GettingStarted
From MIDAS Wiki
Contents |
Concepts
Users & Groups
MIDAS support multiples users. The administrator can add users through the menu My Midas > Administration > Manage Users.
Hierarchy
A bitstream is a file, MIDAS can store many types of bitstreams: conventional images (jpg, png, tiff, ...), medical images (dicom, mha, ...), documents (pdf, doc, txt, ...), video (avi, mpg, flv, ...). Bitstreams can be grouped as resources, this is very useful in the case of DICOM imagery, for example. A resource may also contain only one bitstream, as in the case of a pdf document.
Bitstream and resources are stored within an item. An item can have zero, one or any number of bitstreams and resources.
Collections can store numerous items.
Communities can store numerous collections.
Users & Groups
MIDAS supports multiple users. The administrator can add users through the menu My Midas > Administration > Manage Users. For each Community, collection or item, permissions can be granted to allow user to interact with any subset of communities, collections, etc. within the MIDAS installation.
Script
- First log in as an administrator and create a new community: My Midas > Create top level community.
- Fill in the form, you can add a logo to the community. Click 'create'.
- Once the community is created, add a new collection (Menu Community > Create collection).
- Add a new item to the collection.
Features
Search bitstream
Local upload
Image gallery
Administrator tools
Custom Workflow
Email subscription
Introduction
MIDAS integrates multimedia server technology with Kitware’s open-source image analysis and visualization packages. The multimedia server follows open standards for data storage, access and harvesting. It has been optimized for storing massive collections of large, scientific images and related metadata and reports. A variety of data access methods are provided including web, file system and DICOM server interfaces.
The main features of MIDAS
- Hierarchical organization of data
- Secure connections and user logins
- Extensible support for over 20 data types including XML, PDF and 20 image types
- Friendly and efficient upload tools
- Customizable metadata
- Powerful search engine (searches metadata, file contents and image headers)
- Optionally indexed by Google, Yahoo!
- Conforms to Open Archives Initiative (OAI) and Corporation for National Research Initiatives (CNRI) standards
- 3D interactive slice viewer for volumetric datasets
MIDAS is built upon several open source projects and open standards:
Configuring MIDAS
- In config.php: $MIDAS_SHARE_KEY="Midas$5!" makes the private collections and items accessible to anybody who has the complete URL
Installing MIDAS
Prerequisites
MIDAS runs on top of major web servers (currently, it is being tested with Apache) and requires some packages.
- Apache
- PostgreSQL (http://www.postgresql.org)
- PHP > 5.0 (http://www.php.net)
- ImageMagick (http://www.imagemagick.org/script/download.php)
- phpPgAdmin > 8.0 (recommended: http://phppgadmin.sourceforge.net)
Installation
Once the MIDAS distribution is in the document root of your web browser you will probably have to change several things in the config file.
Open the Midas/midas/config/config.php file and change the values of the following variables :
- $MIDAS_PG_DB_HOST (localhost by default). Hostname of the PostGres database
- $MIDAS_PG_DB_LOGIN (midas by default). Login for PostGres database access
- $MIDAS_PG_DB_PASS(midas by default). Password for PostGres database access
- $MIDAS_PG_DB_NAME (midas by default). Name of the PostGres database
- $MIDAS_PG_DB_PORT (5432 by default). Port of the PostGres database
Create several directories as follows:
- /assestore. Directory where the data is being stored.
- /temp. Temporary directory used by MIDAS.
- /cache. Cache directory used by MIDAS.
Note that these directories can be located outside of the web document root (actually recommended)
- $MIDAS_DSPACE_ASSETSTORE_PATH. This is the full path of the assetstore directory on the server
- $MIDAS_TEMP_DIRECTORY. Temporary directory (should have write access and make directory access)
- $MIDAS_CACHE_DIRECTORY. This is the full path of the cache directory
Also make sure that MIDAS is customized for OSA:
- $MIDAS_CUSTOM_APPLICATION = ’osa’
There are a lot of variables that you can modify in this file. For each of them there is brief commentary in the file which explains what that variable does.
Once you complete all of the changes needed in the config file open your web browser and point to your current MIDAS directory (something like http://www.myhost.com/midas) and follow the instructions. Make sure that you install the OSA tables by checking the box.
Browsing MIDAS
MIDAS groups datasets using a hierarchy:
- Communities are the top level element. A community can contain as many subcommunities as needed.
- Collections are within a community. A collection consists of items and cannot have subcollections.
