistency between the data store and the meta information stored in the PathInfoDB.
+# It sends out an email which contains all differences found. 
+path-info-db-consistency-check.label = Path Info DB consistency check
+path-info-db-consistency-check.dataset-types = .*
+path-info-db-consistency-check.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetAndPathInfoDBConsistencyCheckProcessingPlugin
+
+# ---------------------------------------------------------------------------
+# dropbox configurations
+# ---------------------------------------------------------------------------
+inputs = default-dropbox
+dss-rpc.put-default = default-dropbox
+
+default-dropbox.incoming-dir = ${incoming-root-dir}/incoming-default
+default-dropbox.incoming-data-completeness-condition = auto-detection
+default-dropbox.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JavaTopLevelDataSetHandlerV2
+default-dropbox.program-class = ch.systemsx.cisd.etlserver.registrator.DefaultDropbox
+default-dropbox.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+default-dropbox.validation-script-path = ../core-plugins/default/default-validation-script.py
+
+# ---------------------------------------------------------------------------
+# Archiver configuration (optional)
+# ---------------------------------------------------------------------------
+
+# Configuration of an archiver task. All properties are prefixed with 'archiver.'.
+
+# Archiver class specification (together with the list of packages this class belongs to).
+#archiver.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoArchiver
+
+# ---------------------------------------------------------------------------
+# Imaging database for screening (optional, only used if screening technology switched on)
+# ---------------------------------------------------------------------------
+# Format: <host>[:<port>]. Default: localhost
+# imaging-database.url-host-part =
+# Default: prod.
+imaging-database.kind = test_js_dsu
+
+
+# ---------------------------------------------------------------------------
+#                      INTERNAL CONFIGURATION, 
+# Do not change this part unless you are developing openBIS extensions.
+# ---------------------------------------------------------------------------
+