Querying for shared nodes in JCR (ModeShape) - jcr

I have a JCR content repository implemented in ModeShape (4.0.0.Final). The structure of the repository is quite simple and looks like this:
/ (root)
Content/
Item 1
Item 2
Item 3
...
Tags/
Foo/
Bar/
.../
The content is initially created and stored under /Content as [nt:unstructured] nodes with [mix:shareable] mixin. When a content item is tagged, the tag node is first created under /Tags if it's not already there, and the content node is shared/cloned to the tag node using Workspace.clone(...) as described in the JCR 2.0 spec, section 14.1, Creation of Shared Nodes.
(I don't find this particularly elegant and I did just read this answer, about creating a tag based search system in JCR, so I realize this might not be the best/fastest/most scaleable solution. But I "inherited" this solution from developers before me, so I hope I don't have to rewrite it all...)
Anyway, the sharing itself seems to work (I can verify that the nodes are there using the ModeShape Content Explorer web app or programatically by session.getRootNode().getNode("Tags/Foo").getNodes()). But I am not able to find any shared nodes using a query!
My initial try (using JCR_SQL2 syntax) was:
SELECT * FROM [nt:unstructured] AS content
WHERE PATH(content) LIKE '/Tags/Foo/%' // ISDECENDANTNODE(content, '/Tags/Foo') gives same result
ORDER BY NAME(content)
The result set was to my surprise empty.
I also tried searching in [mix:shareable] like this:
SELECT * FROM [mix:shareable] AS content
WHERE PATH(content) LIKE '/Tags/Foo/%' // ISDECENDANTNODE(content, '/Tags/Foo') gives same result
ORDER BY NAME(content)
This also returned an empty result set.
I can see from the query:
SELECT * FROM [nt:unstructured] AS content
WHERE PATH(content) LIKE '/Content/%' // ISDECENDANTNODE(content, '/Content') works just as well
ORDER BY NAME(content)
...that the query otherwise works, and returns the expected result (all content). It just doesn't work when searching for the shared nodes.
How do I correctly search for shared nodes in JCR using ModeShape?
Update: I upgraded to 4.1.0.Final to see if that helped, but it had no effect on the described behaviour.

Cross-posted from the ModeShape forum:
Shared nodes are really just a single node that appears in multiple places within a workspace, so it's not exactly clear what it semantically means to get multiple query results for that one shareable node. Per Section 14.16 of the JSR-283 (JCR 2.0) specification implementations are free to include shareable nodes in query results at just one or at multiple/all of those locations.
ModeShape 2.x and 3.x always returned in query results only a single location of the shared nodes, as this was the behavior of the reference implementation and this was the feedback we got from users. When we were working on Modeshape 4.0, we tried to make it possible to return multiple results, but we ran into problems with the TCK and uncertainty about what this new expected behavior would be. Therefore, we backed off our goals and implemented query to return only one of the shared locations, as we did with 2.x and 3.x.
I may be wrong, but I'm not exactly sure if any JCR implementation returns multiple rows for a single shared node, but I may be wrong.

Related

Downloading all full-text articles in PMC and PubMed databases

According to one of the answered questions by NCBI Help Desk , we cannot "bulk-download" PubMed Central. However, can I use "NCBI E-utilities" to download all full-text papers in PMC database using Efetch or at least find all corresponding PMCids using Esearch in Entrez Programming Utilities? If yes, then how? If E-utilities cannot be used, is there any other way to download all full-text articles?
First of all, before you go downloading files in bulk, I highly recommend you read the E-utilities usage guidelines.
If you want full-text articles, you're going to want to limit your search to open access files. Furthermore, I suggest also restricting your search to Medline articles if you want articles that are any good. Then you can do the search.
Using Biopython, this gives us :
search_query = 'medline[sb] AND "open access"[filter]'
# getting search results for the query
search_results = Entrez.read(Entrez.esearch(db="pmc", term=search_query, retmax=10, usehistory="y"))
You can use the search function on the PMC website and it will display the generated query that you can copy/paste into your code.
Now that you've done the search, you can actually download the files :
handle = Entrez.efetch(db="pmc", rettype="full", retmode="xml", retstart=0, retmax=int(search_results["Count"]), webenv=search_results["WebEnv"], query_key=search_results["QueryKey"])
You might want to download in batches by changing retstart and retmax by variables in a loop in order to avoid flooding the servers.
If handle contains only one file, handle.read() contains the whole XML file as a string. If it contains more, the articles are contained in <article></article> nodes.
The full text is only available in XML, and the default parser available in pubmed doesn't handle XML namespaces, so you're going to be on your own with ElementTree (or an other parser) to parse your XML.
Here, the articles are found thanks to the internal history of E-utilities, which is accessed with the webenv argument and enabled thanks to the usehistory="y" argument in Entrez.read()
A few tips about XML parsing with ElementTree : You can't delete a grandchild node, so you're probably going to want to delete some nodes recursively. node.text returns the text in node, but only up to the first child, so you'll need to do something along the lines of "".join(node.itertext()) if you want to get all the text in a given node.
According to one of the answered questions by NCBI Help Desk , we cannot "bulk-download" PubMed Central.
https://www.nlm.nih.gov/bsd/medline.html + https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/ will download a good portion of it (I don't know the percentage). It will indeed miss the PMC full-texts articles whose license doesn't allow redistribution as explained on https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/.