- Items are the main element describing the data in MIDAS. Metadata information is related to items.
- Bitstreams are references to files on disk. An item can have several associated bitstreams.
From any page you can access the Help page from the left menu as well as the About MIDAS page.
MIDAS presents several links to browse the database.
- Home: always presented in the top menu bar, allows users to go back to the main page of MIDAS.
- Browse: also always presented in the top menu bar, allows users to see the complete MIDAS hierarchy of communities and collections.
There are several ways to efficiently browse MIDAS : by title, by authors, by keywords and via the image gallery. We describe these options next.
Browse by titles
MIDAS will display all the items ordered by title.
You can enter the first few letters and it will display only the items which match that entry or you can jump to a specific letter in the alphabet and MIDAS will display the items which correspond to that first letter.
Browse by authors
MIDAS will display all the items ordered by title author.
You can enter the first few letters of either the title or the author and it will display only the items which match that entry or you can jump to a specific letter in the alphabet and MIDAS will display the items which correspond to that first letter.
Browse by keywords
MIDAS will display all the items ordered by keyword.
You can enter the first few letters of the keyword and it will display only the items which match that entry or you can jump to a specific letter in the alphabet and MIDAS will display the items which correspond to that first letter.
Image Gallery
The Image Gallery displays all the images in the database as thumbnails. This provides an easy and fun way to navigate the datasets.
Communities
- Collections within this community. Shows all the collections within the community you've selected.
- Xcede Catalog. Creates an XCEDE Catalog listing all the sub-communities, collections, items and bitstreams within the community you've selected.
Collections
- Submitted items. You will be able to see all of the items which are in the collection and have access to them by clicking on on specific thumbnails (see below ‘Click on an item’).
In the ‘Submitted item’ section, you can download the full collection, the Xcede Catalog, or the XML version of the collection.
- Submit an item
- You can submit a new item to the current collection by filling in all of the required fields such as the author(s), title, keyword(s), et. al.
- If you would like to follow changes and/or updates to a specific collection you can subscribe to it by clicking the subscribe button.
- This will allow you to receive e-mails each time something changes in the collections to which you've subscribed.
Items
Most of the information is displayed as a clickable link. For example, when you click on a keyword MIDAS will show you all the items which are related to this keyword displayed in the same manner as a keyword search.
Download an item
To download an item with all its bitstreams there are two options:
- You can click on the first button of the download section causing your files to be downloaded in one tgz file.
- You also can click on the second button of the download section causing your files to be compressed in a unique zip file.
Remember, to be able to download an item you have to have the right policies.
Download a bitstream
To download individual bitstreams instead of the full item, click on the Download button of the bitstream and accept the license.
Searching Midas
Midas includes a performant search tool. You can search any item, or bitstream by just entering in the search toolbar an author, title, etc.
Once Midas generates results, you can narrow your search by focusing on certain aspects like format, the modality, etc., in order to reduce the number of results and get the exact result(s) desired.
User Management
MIDAS uses a user-based session. Anybody can create a MIDAS account. Community, collection and item policies are set to allow users to view, edit and/or add actions. Depending on the community, collection, and item policies, users may be restricted to a view only mode.
Registering to MIDAS
- I don’t have a Midas account. You can create one by simply clicking on Login, then Click here to register and following the instructions.
- You do have a Midas account. Just enter your e-mail address and your password to be connected.
Once you’re registered and connected you have access to your personal data and can upload/download your own data (if you have permissions).
If you forgot your password, you can recover it by simply clicking on click here to recover, and entering your email address.
My MIDAS
- My Submissions. Here you can find all of your previously uploaded data. You have direct access to view or modify the data by editing the information or adding files to the item.
- New Submission. In this section, if a collection already exists, you can create a new item. If no collection exists you will have to create one and then you can create a new item.
Begin by accepting the license. Then select the collection where you want your new item to be submitted. Now you can enter information about this item (e.g., the author(s), title, date). There is a lot of information you can add to describe your new submission.
- My email subscriptions.
MIDAS Administration
Creating a top-level community
To create a Top-Level community, you have to be logged in on your account and have administrative privileges.
- Once you are logged in, go to the My Midas section.
- Click on Create top level community.
- Specify a name for the community (this is mandatory).
- Specify a more complete description of the community (optional).
- Specify introductory text for the community (optional).
- Specify a default copyright (optional).
- Specify any extra links referring to this community (optional).
