Eirods-dav provides access to iRODS servers using the WebDAV protocol and exposes a REST API for accessing and manipulating metadata from within a web browser. It takes the original Davrods module written by Ton Smeele and Chris Smeele, which is a bridge between the WebDAV protocol and the iRODS API. Davrods leverages the Apache server implementation of the WebDAV protocol, mod_dav, for compliance with the WebDAV Class 2 standard.
Eirods-dav adds extra features such as themeable listings and anonymous access for public-facing websites. As well as these features, it also incorporates a REST API for interacting with the metadata stored within an iRODS system. All of these features are implemented as an Apache HTTPD module.
Some of the features that have been added within Eirods-dav are:
- Themeable listings similar to using mod_autoindex.
- Expose and navigate by metadata key-value pairs.
- Search the metadata catalogue.
- REST API for accessing and manipulating the iRODS data and metadata
- Client-side interface to add, edit and delete metadata entries.
- Download all of the metadata for an iRODS entry in various formats.
- Full location breadcrumbs.
- Each user able to have their own custom default root path exposed.
- Users able to log in as well as having a default public user.
As well as features from the original Davrods such as:
- Supports WebDAV Class 2. Locks are local to the Apache server.
- Supports PAM and Native (a.k.a. STANDARD) iRODS authentication.
- Supports SSL encryption for the entire iRODS connection.
- Easy to configure using Apache configuration directives.
- Supports iRODS server versions 4+ and is backwards compatible with 3.3.1.
A working live site of this module showing the themeable listings along with metadata searching and linking is available at the Designing Future Wheat Data Portal.
- For Frictionless Data Packages, any CSV or TSV files are now specified as tabular data resources. For information on how to configure retreiving the required values from the iRODS repository, the details are here. This initial support is for the general column types and support for the format and other fields defined by the Frictionless Data Table Schema will follow in subsequent upgrades.
- Added support for Frictionless Data Data Packages. The details are here.
- Added ability to show the data object checksums in the listings table. See the documentation on the DavRodsShowChecksum and DavRodsChecksumHeading directives for more information. If you are building with an existing user.prefs file, you will need to add the DIR_BOOST and DIR_JANSSON directives to this. See the included example-user.prefs file for more details.
- Added workaround for the fact that mod_dav.so assumes that it is the handler for the REST API calls (https://svn.apache.org/viewvc/httpd/httpd/branches/2.4.x/modules/dav/main/mod_dav.c?revision=1807753&view=markup#l4863)
- Fixed response content-types for the views/... calls
- Object type now included when using the REST API calls that get id information for given paths
- The REST handler now makes sure that the request is really for it before getting the request parameters so it can be used with other modules that are also reading these.
- REST API now accepts POST requests.
- Added REST API for generating virtual directory listings.
- Added Views API for performing searches and generating virtual directory listings directly within the web page.
- Added extra places within the web page where custom HTML sections can be added.
- Added ability to get HTML chunks from any http(s) source such as another web server.
- Added dynamic capabilities to the URL used for getting the HTML chunks using the iRODS ids and metadata values.
- Added ability to customise the headings in the listings table and remove columns.
EIrods-dav requires the following packages to be installed on your server:
- Apache httpd 2.4+
- iRODS 4.x client libraries and headers (in package
irods-runtimeandirods-dev, available from the iRODS website)
Due to the way iRODS libraries are packaged, specifically, its network plugins, one of the following packages must also be installed:
irods-icommandsORirods-icatORirods-resource.
These three packages all provide the necessary libraries in
/var/lib/irods/plugins/network.
For binary installation, download the package for your platform at
https://github.com/billyfish/eirods-dav/releases and copy the module to the
modules directory of your Apache httpd installation. If the binary version
is not available, then you can compile the module from source.
To compile Eirods-dav from source, copy example-user.prefs to user.prefs and edit
it to contain values valid for your system. The file is commented and should be able to
to be set up with a minimum of effort.
Once this is complete, then make followed by make install will create
and install mod_eirods-dav.so to your Apache httpd installation.
See the configuration section for instructions on how to configure Eirods-dav once it has been installed.