Yii Nested Set (Yiiext). Trying to move a root node

I am using the fantastic extension by Yiiext "nested-set-behavior":
https://github.com/yiiext/nested-set-behavior
I am interested to know if anyone can let me know how to move (up or down) a root node when I am running the nested set with multiple roots.
tree example:
Phones (root node)
1.1 Mobile
1.2 Fixed
Cars (root node)
2.1 Fast
2.2 Slow
2.3 Average
Planes (root node)
3.1 Large
3.2 Small
At the moment when I pull out the full tree and show this to the user I get the above result.
I would like to be able to move "Cars" before "Phones".
Is there any way of doing this?
I have tried:
$cars = Category::model()->findByPk($cars_id);
$phones = $cars->prev()->find();
$cars->moveBefore($phones);
This gives me an error in the moveAfter method of the nested set behavior class.
Any one done this before?
Thanks
Dave
As the doc suggest the the prev() method returns :
Array of Active Record objects corresponding to ....
Therefore you have to approach this with different way e.g
$phones = Category::model()->findByPk($phones_id);
$cars = Category::model()->findByPk($cars_id);
$cars->moveBefore($phones);
Or other approach which suits your application scenario
Your code could be fixed by :
$cars = Category::model()->findByPk($cars_id);
$phones = $cars->prev()->find();
foreach($phones as $phone){
$cars->moveBefore($phone);
}
which does not make sense ;)
(p.s: did not test this code)
As I understand, you have 3 nodes, which are the roots.
The problem is that the methods moveAfter() and moveBefore() can not be applied to the main roots. You are trying to move a node, relatively another node, but they are in different trees.
If cars and phones have a common root, it will be success.
In other words, you operate with nodes in different trees, which know nothing about each other.

MVCSiteMap: Should the nodes pickup current request parameter values?

Setup:
I am using MvcSiteMap version 3 in an ASP.NET MVC 4 app.
Problem:
I have a node like this:
<mvcSiteMapNode title="Neighbours" area="MilkyWay" controller="SolarSystems" action="Planets" key="neighbours">
The Planets action on the SolarSystems controller has two parameters, int order, int size, where order states the order of the planets starting from the star. Eg, Mercury would be 1, and size is the order of the planets by size, where the smallest is 1.
For both parameters, -1 means I don't have a clue.
In my route registration, I have something like:
context.MapRoute(
"SolarSystems_Planets",
"SolarSystems/Planets/{order}/{size}",
new { controller = "SolarSystems", action = "Index", order = -1, size = -1 }
);
All works OK, ie, the default values are used...
...EXCEPT when the current page is an action that has the same two parameters with the same names.
In that case, the node will use these two parameters instead of the default values of -1.
For example, If I have a GalaxyClusters controller with an Index action that has two parameters int order and int size, and in the current request, order == 10009985639 and size = 9098 then my planets action tries to find a planet in our solar system with those values.
Obviously, it will fail and we have known that since Galileo's days.
What seems to be happening:
In other words, it seems that MvcSitemap injects the current values of any parameter and if a match is found, then BOOM! This seems wrong to me, so is this the default?
The problem is easily solved by putting in the node the following:
<mvcSiteMapNode title="Neighbours" area="MilkyWay" controller="SolarSystems" action="Planets" order="" size="" key="neighbours">
Is this reliable?!
Note (and questions restated):
I know I have answered what might appear to be my question, but if you think that, before voting to close the question, please read it carefully:
The question I am asking is whether this is the default behaviour? If it is, why? And: is my solution reliable?
Finally, I don't really have an app that catalogs all the galaxies in the Universe (sql server might not like that many records and I would be in receipt of the Nobel prize). I just adapted the problem so that I don't use my client's domain names.
This behavior is not part of MvcSiteMapProvider, but part of the MVC UrlHelper class and they don't intend to fix it.
According to the issue that was submitted about this to the MVC team, this behavior is by design. That is, the URL generation code will pick up ambient values of the request and automatically inject them into the URL if they match.
Their advice about how to work around this issue are the following:
Use named routes to ensure that only the route you want will get used to generate the URL (this is often a good practice, though it won't help in this particular scenario)
Specify all route parameters explicitly - even the values that you want to be empty. That is one way to solve this particular problem.
Instead of using Routing to generate the URLs, you can use Razor's ~/ syntax or call Url.Content("~/someurl") to ensure that no extra (or unexpected) processing will happen to the URL you're trying to generate.
You can accomplish all 3 of these solutions with MvcSiteMapProvider.
<!-- Using a named route -->
<mvcSiteMapNode title="Neighbours" area="MilkyWay" controller="SolarSystems" action="Planets" route="SolarSystems_Planets" key="neighbours">
That won't help in your case, but I am including it here to demonstrate how it can be done.
<!-- Specify parameters explicitly -->
<mvcSiteMapNode title="Neighbours" area="MilkyWay" controller="SolarSystems" action="Planets" order="10009985639" size="9098" key="neighbours">
This means of course you will need a node for each combination of order and size. If the data is coming from some shared resource such as a database, you can implement IDynamicNodeProvider to create a node for each case. This of course assumes that you know in advance what all of the potential values will be.
<!-- Specify the URL explicitly -->
<mvcSiteMapNode title="Neighbours" url="/MilkyWay/SolarSystems/Planets/10009985639/9098" key="neighbours">
Again, you will need a node per URL to accomplish this successfully.
See the issue # GitHub about this for further details.

