WebappConfig > Web Properties file
The web.properties file configures several attributes for the InterMine web application.
| Property | Determines |
| attributeLink | Used to configure hyperlinks, generally to external dbs. See "External Links" section below |
| bag.example.identifiers | Text present in the list upload form. See "List upload examples" section below |
| externallink | Redirect links in query results. See LinkRedirects |
| galaxy | See Galaxy |
| genomicRegionSearch | See GenomeRegionSearch |
| header.links | links at upper right corner |
| meta.keywords | will populate meta tag for keywords. |
| meta.description | will populate meta tag for description. Google uses this in their search results, I think |
| portal.welcome | the message to show when a user arrives at the webapp via the portal action (eg. <something>/portal.do) |
| quickSearch.identifiers | Text displayed in search box |
| theme | Colour scheme for the webapp. Available options are: blue, bright_blue, gold, green, grey, brown, ecoli_blue, metabolic, modmine, ratmine and purple. See Themes. |
| xrefLink | Used to configure hyperlinks for CrossReferences. See below |
Home page
Search box (first box on the left)
| begin.searchBox.title | title of box on left |
| begin.searchBox.description | text in the box on the left |
| begin.searchBox.example | text in the form field |
| textarea.identifiers | Text present on list upload on home page |
List upload box (middle box)
| begin.listBox.title | Title of box |
| begin.listBox.description | Text in box |
| begin.listBox.example | Text in form field |
Third box
| begin.thirdBox.title | Title of box if user is new |
| begin.thirdBox.visitedTitle | Title of box if user has visited before |
| begin.thirdBox.description | Text in box |
| begin.thirdBox.linkTitle | Text for large button |
| begin.thirdBox.link | URL for large button |
Tabs
| begin.tabs.1.id | Name of category, eg. Genes |
| begin.tabs.1.description | Text for that tab |
Templates tagged with each category will appear under the appropriate tab. See Tagging for details on how to tag templates.
List upload examples
Using the bag.example.identifiers key, one can provide a list of keyword examples on the list create/upload page. This could lead to a mixed list of items being updated and only, say Protein or Gene, identifiers being uploaded.
If one wants to provide different example identifiers per different types, like Genes, Proteins, SNPs, you can do so by using the following key:
bag.example.identifiers.gene, bag.example.identifiers.protein etc.
Then, when the user selects a Genes from a dropdown select box for type and choose the Example list link, the text box will be populated keywords associated only with bag.example.identifiers.gene key in the config file.
External links
You can add links to other websites by adding entries to the web.properties file.
The format for this property is:
# on the report page - a single identifier 'attributelink' + unique_name + class + taxonId + attributeName + (url|imageName|text) # on the list analysis page - a list of identifiers 'attributelink' + unique_name + class + taxonId + attributeName + 'list' + (url|imageName|text)
| unique_name | used to distinguish between multiple configurations for the same attribute/organism/class combination |
| class | class of object to link, eg. Protein |
| taxonId | either a proper id or '*' when no assumptions is made regarding the organism. |
| list | indicates the link will have a list of identifiers |
| url | url to link to |
| imageName | name of logo (optional), must be in /model directory |
| text | text that will appear next to the logo |
The value of the attribute (for the current object) is substituted anywhere the string "<<attributeValue>>" occurs in the text or the url
example:
attributelink.flybase.Gene.7227.primaryIdentifier.url=http://www.flybase.org/.bin/fbidq.html?<<attributeValue>> attributelink.flybase.Gene.7227.primaryIdentifier.text=FlyBase: <<attributeValue>>
In this case Gene pages for Drosophila melanogaster will have a link that uses the organismDbId field.
A list example:
attributelink.flymine.Gene.*.primaryIdentifier.list.url=http://www.flymine.org/query/portal.do?externalid=<<attributeValue>>&class=Gene attributelink.flymine.Gene.*.primaryIdentifier.list.text=FlyMine attributelink.flymine.Gene.*.primaryIdentifier.list.imageName=flymine_logo_link.gif
Only if a taxonId is specified the code will check if the link to the external db is relevant.
Settings for the xrefLink property
You can configure the URLs for querying CrossReference? from external sources by adding entries to the web.properties file.
The format for this property is:
# on the report page 'xreflink' + dataSource_name + (url|imageName)
| dataSource_name | the name of the external database |
| url | url to link to |
| imageName | name of logo (optional), must be in /model directory |
example:
xreflink.PFAM.url=http://pfam.sanger.ac.uk/family? xreflink.PIRSF.url=http://pir.georgetown.edu/cgi-bin/ipcSF?id=
Cross references represent identifiers used in external databases, eg. FlyBase?, UniProt. An object in InterMine which has CrossReference? will have a identifier and data source for that cross reference. In order to find the cross reference in that data source, a url is required to link to and the full path should look like url+identifier, e.g. http://pfam.sanger.ac.uk/family?PF00001. In web.properties, the first part of the full path could be configured as in "url", and identifier will be added programmatically to the rear of it. The dataSource_name should be consistent with the source name of the CrossReferences? in the InterMine database.
See: ModMine's web.properties file, FlyMine's web.properties file
Overriding properties
- global.web.properties - used by all mines. Properties set here will be available to everyone, even the test model mine.
- bio.web.properties - used by all bio-mines. Properties set here will be available to all mines that use the bio layer. so not the test model model. Can overwrite properties in the global.web.properties file.
- web.properties - used by a mine. Properties set here will be available to only that specific mine. Can create mine-specific properties or overwrite properties in the above two files.
See: WebappConfig
