what is a proper way of organizing files in a wcm that is using JCR. Let's say the total file count is 100,000+ files and total file size is about 50-70GB.
Is it better to organize files by fie types ( and create sub directories to further group the files by some category)
What are the advantages. Does it make any difference while using query api, maintenance, or something.
Proposal 1:
--shared
------images
------pdf
------movies
--location1
------images
------pdf
------movies
--location2
------images
------pdf
------movies
Proposal 2:
--pdf
-------shared
-------location1
-------location2
--images
--------shared
--------location1
--------location2
.. etc
Take a look at this: David's Model: A guide for content modeling
Some highlights:
Data First, Structure Later. Maybe.
Drive the content hierarchy, don't let it happen.
Workspaces are for clone(), merge() and update().
Beware of Same Name Siblings.
References considered harmful.
Files are Files are Files.
ID's are evil.
Whatever you do, make sure you don't end up with more than a 1000 child nodes under any given node.
Just as in any (real) file system, when you want to list a folder with a lot of files/subfolders in it, it can take some time.
By default Jackrabbit 2.x will now hash up the user space.
ie:
/users/s/sa/sandra
/users/s/si/simong
...
I would personally go for your first proposal as it makes more sense.
We have a webapp where all our users can upload/delete/modify their files in JCR and did it this way:
/_users/s/si/simon/public
/_users/s/si/simon/public/My Pictures
/_users/s/si/simon/public/My Pictures/2010/06/Trip to the US
/_users/s/si/simon/public/My Pictures/2010/06/Trip to the US/DC1001.jpg
/_users/s/si/simon/private/account_details.txt
...
We're loosely following the way home folders are done in UNIX-like systems.
We try to hash up all the things we (reasonably) can. Like the for example the user space (/s/si/simong) but also things like messages:
/_users/s/si/simong/messages/2009/12/25/ab34ed87dee
/_users/s/si/simong/messages/2010/03/12/e4f1de3cd48
...
However it's up to the individual user to not have more then 1000 child files in a given folder (we do warn them though.)
Doing it this way also gives you a nice benefit of exercising Access Control.
ie: everthing under ~/private is only read- and writeable by the current user, ~/public is readable by everybody.
Related
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/.
I have a content directory called foo and I want all files under that directory to have an extra metadata item foovar: default, unless explicitly overridden in the file header. I think I'm supposed to do this with EXTRA_PATH_METADATA, but I can't figure out what incantation it wants.
(for my current use case I'm trying to apply template: sometemplate within this dir, but I'm interested in solving the general case as it would make several related headaches go away)
I think what you're looking for is actually DEFAULT_METADATA. Check out this portion of the documentation:
DEFAULT_METADATA = {}
The default metadata you want to use for all articles and pages.
So, in your case it might look something like this in your config file:
DEFAULT_METADATA = {'foovar': 'default'}
Then to assign your custom template(s), see this portion of the documentation.
This wasn't possible at the time I asked. I've since sent the devs a PR adding support, and it's been merged to master. Presumably it will go out in the next release. It makes EXTRA_PATH_METADATA recursive, so you can apply settings to a subdir like this:
EXTRA_PATH_METADATA = {'dirname/subdir': {'status': 'hidden'}}
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.
User is selecting rather hefty single XML files via an NSOpenPanel. The application is making moderate changes to the file so I'd like to include an option of creating a backup in a subfolder based on the directory the original file was selected. Creating the new subfolder is no problem but does anybody have a good way to to create a backup of said foo.xml, is there a practice for such thing or is it as simple as creating a duplicate and renaming it foo.back01.xml?
Not sure, how much this Approach will fit with your requirement, but this is what i was doing,
-- Have a directory in the Temporary folder of the System : Assuming once the Application is closed all this files will be deleted,
-- To have the uniqueness in the file, generate file name with following pattern , have a function say [+(NSString *) generateFileNameForExtension:(NSString *)extension Create:(bool)bCreate]
Assuming input is .xml and false , it might give fileName something like this,
AppName128908765445.xml , i.e. [AppName][UTCTimeStamp].[Fileextension]
-- Once you think its done, there could be Function call [self addToDeleteList:(NSString *)fileName] which will add a file to delete list,
-- There would be a function, which shall invoke a timer for 1 minute and every one minute it will read all the files gets added into delete list then delete it.
Will share the code with you if needed...
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.