Map blank nodes from stardog to pubby

So I have this .rdf that I have loaded onto Stardog and then I am using Pubby running over Jetty, to browse the triple store.
In my rdf file, I have several blank nodes which is given a blank node identifier by stardog. So this is a snippet of the rdf file.
<kbp:ORG rdf:about="http://somehostname/resource/res1">
<kbp:canonical_mention>
<rdf:Description>
<kbp:mentionStart rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1234</kbp:mentionStart>
<kbp:mentionEnd rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1239</kbp:mentionEnd>
</rdf:Description>
</kbp:canonical_mention>
So basically I have some resource "res1" which has links to blank node which has a mention start and mention end offset value.
The snippet of the config.ttl file for Pubby is shown below.
conf:dataset [
# SPARQL endpoint URL of the dataset
conf:sparqlEndpoint <http://localhost:5822/xxx/query>;
#conf:sparqlEndpoint <http://localhost:5822/foaf/query>;
# Default graph name to query (not necessary for most endpoints)
conf:sparqlDefaultGraph <http://dbpedia.org>;
# Common URI prefix of all resource URIs in the SPARQL dataset
conf:datasetBase <http://somehostname/>;
...
...
So the key thing is the datasetBase which maps URIs to URL.
When I try to map this, there is an "Anonymous node" link but upon clicking, nothing is displayed. My guess is, this is because the blank node has some identifier like _:bnode1234 which is not mapped by Pubby.
I wanted to know if anyone out there knows how to map these blank nodes.
(Note: If I load this rdf as a static rdf file directly onto Pubby, it works fine. But when I use stardog as a triple store, this mapping doesn't quite work)
It probably works in Pubby because they are keeping the BNode id's available; generally, the SPARQL spec does not guarantee or require that BNode identifiers are persistent. That is, you can issue the same query multiple times, which brings back the same result set (including bnodes) and the identifiers can be different each time. Similarly, a bnode identifier in a query is treated like a variable, it does not mean you are querying for that specific bnode.
Thus, Pubby is probably being helpful and making that work which is why using it directly works as opposed to a third party database.
Stardog does support the Jena/ARQ trick of putting a bnode identifier in angle brackets, that is, <_:bnode1234> which is taken to mean, the bnode with the identifier "bnode1234". If you can get Pubby to use that syntax in queries for bnodes, it will probably work.
But generally, I think this is something you will have to take up with the Pubby developers.

Eclipse RCP: How to order perspective buttons belonging to different plugins?