If the machine on which you install Eirods-dav is protected by SELinux, you may need to make changes to your policies to allow Eirods-dav to run:
- Apache HTTPD must be allowed to connect to TCP port 1247
- Eirods-dav must be allowed to dynamically load iRODS client plugin libraries in /var/lib/irods/plugins/network
For example, the following two commands can be used to resolve these requirements:
setsebool -P httpd_can_network_connect true
chcon -t lib_t /var/lib/irods/plugins/network/lib*.so
Eirods-dav is configured in two locations: an HTTPD configuration file, which is the main configuration file and in an iRODS environment file used for iRODS client library configuration, similar to the configuration of icommands.
The Eirods-dav RPM distribution installs a commented out vhost template
in davrods-vhost.conf. With the comment marks
(#) removed, this provides you with a sane default configuration
that you can tune to your needs. The Eirods-dav configuration
options are documented in this file and can be changed to your liking.
As well as that documentation, the new features are also described
below.
If you wish to run Eirods-dav without the need for authentication, it
can be set up to run as a normal public-facing website. This is done by
specifying a user name and password for the iRODS user whose data you
wish to display. The directives for these are DavRodsDefaultUsername
and DavRodsDefaultPassword.
For example, to display the data for a user with the user name anonymous and password foobar the configuration directives would be:
DavRodsDefaultUsername anonymous
DavRodsDefaultPassword foobar
- DavRodsAddExposedRoot: This directive allows you to specify the default exposed roots on a per-user basis. When a logged-in user hasn't been added using this directive, the DavRodsExposedRoot will be used instead.
DavRodsAddExposedRoot lars /tempZone/home/lars/private
DavRodsAddExposedRoot james /tempZone/home/admin
By default, the html listings generated by mod_davrods do not use any styling. It is possible to style the listings much like mod_autoindex. There are various directives that can be used.
- DavRodsThemedListings: This directive is a global on/off switch which toggles the usage of themed listings. Unless this is set to true then none of the following directives in this section will work. To turn it on, use the following directive:
DavrodsThemedListings true
There are various points in the web pages generated by Eirods-dav where custom HTML can be inserted. Each of these configuration directives take three different types of different data:
- text: Treat the configuration value as raw HTML that will get used. This can either be a single-line directive or if you want to define this across multiple lines of text you will need a backslash (\) at the end of each line. An example is
DavRodsHTMLHead <link rel="stylesheet" type="text/css" \
media="all" href="/eirods_dav_files/styles/styles.css">
- file: A file whose content will be used for the required HTML chunk by beginning your value with "file:", e.g. to use the content of a file at /opt/apache/eirods_dav_head.html:
DavRodsHTMLTop file:/opt/apache/eirods_dav_head.html
If a file is used, then it will be re-read for each incoming request. So any changes you make to the file won't need a restart of Apache to be made live.
- http(s): A web page that is available via an http or https request. Eirods-dav will download all of the html and use this as the data that will be inserted into its listing page. The configuration value needs to begin with the appropriate protocol, e.g. http or https. For example to use the content of a web page at https://grassroots.tools/eirods_dav_bottom.html
DavRodsHTMLBottom https://grassroots.tools/eirods_dav_bottom.html
So each of these examples all point to static resources in that the content is always the same regardless of the listing that Eirods-dav is currently displaying. One of the new features of Eirods-dav is that it can now use its internal variables to use dynamic resources. It currently has two types of internal variables
- id: This is the iRODS id for the collection that Eriods-dav is currently displaying.
- metadata: This is used to get a given value from the metadata for the current collection. For example if the collection had metadata key called method, then the value for this would be referred to by metadata:method.
Each variable is denoted within a configuration directive by placing it in inside a @{ } block. So an example directive might be so to set URL parameters of project to the metadata value for the current collection's metadata key of project_id and setting a parameter of irods_id to the current collection's iRODS id would be:
DavRodsHTMLTop https://test.server?project=@{metadata:project_id}&irods_id=@{id}
and, for example, if the id of the current collection was 2.123 and it had a metadata key-value pair of project_id = mariner1, then Eirods-dav would convert this web address into
https://test.server?project=mariner1&irods_id=2.123
Each of the configuration directives for these options to insert HTML into the web page are listed below:
-
DavRodsHTMLHead: This is an HTML text that will be placed within the <head> directive of the HTML pages generated by Eirods-dav. More information on the types of values that this can take is described in the themed listings section.
-
DavRodsHTMLTop: You can specify a chunk of HTML to appear above each listing using this directive. More information on the types of values that this can take is described in the themed listings section.
