Commit c9192e1c authored by Piotr Gawron's avatar Piotr Gawron
Browse files

Merge branch 'devel_11.1.x' of https://git-r3lab.uni.lu/piotr.gawron/minerva into devel_11.1.x

parents 5d0b91ec 9e4c1472
minerva (11.0.3) stable; urgency=medium
* Bug fix: removing empty project removed images from all projects
* Bug fix: clicking on map when left panel was hidden threw error
* Bug fix: links to invalid annotations were opening invalid web page
* Bug fix: service resolving miriam resources doesn't worki over http
anymore
* Bug fux: chebi annotator doesn't work over http anymore
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 19 Oct 2017 13:50:00 +0200
minerva (11.0.2) stable; urgency=medium
* Bug fix: login issues when default page is in secure area
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 25 Sep 2017 12:00:00 +0200
minerva (11.0.1) stable; urgency=medium
* Bug fix: logout caused issues with session data
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 08 Sep 2017 12:00:00 +0200
minerva (11.0.0) stable; urgency=medium
* Bug fix: security issue - access to specific map can be restricted
by the userlogin
* Bug fix: sbgn import
* Bug fix: mesh connector
* Rest API (documentation can be found here:
https://git-r3lab.uni.lu/piotr.gawron/minerva/blob/master/README.md)
* Selecting an element on the map shows info about it in the bottom left
corner (when Search tab is not open)
* Upload of data overlays allows to upload just names of the proteins
(or other elements), it can be done via file or just by typing in the
proper text box
* Layout changes: the main one is that there are only 3 tab panels
(search, overlay, info), so it should be easier to navigate
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 28 Aug 2017 12:00:00 +0200
minerva (10.0.5) stable; urgency=medium
* Bug fix: interacting drugs can be found for RNAs
* Bug fix: error handling improved on map upload
* Bug fix: taxonomy ncbi server switched to https
* Overlay presents description field if possible
-- Piotr Gawron <piotr.gawron@uni.lu> Sat, 04 Mar 2017 12:00:00 +0200
minerva (10.0.4) stable; urgency=medium
* Bug fix: overlays colors are centered in white (not black)
* Bug fix: export to CellDesigner fixed
* Bug fix: DrugBank connector updated due to change in DrugBank website
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 29 Dec 2016 17:01:16 +0200
minerva (10.0.3) stable; urgency=medium
* Bug fix: login cannot contain whitespace
* Bug fix: search for multiple drugs will not return more drugs than
queried for
* Bug fix: drug list for some proteins (like RHOA) hung webpage
* Bug fix: comments on submaps issue
* Bug fix: link to submap from comment panel
* Overlay coloring can be defined in Configuration
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 15 Dec 2016 15:01:16 +0200
minerva (10.0.2) stable; urgency=medium
* Bug fix: markers for mirna targets visibility
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 29 Sep 2016 10:01:16 +0200
minerva (10.0.1) stable; urgency=medium
* Bug fix: export to image
* Bug fix: trigger reaction and physical stimulation reactions are no
longer allowed (CellDesigner data model issue)
* Bug fix: clicking on reactions in submaps
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 21 Sep 2016 13:01:16 +0200
minerva (10) stable; urgency=medium
* Project info tab available for users
* Management of overlays in admin panel
* Bug fix: Visualization of text mining
* Bug fix: Exception when accessing non-existing project
* Bug fix: Zooming issue when searching for results on submaps
* Bug fix: Out of memory when caching a lot of data
* Bug fix: Corrupted drug names
* Bug fix: Unexpected errors when uploading layouts
* Bug fix: Coordinates in url
* Bug fix: Hiding left panel
* Bug fix: CellDesigner font size is processed properly
* Bug fix: Search by reaction id is not case sensitive
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 22 Aug 2016 13:01:16 +0200
minerva (9) stable; urgency=medium
* Fix on install script of version 8 that crashed some new installations
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 29 Jun 2016 09:58:34 +0200
minerva (8) stable; urgency=medium
* Micro RNA interface
* Toxic chemicals interdace
* Data sets (layouts) visualized dynamically in the browser
* Reverse query for drugs, chemicals, micro RNAs interfaces
* Small bug fixes
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 14 Apr 2016 13:03:55 +0200
minerva (7) stable; urgency=low
* Uploaded datasets are available for download
* Entrez annotator
* Ensembl annotator