Once you are satisfied with your content, click on the Create community link. If you change your mind and no longer wish to create the community, click on the back button. Once your new community has been created you can then create a subcommunity, a collection or edit the community. Additionally, you can add specific policies for that community. By default, all policies are set to the person who created the community.
Editing a community
If you are the owner of a community or have administrative privileges you can edit a community.
- Browse to the community you want to edit.
- Click on Edit Community.
- You can add a logo for the community by browsing your computer for the desired file and clicking on Upload Logo.
- Once you make all desired modifications click on Update community.
If you want to add the same copyright to all the items you created in that community use the Propagate Copyright to All Items link.
If you want to delete the community, click on Delete Community. Then confirm this selection by clicking on ‘OK’. Remember, if you delete a community you will delete any sub-communities, collections and items in that community as well.
Creating a sub-community
If you are the owner of a community or have administrative privileges you can create sub-communities within a community.
- Browse to the community you want to edit.
- Click on Create SubCommunity.
- Enter a name for the subcommunity (mandatory) the same way you would if you were creating a new community.
- Enter any optional descriptions, links and default copyrights.
- Click on Create community.
Adding an agreement to a community
If you are the owner of a community or have administrative privileges you can create or edit an agreement. You can add an agreement to a community when either creating or editing it. Let's assume you are creating a new one. (see above creation of community paragraphs)
Once you are in the create community page:
- Click on Add group agreement. A text area, a drop-down box and a "create group" button appear.
- Write the agreement in the text area. You can also click on html to write a html text. If you do it, once you're done, click on Update.
- You MUST select a group that will be related to the community. You can either select it from the drop-down box or click on create group to create a new one. If you do that, the box and the button are replaced by a field, where you can write the new group, and a new button select existing group that lets you go back to the previous view. If you don't select a group, set an agreement and try to create the community, it won't work and you will loose the agreement text that might be long.
- Once you selected the group and wrote the agreement, click on Create community
If you are editing a community, once you are in the edit community page, follow the same instructions.
If you want to delete the agreement, go to the edit community page, remove the agreement and then click on Update community.
Creating a collection
If you are the owner of a community or have administrative privileges you can create a collection within a community.
- Log into MIDAS
- Browse to the community in which you want to create the collection
- Click on Create Collection
- Specify a name for the collection (this is mandatory)
- Specify a more complete description of the collection (optional)
- Specify introductory text for the collection (optional)
- Specify a default copyright (optional)
- Specify a license for this collection. By specifying a license for the collection any users who upload data to it will have to agree to license the data for redistribution.
- Specify extra links referring to this collection (optional)
- Select or deselect the Create default group for this collection, this means that MIDAS will create a group for this collection and put the owner of the collection in that group.
Once you are satisfied with your content, click on the Create collection. If you change your mind and no longer want to create the collection, click on the back button. Once your new collection has been created you can add items to or edit items in the collection. Additionally, you can add collection specific policies. By default, all policies are set to the person who created the collection.
Editing a collection
If you are owner of a collectionor have administrative privileges you can edit a collection.
- Browse to the collection you want to edit.
- Click on Edit Collection.
- You can add a logo for the collection by browsing your computer, and clicking on Upload Logo.
- Once you did all the modifications you wanted, click on Update collection.
If you want to add the same copyright to all the items you created in that collection, use the Propagate Copyright to All Items.
If you want to delete the community, click on Delete Collection. Then confirm by clicking on ‘OK’. Remember, if you delete a collection, then all the items in that collection will be deleted as well.
Creating an item
- You have two options to create an item:
- Go to My Midas section and click on New Submission.
- Browse to the desired collection and click on Add item to this collection
- Read the license (if specified) and grant it to be able to add an item
- Select the collection where you want to submit your item by scrolling the selection menu (if not specified already)
Moreover, you can select several collections where the publication belongs by checking the corresponding boxes.
- Fill in all the related information. Keywords could be useful when you want to to a search into the database.
- Click next
- Select the files you want to upload by clicking on Select Files...
- Click on Start Upload. You can upload several files, at the same time, or one by one.
- Once you have uploadd all the files, click on Finish Submission.
Your new item item is now uploaded on the MIDAS database.
Editing an Item
If you are owner of an item or have administrative privileges you can edit an item.
- Browse to the item you want to edit.
- Click on Edit Item.
- Once you did all the modifications you wanted, click on Update item.
If you want to update or delete bitstreams (files) for the given item you can click directly on Add/Modify files (without updating main item)
- You can delete the item by clicking on Remove Item and confirm.