-
DavRodsPreListingsHtml: You can specify a chunk of HTML to appear directly prior to the directory listing using this directive. More information on the types of values that this can take is described in the themed listings section.
-
DavRodsPostListingsHtml: You can specify a chunk of HTML to appear directly after to the directory listing using this directive. More information on the types of values that this can take is described in the themed listings section.
-
DavRodsHTMLBottom: You can specify a chunk of HTML to appear below each listing using this directive. More information on the types of values that this can take is described in the themed listings section.
-
DavRodsPreCloseBodyHtml: You can specify a chunk of HTML to appear just before the closing </body> tag using this directive. More information on the types of values that this can take is described in the themed listings section.
-
DavRodsZoneLabel: This directive allows you specify an alternative value instead of the iRODS zone name. For example to set this to be public data, then the directive would be:
DavRodsZoneLabel public data
The directory listings can be customised using a variety of configuration directives.
- DavRodsHTMLListingClass: The list of collections and data objects displayed by Eirods-dav are within an HTML table. If you wish to specify CSS classes for this table, you can use this directive. For instance, if you wish to use the CSS classes called table and table-striped, then you could use the following directive:
DavRodsHTMLListingClass table table-striped
The listings table defaults to displaying five columns:
- Name
- Owner
- Size
- Date
- Properties
Each of these headings can be changed to one of your choice using the following configuration directives. If you would like a column to be hidden then set the value of any of these directives to !. For example
DavRodsOwnerHeading !
would hide the Owner column.
- DavRodsNameHeading: If you want to change the column heading for the Name column then you can use this directive. For instance to change it to Object
DavRodsNameHeading Object
- DavRodsSizeHeading: If you want to change the column heading for the Size column then you can use this directive. For instance to change it to File size
DavRodsSizeHeading File size
- DavRodsOwnerHeading: If you want to change the column heading for the Owner column then you can use this directive. For instance to hide it
DavRodsOwnerHeading !
- DavRodsDateHeading: If you want to change the column heading for the Date column then you can use this directive. For instance to change it to Last modified
DavRodsDateHeading Last modified
- DavRodsPropertiesHeading: If you want to change the column heading for the Properties column then you can use this directive. For instance to change it to Metadata
DavRodsPropertiesHeading Metadata
- DavRodsShowChecksum: If you wish to add a column for displaying the file checksums, set this directive to true. By default it is false and checksums will not be displayed.
DavRodsShowChecksum true
- DavRodsChecksumHeading: If you want to change the column heading for the Checksum column then you can use this directive. For instance to change it to MD5
DavRodsChecksumHeading MD5
- DavRodsHTMLCollectionIcon:
If you wish to use a custom image to denote collections, you can use this
directive. This can be superseded by a matching call to the
DavRodsAddIcondirective. For instance, to use /eirods_dav_files/images/drawer for all collections, the directive would be:
DavRodsHTMLCollectionIcon /eirods_dav_files/images/drawer
- DavRodsHTMLObjectIcon:
If you wish to use a custom image to denote data objects, you can use
this directive. This can be superseded by a matching call to the
DavRodsAddIcondirective. For instance, to use /eirods_dav_files/images/file for all data objects, the directive would be:
DavRodsHTMLObjectIcon /eirods_dav_files/images/file
- DavRodsAddIcon: This directive allows you to specify icons that will be displayed in the listing for matching collections and data objects. This directive takes two or more arguments the first of which is the path to the image file to use. The remaining arguments are the file suffices that will be matched and use the given icon. For example, to use an archive image for various compressed files and a picture image for image files, the directives would be:
DavRodsAddIcon /eirods_dav_files/images/archive .zip .tgz
DavRodsAddIcon /eirods_dav_files/images/image .jpeg .jpg .png
Each data object and collection can also display its metadata AVUs and have these as clickable links to allow a user to browse all data objects and collections with matching metadata too.
-
DavRodsHTMLMetadata: This directive is toggles the usage of metadata within the listings. It can take one of the following values:
- full: All of the metadata for each entry will get sent in the HTML page for each request.
-
on_demand: None of the metadata is initially included with the HTML pages sent by Eirods-dav. Instead they can be accessed via AJAX requests from these pages.