* Valid/required annotations and used annotations saved in user profile
* Export to pdf/png/jpg/svg
* New web interface
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 3 Dec 2015 22:00:00 +0200
minerva (6) stable; urgency=low
* Searching by annotations
* Errors from parsing data forwarded to client
* Notification email system added
* Warnings are downloadable
* Complex map (composed from many small maps)
* Visualization of Recon specific annotations
* Versioning system
* Galaxy connector
* Miriam types report
* Advanced annotation options
* Uniprot annotation module
* Customized validation of miriam annotations
* Recon annotation service
* Bug fix: Data autofill problem in user management
* Bug fix: User privileges for adding project
* Bug fix: Problem with some miriam entries in RDF format
* Bug fix: Reporting of drawing problems
* Bug fix: Visualization of posttranslationa modification
* Bug fix: Drugbank problem after update of Drugbank interface
* Bug fix: Session scope fixed (browsing many maps at the same time)
* Bug fix: Asynchronous removing/adding maps
* Bug fix: Export to CellDesigner rarely produced corrupted CellDesigner file
* Bug fix: Recon annotations of reactions
* Bug fix: Login problem when browsing not default map
* Bug fix: Multimers are available for every element
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 21 Jul 2015 22:00:00 +0200
minerva (5) stable; urgency=low
* Additional checkboxes in upload model: annotate automatically, cache data, verify annotations
* Popup window in admin panel that list warnings
* Information about build
* Parsing and annotation warnings for models in admin panel
* Custom reaction visualization in upload overlay
* Bug fix: Problem with touch interface on Windows 8.1
* Bug fix: Google Maps API problem with floating bubbles
* Bug fix: Error handling in admin panel
* Bug fix: Reaction color in CellDesigner file
* Bug fix: Reaction line width
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 18 Dec 2014 22:00:00 +0200
minerva (4) stable; urgency=low
* Export of the part of the map into CellDesigner file
* Logo files managable via config webpage
* Import data from GO
* Custom overlay upload
* Additional structural information imported from annotation service
* Bug fix: Fonts and lines in hierarchical view
* Bug fix: Visualization of residues in rna, antisense rna, proteins
* Bug fix: Problem with touching bubbles on touch interface
* Bug fix: Problem with special UTF-8 characters in CellDesigner file
* Bug fix: Problem with users and session expire
* Bug fix: Export problem
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 11 Sep 2014 22:00:00 +0200
minerva (3) stable; urgency=low
* Drug targeting interface
* Export to CellDesigner
* Status page of all dependent services
* Configuration page
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 5 Jun 2014 22:00:00 +0200
minerva (2) stable; urgency=low
* Upload of the CellDesigner map
* Bug fix: Problem with touch interface after update of browsers engine
* Bug fix: Problem in Safari when searching for elements
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 2 Apr 2014 22:00:00 +0200
minerva (1) stable; urgency=low
* Initial release
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 4 Dec 2013 22:00:00 +0200
minerva (11.0.3) stable; urgency=medium
* Bug fix: removing empty project removed images from all projects
* Bug fix: clicking on map when left panel was hidden threw error
* Bug fix: links to invalid annotations were opening invalid web page
* Bug fix: service resolving miriam resources doesn't worki over http
anymore
* Bug fux: chebi annotator doesn't work over http anymore
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 19 Oct 2017 13:50:00 +0200
minerva (11.0.2) stable; urgency=medium
* Bug fix: login issues when default page is in secure area
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 25 Sep 2017 12:00:00 +0200
minerva (11.0.1) stable; urgency=medium
* Bug fix: logout caused issues with session data
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 08 Sep 2017 12:00:00 +0200
minerva (11.0.0) stable; urgency=medium
* Bug fix: security issue - access to specific map can be restricted
by the userlogin
* Bug fix: sbgn import
* Bug fix: mesh connector
* Rest API (documentation can be found here:
https://git-r3lab.uni.lu/piotr.gawron/minerva/blob/master/README.md)
* Selecting an element on the map shows info about it in the bottom left
corner (when Search tab is not open)
* Upload of data overlays allows to upload just names of the proteins
(or other elements), it can be done via file or just by typing in the