My application has 5 plugins. Each plugin has a perspective of it's own and hence each perspective extension definition is under individual plugin's plugin.xml.
Now, I want to control the order in which these perspectives appear in my application. How to do it?
There is one main plugin that holds "ApplicationWorkBenchAdvisor.java". This has initialize() method in which I am iterating through the perspective registry using
PlatformUI.getWorkbench().getPerspectiveRegistry().getPerspectives();
and then appending perspective ids in a comma separated fashion to a String variable (pbar) which is used later like this.
PlatformUI.getPreferenceStore().setDefault(IWorkbenchPreferenceConstants.PERSPECTIVE_BAR_EXTRAS, pbar);
PlatformUI.getPreferenceStore().setValue(IWorkbenchPreferenceConstants.PERSPECTIVE_BAR_EXTRAS, pbar);
When iterating thourgh the perspective registry, I can compare perspective ids and sort it(when adding to 'pbar' by comparing ids) the way I want it to appear but, I don't want to do this ordering here as it appears like a dirty way.
Is there any other place where we can fix the order in which perspectives appear? (Each perspective resides in different plugin).
ADDED
1) Could we also control the ordering in the perspective switcher?
2) Is there a way to control entry into perspective registry to in inflict the desired order. If not could we write back into perspective registry?
If your application is encapsulated as an eclipse product, you may tweak the plugin.properties/plugin_customization.ini file.
(file referenced by the 'preferenceCustomization' property in your product extension point.)
This file is a java.io.Properties format file. Typically this file is used to set the values for preferences that are published as part of a plug-in's public API.
(Example of such a file for org.eclipse.platform)
So if the string representing the order of perspective can be referenced as a property, you can define the default order in there.
Since the source code of IWorkbenchPreferenceConstants mentions:
/**
* Lists the extra perspectives to show in the perspective bar.
* The value is a comma-separated list of perspective ids.
* The default is the empty string.
*
* #since 3.2
*/
public static final String JavaDoc PERSPECTIVE_BAR_EXTRAS = "PERSPECTIVE_BAR_EXTRAS"; //$NON-NLS-1$
Maybe a line in the plugin_customization.ini file:
org.eclipse.ui/PERSPECTIVE_BAR_EXTRAS=perspectiveId1,perspectiveId2,perspectiveId3
would allow you to specify that order without having to hard-code it.
Additional notes:
IPerspectiveRegistry (or PerspectiveRegistry) is not made to write anything (especially for perspective defined in an extension)
Ordering may be found in the state of the workbench (stored in the workspace and then restored when its launched again, .metadata/.plugins/org.eclipse.ui.workbench/workbench.xml)
Do you confirm that:
IPerspectiveRegistry registry = PlatformUI.getWorkbench().getPerspectiveRegistry();
IPerspectiveDescriptor[] perspectives = registry.getPerspectives();
is not in the right order when the plugin_customization.ini does define that order correctly ?
Liverpool 5 - 0 Aston Villa does confirm that (in the comments), but also indicates the (ordered) ini file entries internally get recorded into preference store, which means they can be retrieved through the preference store API:
PatformUI.getPreferenceStore().getDefault(
IWorkbenchPreferenceConstants.PERSPECTIVE_BAR_EXTRAS)
Liverpool 5 - 0 Aston Villa then add:
perspective registry (the initial "PlatformUI.getWorkbench().getPerspectiveRegistry().getPerspectives();" bit) remains unaltered (and unordered).
But, you still can "readily access to ordered list of perspectives" through preference store.
So, for other tasks, instead of iterating though perspective registry (which is still unordered), we can use the ordered variable that stores list of ordered perpective ids.
.
.
.
.
Note: another possibility is to Replace the Perspective-Switcher in RCP apps
=> to:
You can more easily define the order in a menu or in buttons there.
Extreme solution: re-implement a perspective switcher.
To sum up all the observations and findings,
1) It is not possible to alter entries in the perspective registry. It is read-only.
2) To make perspective appear in the order that we want on perspective bar, we can achieve it by adding an entry in plugin_customization.ini (or preferences.ini) as shown below.
org.eclipse.ui/PERSPECTIVE_BAR_EXTRAS=perspectiveId1,perspectiveId2,perspectiveId3
3) If we want to fetch this ordered list, we can't fetch it directly. But as this ini file entry internally gets recorded in PreferenceStore we can fetch the same value from PreferenceStore using the following API as shown below.
PlatformUI.getPreferenceStore().getDefault(
IWorkbenchPreferenceConstants.PERSPECTIVE_BAR_EXTRAS);
Why would someone need to access the entry defined in ini file at all?
Well, in my case I had a view in which i had to display links to every perspective. As my perspective bar was sorted in desired order, I also wanted to maintain the same order in my view while displaying links to perspectives.
4) There is no known way to inflict the same sort order in the display of default perspective switcher. While a new custom perspective switcher can be written to achieve the desired effect.