-
none: No metadata information will be made available. So to set the metadata to be available on demand, the directive would be:
DavRodsHTMLMetadata on_demand
- DavRodsHTMLMetadataEditable: This directive specifies whether the client-side functionality for editing the metadata by accessing REST API calls is active or not. By default, it is off and can be turned on by setting this directive to true.
DavRodsHTMLMetadataEditable true
- DavRodsHTMLAddMetadataImage:
If
DavRodsHTMLMetadataEditableis set to true, then you can use this directive to specify the image used for the button to add metadata to a particular data object or collection.
DavRodsHTMLAddMetadataImage /eirods_dav_files/images/list_add
- DavRodsHTMLDeleteMetadataImage:
If
DavRodsHTMLMetadataEditableis set to true, then you can use this directive to specify the image used for the button to delete metadata from a particular data object or collection.
DavRodsHTMLDeleteMetadataImage /eirods_dav_files/images/list_delete
- DavRodsHTMLEditMetadataImage:
If
DavRodsHTMLMetadataEditableis set to true, then you can use this directive to specify the image used for the button to edit metadata for a particular data object or collection.
DavRodsHTMLEditMetadataImage /eirods_dav_files/images/list_edit
- DavRodsHTMLDownloadMetadataImage: You can use this directive to specify the image used for the button to download all of the metadata for a particular data object or collection.
DavRodsHTMLDownloadMetadataImage /eirods_dav_files/images/list_download
- DavRodsHTMLOkImage:
If
DavRodsHTMLMetadataEditableis set to true, then you can use this directive to specify the image used for the "OK" button of the metadata editor.
DavRodsHTMLOkImage /eirods_dav_files/images/list_ok
- DavRodsHTMLCancelImage:
If
DavRodsHTMLMetadataEditableis set to true, then you can use this directive to specify the image used for the "Cancel" button of the metadata editor.
DavRodsHTMLCancelImage /eirods_dav_files/images/list_cancel
Eirods-dav has a REST API for accessing and manipulating the iRODS metadata catalog. You can specify the reserved address that Eirods-dav will use to have its REST API available on.
- DavRodsAPIPath: This directive specifies the path used within Eirods-dav to link to the various REST API functionality such as the metadata search. To specify it as /api/, which is a good default, use the following directive:
DavRodsAPIPath /api/
Then the various REST API endpoints would all begin with /api/ e.g. /api/metadata/search for the search function.
Currently the REST API has the following functions:
-
metadata/get: This is for getting all of the associated metadata for an iRODS item. It takes two parameter, the first is id, which is the iRODS id of the data object or collection that you wish to get the metadata pairs for. The second parameter is output_format which specifies the format that the metadata will be returned in. It currently can take one of the following values:
- json: This will return the metadata as a JSON (JavaScript Object Notation) array with each entry in the array having attribute, value, and where appropriate, units keys for its key-value pairs.
- csv: This will return the metadata as a table of comma-separated values with the order of the columns being attribute, value, units. Each of these entries will be contained within double quotes to allow for commas within their values without causing errors.
- tsv: This will return the metadata as a table of tab-separated values with the order of the columns being attribute, value, units. Each of these entries will be contained within double quotes to allow for commas within their values without causing errors.