proper text box
* Layout changes: the main one is that there are only 3 tab panels
(search, overlay, info), so it should be easier to navigate
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 28 Aug 2017 12:00:00 +0200
minerva (10.0.5) stable; urgency=medium
* Bug fix: interacting drugs can be found for RNAs
* Bug fix: error handling improved on map upload
* Bug fix: taxonomy ncbi server switched to https
* Overlay presents description field if possible
-- Piotr Gawron <piotr.gawron@uni.lu> Sat, 04 Mar 2017 12:00:00 +0200
minerva (10.0.4) stable; urgency=medium
* Bug fix: overlays colors are centered in white (not black)
* Bug fix: export to CellDesigner fixed
* Bug fix: DrugBank connector updated due to change in DrugBank website
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 29 Dec 2016 17:01:16 +0200
minerva (10.0.3) stable; urgency=medium
* Bug fix: login cannot contain whitespace
* Bug fix: search for multiple drugs will not return more drugs than
queried for
* Bug fix: drug list for some proteins (like RHOA) hung webpage
* Bug fix: comments on submaps issue
* Bug fix: link to submap from comment panel
* Overlay coloring can be defined in Configuration
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 15 Dec 2016 15:01:16 +0200
minerva (10.0.2) stable; urgency=medium
* Bug fix: markers for mirna targets visibility
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 29 Sep 2016 10:01:16 +0200
minerva (10.0.1) stable; urgency=medium
* Bug fix: export to image
* Bug fix: trigger reaction and physical stimulation reactions are no
longer allowed (CellDesigner data model issue)
* Bug fix: clicking on reactions in submaps
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 21 Sep 2016 13:01:16 +0200
minerva (10) stable; urgency=medium
* Project info tab available for users
* Management of overlays in admin panel
* Bug fix: Visualization of text mining
* Bug fix: Exception when accessing non-existing project
* Bug fix: Zooming issue when searching for results on submaps
* Bug fix: Out of memory when caching a lot of data
* Bug fix: Corrupted drug names
* Bug fix: Unexpected errors when uploading layouts
* Bug fix: Coordinates in url
* Bug fix: Hiding left panel
* Bug fix: CellDesigner font size is processed properly
* Bug fix: Search by reaction id is not case sensitive
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 22 Aug 2016 13:01:16 +0200
minerva (9) stable; urgency=medium
* Fix on install script of version 8 that crashed some new installations
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 29 Jun 2016 09:58:34 +0200
minerva (8) stable; urgency=medium
* Micro RNA interface
* Toxic chemicals interdace
* Data sets (layouts) visualized dynamically in the browser
* Reverse query for drugs, chemicals, micro RNAs interfaces
* Small bug fixes
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 14 Apr 2016 13:03:55 +0200
minerva (7) stable; urgency=low
* Uploaded datasets are available for download
* Entrez annotator
* Ensembl annotator
* Valid/required annotations and used annotations saved in user profile
* Export to pdf/png/jpg/svg
* New web interface
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 3 Dec 2015 22:00:00 +0200
minerva (6) stable; urgency=low
* Searching by annotations
* Errors from parsing data forwarded to client
* Notification email system added
* Warnings are downloadable
* Complex map (composed from many small maps)
* Visualization of Recon specific annotations
* Versioning system
* Galaxy connector
* Miriam types report
* Advanced annotation options
* Uniprot annotation module
* Customized validation of miriam annotations
* Recon annotation service
* Bug fix: Data autofill problem in user management
* Bug fix: User privileges for adding project
* Bug fix: Problem with some miriam entries in RDF format
* Bug fix: Reporting of drawing problems
* Bug fix: Visualization of posttranslationa modification
* Bug fix: Drugbank problem after update of Drugbank interface
* Bug fix: Session scope fixed (browsing many maps at the same time)
* Bug fix: Asynchronous removing/adding maps
* Bug fix: Export to CellDesigner rarely produced corrupted CellDesigner file
* Bug fix: Recon annotations of reactions
* Bug fix: Login problem when browsing not default map
* Bug fix: Multimers are available for every element
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 21 Jul 2015 22:00:00 +0200
minerva (5) stable; urgency=low
* Additional checkboxes in upload model: annotate automatically, cache data, verify annotations