Manage SSHFS
If you want to export Midas’s items through sshfs or scp/sfp, you can use this panel to do it. You select the community/collection where you want to add your item, put its link.
Users Quota
Here you can manage quotas for the different users. That means you can define for each user, how many MB one is allowed to upload on the database. By default, this value is set to 10240MB.
Manage Groups
In Midas, as an administrator, you can create groups with specific users. By default there are two groups: Anonymous and Administrator and the default administrator is in the Administrator group. We really recommend that you change the name and password of the main administrator of MIDAS.
This notion of Group is very useful when you want to display full communities or specific items only to some persons. For example if you created a community which contains personal data you want to share only with a group of people, you can create a group including that people, and add policies for that group in the community.
Upgrading Midas
Some update of MIDAS requires modification to the database. Therefore an upgrade script is provided and you should see some warning messages on the main page of MIDAS. In that case.
- Login as administrator
- Go to My Midas
- Click on 'Administration
- Click on Upgrade Midas
- Click on Upgrade
Note: depending on the size of the database and the nature of the database schema modifications, the upgrade can take a long time.
MIDAS Policies
MIDAS has different policies depending on Communities, Collections and Items. Moreover, policies can be set for individual users or a group of users. Policies can be propagated down to Collections and Items by using the Propagate policies button.
Community
- Read. The community is visible.
- Edit. The community information can be edited.
- Delete. The community can be deleted.
- Add Collections. Collections can added to the community
- Remove Collections. Collections can be removed from the community
Collection
- Read. The collection is visible.
- Edit. The collection information can be edited.
- Delete. The collection can be deleted.
- Add Items. Items can added to the collection
- Remove Items. Items can be removed from the collection
Item
- Read. The item is visible.
- Edit. The item information can be edited.
- Delete. The item can be deleted.
- Add Bitstreams. Bitstreams can added to the community
- Remove Bitstreams. Bitstreams can be removed from the community
MIDAS Comments and ratings
To allow its users to give feedbacks on the available datas, MIDAS provide a generic comments and ratings system. These features can be enabled/disabled by turning on/off the designated variables in the main config file (config.php in midas/config) and are disabled by default. Comments and ratings are visible to every single visitor of MIDAS but the users need to be logged in to post a comment or submit a rating.
Comments
- to enable the comments set the variable $MIDAS_ENABLE_COMMENT to "true"
- There are two possible configurations depending on how much control the MIDAS administrator wants to have over the comments :
- Set $MIDAS_USE_APPROVE_COMMENT to "true" if you want to be able to review the comment before making them public. All the admins will receive an e-mail notification when a new comment is posted (make sure to enter your smtp server information in midas/config/config_smtp.php). The admin can just click on the link, log in to MIDAS and either remove or approve the comment by clicking on the button on the top right corner of the comment.
- Set $MIDAS_USE_APPROVE_COMMENT to "false" if you want to make the comments public automatically as they are posted. This configuration implies that we trust the users enough to allow them to leave any comments without any review from an admin. (Note that an admin can still remove the comments once posted)
Ratings
- to enable the ratings set the variable $MIDAS_ENABLE_RATING to "true"
- By default, users can give a rating to the following resources : items, collections and communities.
- The ratings are located on the top right corner of the "view" page of the resource. If there is a global rating for the resource it is displayed in the stars, in blue (from 1 to 5), if not all the stars are empty.
- submit your rating (fronm 1 to 5) by clicking on the stars
- If the user has rated the resource a green checkbox appears next to the stars, he can check what his rating is by sliding the mouse over the checkbox, his rating will appear as green stars. He can change his ratings by clicking again on the stars
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- MIDAS ratings system uses two types of ratings that are transparent for the users: a record of the users' ratings on each resource and a global rating for each resource that is computed automatically based upon all the ratings of its children by the main formula :
- To give more importance to the ratings on a parent resource than on all its children resources, we multiply the sum and the total number of the ratings on the parent resource by a Nrc factor, which represent the number of rated resources within the parent resource.
- We determine the max between Nrc and 1, as a mulitplying factor, in case there isn't any rated resource within the parent resource. In that case the global rating is due only to the ratings on the parent resource itself. The formula becomes:
- Also, if the parent resource has not been rated but its children have, then its global rating is due only to the ratings on its children,
- Anything that has a unique ID could possibly be rated via the ratings system. Developpers would just include the element ratings.thtml in the view where they want to see ratings appear. They might also want to define how these ratings are going to affect the global rating of the rest of the tree by writing the function that will compute the global rating for this resource.