For example to get the metadata for a data object with the id of 1.10021 in a JSON output format, the URL to call would be
/eirods-dav/api/metadata/get?id=1.10021&output_format=json
- metadata/search: This API call is for getting a list of all data objects and collections that have a given metadata attribute-value pair. It takes two parameters: key, which is the attribute to search for and, value, which specifies the metadata value. There is a third optional parameter, units for specifying the units that the metadata attribute-value pair must also have. So to search for all of the data objects and collections that have an attribute called volume with a value of 11, the URL to call would be
/eirods-dav/api/metadata/search?key=volume&value=11
- metadata/edit: This API call is for editing a metadata attribute-value pair for a data object of collection and replacing one or more of its attribute, value or units. It takes the following required parameters: id, which is the iRODS id of the data object or collection to delete the metadata from, key, which is the attribute to edit, value, which specifies the metadata value to edit. Again, there is an optional parameter, units for specifying the units that the metadata attribute-value pair must also have to match. There must also be one or more of the following parameters to specify how the metadata will be altered: new_key, which is for specifying the new name for the attribute, new_value, for specifying the new metadata value and new_units for specifying the units that the metadata attribute-value pair will now have. So to edit an attribute called volume with a value of 11 and units of decibels for a data object with the id of 1.10021 and give it a new value of 8 and units of litres, the URL to call would be
/eirods-dav/api/metadata/edit?id=1.10021&key=volume&value=11&units=decibels&new_value=8&new_units=litres
- metadata/add: This API call is for adding a metadata attribute-value pair to a data object of collection. It takes three parameters: id, which is the iRODS id of the data object or collection to add the metadata to, key, which is the attribute to add and, value, which specifies the metadata value to be added. As with the search call listed above, there is a fourth optional parameter, units for specifying the units that the metadata attribute-value pair will have. So to add an attribute called volume with a value of 11 to a data object with the id of 1.10021, the URL to call would be
/eirods-dav/api/metadata/add?id=1.10021&key=volume&value=11
- metadata/delete: This API call is for deleting a metadata attribute-value pair from a data object of collection. It takes three parameters: id, which is the iRODS id of the data object or collection to delete the metadata from, key, which is the attribute to delete for and, value, which specifies the metadata value to delete. As before, there is a third optional parameter, units for specifying the units that the metadata attribute-value pair must also have to match. So to delete an attribute called volume with a value of 11 and units of decibels from a data object with the id of 1.10021, the URL to call would be
/eirods-dav/api/metadata/delete?id=1.10021&key=volume&value=11&units=decibels
- metadata/keys: This API call is for getting a list of the metadata keys that have a partial match with a given key parameter denoted by key. For example, to get a list of all keys containing the phrase proj, the URL to call would be
/eirods-dav/api/metadata/keys?key=proj
- metadata/values: This API call is for getting a list of the metadata key-value pairs that have a partial match for the value given by the parameter value for a given key parameter denoted by key. For example, to get a list of all key-value pairs for a key called name and a value containing the phrase ob so that it would match Robert, Bob, etc., the URL to call would be
/eirods-dav/api/metadata/values?key=name&value=ob
- general/info: This API call is for getting information such as id, path, file size, etc. on a given iRODS data object or collection. The parameter, path, specifies the object or collection to get the details for. For example, to get the information for the item at /test/test.txt, the URL to call would be
/eirods-dav/api/general/info?path=/test/test.txt
- general/list: This API call is for getting information such as id, path, file size, etc. for a list of given iRODS data object or collection ids. The parameter, ids, specifies a space- or comma-separated list of ids. For example to get the information for the ids 1.123 and 2.234, the URL to call would be
/eirods-dav/api/general/list?ids=1.123%202.234
As the REST API returns its results in JSON and other delimited formats, it's also useful to display the information from these API functions in the web page so Eirods-dav has views for some of these functions.
DavRodsViewsPath: This directive specifies the path used within Eirods-dav to link to the various HTML views that use the REST API functionality such as the metadata search functionality. To specify it as /views/, which is a good default, use the following directive:
DavRodsViewsPath /views/
Then the various views endpoints would all begin with /views/ e.g. /views/search for the search view.
Currently there are the following views:
- search: This generates a web page based upon the results of the REST metadata search function. It takes two parameters: key, which is the attribute to search for and, value, which specifies the metadata value. There is a third optional parameter, units for specifying the units that the metadata attribute-value pair must also have. So to search for all of the data objects and collections that have an attribute called volume with a value of 11, the URL to call would be
/eirods-dav/views/search?key=volume&value=11
- list: This generates a web page based upon the results of the REST list function described in the general section of the REST API documentation. It displays a virtual directory listing for a list of given iRODS data object or collection ids. The parameter, ids, specifies a space- or comma-separated list of ids. For example to get the information for the ids 1.123 and 2.234, the URL to call would be
/eirods-dav/views/list?ids=1.123%202.234
Frictionless Data is an open source toolkit and set of standards to make data integration as simple as possible. The standards cover datasets, files and tabular data and over time the goal is to cover all of these. For now though, we are starting with datasets which are covered by the Data Package format. So for each configured iRODS collection, a virtual Data Package will be created and appear in the listings as a normal file available for download.