* Popup window in admin panel that list warnings
* Information about build
* Parsing and annotation warnings for models in admin panel
* Custom reaction visualization in upload overlay
* Bug fix: Problem with touch interface on Windows 8.1
* Bug fix: Google Maps API problem with floating bubbles
* Bug fix: Error handling in admin panel
* Bug fix: Reaction color in CellDesigner file
* Bug fix: Reaction line width
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 18 Dec 2014 22:00:00 +0200
minerva (4) stable; urgency=low
* Export of the part of the map into CellDesigner file
* Logo files managable via config webpage
* Import data from GO
* Custom overlay upload
* Additional structural information imported from annotation service
* Bug fix: Fonts and lines in hierarchical view
* Bug fix: Visualization of residues in rna, antisense rna, proteins
* Bug fix: Problem with touching bubbles on touch interface
* Bug fix: Problem with special UTF-8 characters in CellDesigner file
* Bug fix: Problem with users and session expire
* Bug fix: Export problem
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 11 Sep 2014 22:00:00 +0200
minerva (3) stable; urgency=low
* Drug targeting interface
* Export to CellDesigner
* Status page of all dependent services
* Configuration page
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 5 Jun 2014 22:00:00 +0200
minerva (2) stable; urgency=low
* Upload of the CellDesigner map
* Bug fix: Problem with touch interface after update of browsers engine
* Bug fix: Problem in Safari when searching for elements
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 2 Apr 2014 22:00:00 +0200
minerva (1) stable; urgency=low
* Initial release
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 4 Dec 2013 22:00:00 +0200
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE module PUBLIC "-//Puppy Crawl//DTD Check Configuration 1.3//EN" "http://www.puppycrawl.com/dtds/configuration_1_3.dtd">
<!--
This configuration file was written by the eclipse-cs plugin configuration editor
<!--
This configuration file was written by the eclipse-cs plugin configuration editor
-->
<!--
Checkstyle-Configuration: MapViewer checkstyle
Description: none
<!--
Checkstyle-Configuration: MapViewer checkstyle
Description: none
-->
<module name="Checker">
<property name="severity" value="warning"/>
......
......@@ -9,6 +9,8 @@ versionCompLt() {
[ "$1" = "$2" ] && return 1 || versionCompLte $1 $2
}
# file with bash code generating DB schema diffs for different versions
dbschemadiff=management_scripts/db_schema_and_diff.sh
#Where source file of the debian package should be placed
SRC_DIR=debian/src
......@@ -54,22 +56,9 @@ cp debian/scripts/common.sh $SRC_DIR/
#copy changelog file
cp CHANGELOG $ROOT_DIR/debian/template/changelog
#this variable will contain all available versions of the package
versions=();
#this is current (latest) version of the package
current_version=-1;
#find all available versions
for version in `ls $DB_SCHEMA_DIR | sort -V`;
do
if [ -d "$DB_SCHEMA_DIR/$version" ]
then
versions+=($version);
current_version=$version;
fi
done
# set $versions and $current_version; generate upgrade scripts in SRC_DIR
DBSCRIPT_DEST_DIR=$SRC_DIR
source $dbschemadiff
echo "Current version: " $current_version
......@@ -81,47 +70,6 @@ then
exit 1;
fi
#--------------------------------------
# GENERATE DB schemas and diff files
#--------------------------------------
#last version (used for generating db diff files)
last_version=-1;
for version_A in ${versions[*]}
do
#main update file (used to create this version - it's a diff
#between base.sql and current version)
update_file=$SRC_DIR/db_0_to_$current_version".sql";
#now iterate through all versions
for file in `ls $DB_SCHEMA_DIR/$version_A | sort -V`;
do
if [ -f "$DB_SCHEMA_DIR/$version_A/$file" ]
then
#add differemce tp current db schema diff
printf "\n\n-- UPDATE $version_A/$file\n\n" >>$update_file;
cat $DB_SCHEMA_DIR/$version_A/$file >> $update_file;
#and now iterate again through all versions to add diffs
#between previous versions and current one
for version_B in ${versions[*]}
do
#update from version_B should contain all db changes that appeard
#after #version_B (so version_A must be later)
if versionCompLt $version_B $version_A
then
upd_file=$SRC_DIR/db_"$version_B"_to_$current_version".sql";
printf "\n\n-- UPDATE $version_A/$file\n\n" >>$upd_file;
cat $DB_SCHEMA_DIR/$version_A/$file >> $upd_file;
fi
done
fi
done
last_version=$version_A
done
#------------------------------------------
# Now we have all db schema diff files. Let's start preparing
# debian package
......