To populate the various parts of the data package specification for a given collection, eirods-dav will query the collection's iRODS metadata. This is for values such as the license, authors, title, description, etc. By default, the metadata keys used are:
| Data Package field | Default iRODS metadata key |
|---|---|
| license_name | license |
| license_url | license_url |
| description | description |
| name | name |
| authors | authors |
| title | title |
| id | id |
-
DavRodsFrictionlessData: If
DavRodsFrictionlessDatais set to true, then the Frictionless Data support is enabled. -
DavRodsFDResourceNameKey: This is the key to use when querying iMeta catalog for the value to use for the name field in the data package. If thie configuration variable is not set, then the default key name of name will be used to search in iMeta. For example, to get the value associated with the metadata key project_name, you would need the following configuration setting:
DavRodsFDResourceNameKey project_name
- DavRodsFDResourceLicenseNameKey: This is the key to use when querying iMeta catalog for the value to use for the license field in the data package. If thie configuration variable is not set, then the default key name of license will be used to search in iMeta. For example, to get the value associated with the metadata key project_license_name, you would need the following configuration setting:
DavRodsFDResourceLicenseNameKey project_license_name
- DavRodsFDResourceLicenseUrlKey: If this is set, then this key will be queried in the iMeta catalog for this collection. If it is not set, then the default key name of license_url will be used. For example, to get the value associated with the metadata key project_license_web, you would need the following configuration setting:
DavRodsFDResourceLicenseUrlKey project_license_web
- DavRodsFDResourceTitleKey: This is the key to use when querying iMeta catalog for the value to use for the title field in the data package. If thie configuration variable is not set, then the default key name of title will be used to search in iMeta. For example, to get the value associated with the metadata key project_title, you would need the following configuration setting:
DavRodsFDResourceTitleKey project_title
- DavRodsFDResourceAuthorsKey: If this is set, then this key will be queried in the iMeta catalog for this collection. If it is not set, then the default key name of authors will be used. For example, to get the value associated with the metadata key project_authors, you would need the following configuration setting:
DavRodsFDResourceAuthorsKey project_authors
- DavRodsFDResourceDescriptionKey: This is the key to use when querying iMeta catalog for the value to use for the description field in the data package. If thie configuration variable is not set, then the default key name of description will be used to search in iMeta. For example, to get the value associated with the metadata key project_description, you would need the following configuration setting:
DavRodsFDResourceDescriptionKey project_description
- DavRodsFDResourceIdKey: This is the key to use when querying iMeta catalog for the value to use for the id field in the data package. If thie configuration variable is not set, then the default key name of id will be used to search in iMeta. For example, to get the value associated with the metadata key project_id, you would need the following configuration setting:
DavRodsFDResourceIdKey project_id
- DavRodsFDDataPackageImage: You can use this directive to specify the image used for the data package.
DavRodsFDDataPackageImage /eirods_dav_files/images/archive
- DavRodsFDSaveDataPackages: By default, the datapackage.json files are virtual and generated on the fly. Although this may be fine for smaller datasets, you may find that the time that is taken to generate these files is too long. So this configuration directive can be used to store the datapackage.json file within the relevant collection. This is equivalent to running the iRODS command iput. So you must make sure that the iRODS user configured by DavRodsDefaultUsername or the currently logged in user has the permissions to be able to write files to the given collection. By default, this directive is false. To enable it, set it to true.
DavRodsSetSaveFDDataPackages true
These keys can be concatenated so that multiple metadata values can be combined where necessary as a comma-separated string. For instance, if the value that you wish to use for the description is the combination of short_info and detailed_info metadata keys, then the configuration would be.
DavRodsFDResourceDescriptionKey short_info,detailed_info
As well as specifying the keys, white space or full stops can be specified in the configuration value too. With the example above, if you would like to have s the short_info, a full stop, two blank lines, the detailed_info, a space and the footnote metadata value, the configuration would be
DavRodsFDResourceDescriptionKey short_info,.,\n,\n,detailed_info, ,footnote
Any csv or tsv files in a Frictionless Data package can now be configured to display their tabular-specific data fields within a datapackage.json file. This is done by querying the iMeta catalog for the given data object. The first required key is column_headings which has a comma-separated list of the column headings for the tabular file. For each of these headings an additional key-value pair specify the type of data in the given column of the file. The keys for these are the column name with a _type suffix and the values being ones of the types defined here.