# shell snippet which extracts all available MINERVA versions from
# subdirectories available in DB_SCHEMA_DIR (typically
# `persist/src/db`) and generates database upgrade scripts (diff
# files)
# Precondition: the following variables have to be correctly initialised
# * DB_SCHEMA_DIR set to the directory containing database initialisation and upgrade sql commands
# * DBSCRIPT_DEST_DIR set to the directory that will be populated with database upgrade scripts
# Postcondition:
# * versions is set to the available MINERVA versions (bash array)
# * current_version is set to the latest available version
# * DBSCRIPT_DEST_DIR contains script to initialise the database from any version to the current version
#this variable will contain all available versions of the package
versions=();
#this is current (latest) version of the package
current_version=-1;
#find all available versions
for version in `ls "$DB_SCHEMA_DIR" | sort -V`;
do
if [ -d "$DB_SCHEMA_DIR/$version" ]
then
versions+=($version);
current_version=$version;
fi
done
#--------------------------------------
# GENERATE DB schemas and diff files
#--------------------------------------
versionCompLte() {
[ "$1" = "`echo -e "$1\n$2" | sort -V | head -n1`" ]
}
versionCompLt() {
[ "$1" = "$2" ] && return 1 || versionCompLte $1 $2
}
#last version (used for generating db diff files)
for version_A in ${versions[*]}
do
#main update file (used to create this version - it's a diff
#between base.sql and current version)
update_file="$DBSCRIPT_DEST_DIR/db_0_to_${current_version}.sql";
#now iterate through all versions
for file in `ls "$DB_SCHEMA_DIR/$version_A" | sort -V`;
do
if [ -f "$DB_SCHEMA_DIR/$version_A/$file" ]
then
#add difference to current db schema diff
printf "\n\n-- UPDATE $version_A/$file\n\n" >> "$update_file";
cat "$DB_SCHEMA_DIR/$version_A/$file" >> "$update_file";
#and now iterate again through all versions to add diffs
#between previous versions and current one
for version_B in ${versions[*]}
do
#update from version_B should contain all db changes that appeared
#after #version_B (so version_A must be later)
if versionCompLt $version_B $version_A
then
upd_file="$DBSCRIPT_DEST_DIR/db_${version_B}_to_${current_version}.sql";
printf "\n\n-- UPDATE $version_A/$file\n\n" >> "$upd_file";
cat "$DB_SCHEMA_DIR/$version_A/$file" >> "$upd_file";
fi
done
fi
done
done
MINERVA installation instructions using RPM Package Manager
===========================================================
These instructions guide you through the installation process of
`MINERVA <https://git-r3lab.uni.lu/piotr.gawron/minerva>`_ on Red Hat
Enterprise Linux 7 or CentOS 7. The server will also host the database
required for the functioning of MINERVA.
.. note::
Content visualization of MINERVA platform is supported by Google
Maps API. Users of MINERVA platform are obliged to comply with the
`Google Maps/Google Earth APIs Terms of Service
<https://www.google.com/intl/en-US_US/help/terms_maps.html>`_.
Overview
--------
The main steps are
* Install `Oracle Java SE Development Kit 8 <http://www.oracle.com/technetwork/java/javase/downloads/index.html>`_.
* Install `PostgreSQL <https://www.postgresql.org/>`_ and set up a
database.
* Install and configure `Apache Tomcat <https://tomcat.apache.org/>`_.
* Install the MINERVA RPM.
Java SE Development Kit
-----------------------
Red Hat Enterprise Linux 7
``````````````````````````
Follow the instructions at https://access.redhat.com/solutions/732883
to install ``java-1.8.0-oracle``.
CentOS 7
````````
Follow the link for ``Java SE Development Kit 8`` at