So, using this example file data.csv which has three columns containing a string, an integer and a floating point number respectively, shown below
var1,var2,var3
A,1,2.1
B,3,4.5
the required imeta fields would be
- column_headings: var1,var2,var3
- var1_type: string
- var2_type: integer
- var3_type: number
The required imeta data would be
billy@desktop:~/$ imeta ls -d datasets/tabular/data.csv
AVUs defined for dataObj /grassrootsZone/home/rods/datasets/tabular/data.csv:
attribute: column_headings
value: var1,var2,var3
units:
----
attribute: var1_type
value: string
units:
----
attribute: var2_type
value: integer
units:
----
attribute: var3_type
value: number
units:
The Frictionless Data support can be configured to only be active at particular points in the directory hierarchy. For example, to have the data packages appear in all of the child directories of /data, the configuration might be
# Generate Data Packages for all child directories directly below /data
<LocationMatch "/data/[^\/]+/">
DavRodsFrictionlessData true
DavRodsFDResourceTitleKey projectName
DavRodsFDResourceIdKey uuid
DavRodsFDResourceDescriptionKey projectName,.,\n,\n,description
DavRodsFDDataPackageImage /images/archive
</LocationMatch>
# Since Data Packages are generated for the child directories configured in
# the line above, exclude all directories further down
<LocationMatch "/data/[^\/]+/[^\/]+/">
DavRodsFrictionlessData false
</LocationMatch>
The binary distribution installs the irods_environment.json file in
/etc/httpd/irods. In most iRODS setups, this file can be used as
is.
Importantly, the first seven options (from irods_host up to and
including irods_zone_name) are not read from this file. These
settings are taken from their equivalent Eirods-dav configuration
directives in the vhost file instead.
The options in the provided environment file starting from
irods_client_server_negotiation do affect the behaviour of
Eirods-dav. See the official documentation for help on these settings.
For instance, if you want Eirods-dav to connect to iRODS 3.3.1, the
irods_client_server_negotiation option must be set to "none".
To build from source, the following build-time dependencies must be installed (package names may differ on your platform):
httpd-devel >= 2.4apr-develapr-util-develirods-dev
Additionally, the following runtime dependencies must be installed:
httpd >= 2.4which can either be installed using the platform package provider or downloaded and built from the httpd website.irods-runtime >= 4.1.8janssonboostboost-systemboost-filesystemboost-regexboost-threadboost-chrono
First, browse to the directory where you have unpacked the Eirods-dav source distribution.
Running make without parameters will generate the Davrods module .so
file in the .libs directory. make install will install the module
into Apache's modules directory.
If you are using the httpd provided by your platform, then copy the davrods.conf
file into /etc/httpd/conf.modules.d/. If you are using an httpd installed from a source package, then copy davrods-vhost.confto theconf/extra` folder
inside httpd and enable it by adding
include conf/extra/davrods-vhost.conf
to conf/httpd.conf.
Note: Non-Redhat platforms may have a different convention for the location of the above file and the method for enabling/disabling modules, consult the respective documentation for details.
Create an irods folder in a location where Apache HTTPD has read
access (e.g. /etc/httpd/irods). Place the provided
irods_environment.json file in this directory. For most setups, this
file can be used as is (but please read the configuration
section).
Finally, set up httpd to serve Eirods-dav where you want it to. An example vhost config is provided for your convenience.
If you are dealing with big files, you will almost certainly want to enable Apache's compression functionality using mod_deflate.
For instance, to enable compressed response bodies from Apache, you might want a configuration such as
LoadModule deflate_module modules/mod_deflate.so
SetOutputFilter DEFLATE
SetEnvIfNoCase Request_URI "\.(?:gif|jpe?g|png|gzip|zip|bz2)$" no-gzip
Please report any issues you encounter on the issues page.
Simon Tyrrell and Chris Smeele.
For questions or support on the WebDAV functionality, Simon Tyrrell, Chris Smeele or Ton Smeele either directly. For questions or support on the themes and REST API, contact Simon Tyrrell directly or via the Earlham Institute page.
Copyright (c) 2017-20, Earlham Institute and (c) 2016 Utrecht University.
EIrods-dav is licensed under the GNU Lesser General Public License version 3 or higher (LGPLv3+). See the COPYING.LESSER file for details.
The lock_local.c file was adapted from the source of mod_dav_lock,
a component of Apache HTTPD, and is used with permission granted by
the Apache License. See the copyright and license notices in this file
for details.