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q<X���DataONE R Client Packageq=…q>}q?(h"h8h$h6ubaubh)q@}qA(h"U�h$h h%h&h'h(h)}qB(h+]h,]h-]h.]qChah0]qDhauh2Kh3hh]qE(h5)qF}qG(h"X���SynopsisqHh$h@h%h&h'h9h)}qI(h+]h,]h-]h.]h0]uh2Kh3hh]qJh<X���SynopsisqK…qL}qM(h"hHh$hFubaubcdocutils.nodes
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qN)qO}qP(h"X³��Environmental scientists commonly use the `R Project`_ software system for
statistical analysis and modeling. The R framework is a flexible statistical
computing environment with robust, extensive packages to perform a large
variety of analysis and modeling tasks. Because R is open source and
extensible, it has been widely adopted by the environmental science community,
and it is easy to extend to provide new analysis capabilities.h$h@h%h&h'U	paragraphqQh)}qR(h+]h,]h-]h.]h0]uh2Kh3hh]qS(h<X*���Environmental scientists commonly use the qT…qU}qV(h"X*���Environmental scientists commonly use the h$hOubcdocutils.nodes
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qW)qX}qY(h"X���`R Project`_UresolvedqZKh$hOh'U	referenceq[h)}q\(UnameX	���R ProjectUrefuriq]X���http://www.r-project.orgq^h.]h-]h+]h,]h0]uh]q_h<X	���R Projectq`…qa}qb(h"U�h$hXubaubh<X}�� software system for
statistical analysis and modeling. The R framework is a flexible statistical
computing environment with robust, extensive packages to perform a large
variety of analysis and modeling tasks. Because R is open source and
extensible, it has been widely adopted by the environmental science community,
and it is easy to extend to provide new analysis capabilities.qc…qd}qe(h"X}�� software system for
statistical analysis and modeling. The R framework is a flexible statistical
computing environment with robust, extensive packages to perform a large
variety of analysis and modeling tasks. Because R is open source and
extensible, it has been widely adopted by the environmental science community,
and it is easy to extend to provide new analysis capabilities.h$hOubeubhN)qf}qg(h"X»��The `DataONE R Client Package`_ is an R package that provides access to the
DataONE services that are present at Coordinating Nodes and Member Nodes. The
tool will allow an R user to easily load the d1r package (using CRAN_) and
then use functions in R to search the DataONE system, locate data of interest,
load that data into the R environment, process it using R's various tools, and
then upload derived data and metadata back into DataONE.h$h@h%h&h'hQh)}qh(h+]h,]h-]h.]h0]uh2Kh3hh]qi(h<X���The qj…qk}ql(h"X���The h$hfubhW)qm}qn(h"X���`DataONE R Client Package`_hZKh$hfh'h[h)}qo(UnameX���DataONE R Client Packageh.]h-]h+]h,]h0]Urefidqphuh]qqh<X���DataONE R Client Packageqr…qs}qt(h"U�h$hmubaubh<X»��� is an R package that provides access to the
DataONE services that are present at Coordinating Nodes and Member Nodes. The
tool will allow an R user to easily load the d1r package (using qu…qv}qw(h"X»��� is an R package that provides access to the
DataONE services that are present at Coordinating Nodes and Member Nodes. The
tool will allow an R user to easily load the d1r package (using h$hfubhW)qx}qy(h"X���CRAN_hZKh$hfh'h[h)}qz(UnameX���CRANh]X���http://cran.r-project.orgq{h.]h-]h+]h,]h0]uh]q|h<X���CRANq}…q~}q(h"U�h$hxubaubh<XÜ���) and
then use functions in R to search the DataONE system, locate data of interest,
load that data into the R environment, process it using R's various tools, and
then upload derived data and metadata back into DataONE.q€…q}q‚(h"XÜ���) and
then use functions in R to search the DataONE system, locate data of interest,
load that data into the R environment, process it using R's various tools, and
then upload derived data and metadata back into DataONE.h$hfubeubhN)qƒ}q„(h"X¤��By targeting R in the Investigator Toolkit, we enable a wide variety of
scientists to harness data within the network of Member Nodes, and to
reference the data sets within their R scripts using their unique identifiers
from DataONE. This allows anyone to execute the R script from a paper or
analysis, and the `dataone` library handles the details of finding and accessing
the data needed for analysis or visualization.h$h@h%h&h'hQh)}q…(h+]h,]h-]h.]h0]uh2Kh3hh]q†(h<X7��By targeting R in the Investigator Toolkit, we enable a wide variety of
scientists to harness data within the network of Member Nodes, and to
reference the data sets within their R scripts using their unique identifiers
from DataONE. This allows anyone to execute the R script from a paper or
analysis, and the q‡…qˆ}q‰(h"X7��By targeting R in the Investigator Toolkit, we enable a wide variety of
scientists to harness data within the network of Member Nodes, and to
reference the data sets within their R scripts using their unique identifiers
from DataONE. This allows anyone to execute the R script from a paper or
analysis, and the h$hƒubcdocutils.nodes
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qŠ)q‹}qŒ(h"X	���`dataone`h)}q(h+]h,]h-]h.]h0]uh$hƒh]qŽh<X���dataoneq…q}q‘(h"U�h$h‹ubah'Utitle_referenceq’ubh<Xd��� library handles the details of finding and accessing
the data needed for analysis or visualization.q“…q”}q•(h"Xd��� library handles the details of finding and accessing
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q–)q—}q˜(h"X'���.. _R Project: http://www.r-project.orgh#Kh$h@h%h&h'Utargetq™h)}qš(h]h^h.]q›hah-]h+]h,]h0]qœhauh2Kh3hh]ubh–)q}qž(h"X#���.. _CRAN: http://cran.r-project.orgh#Kh$h@h%h&h'h™h)}qŸ(h]h{h.]q hah-]h+]h,]h0]q¡h
auh2Kh3hh]ubeubh)q¢}q£(h"U�h$h h%h&h'h(h)}q¤(h+]h,]h-]h.]q¥hah0]q¦hauh2K h3hh]q§(h5)q¨}q©(h"X���User storiesqªh$h¢h%h&h'h9h)}q«(h+]h,]h-]h.]h0]uh2K h3hh]q¬h<X���User storiesq­…q®}q¯(h"hªh$h¨ubaubcdocutils.nodes
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q·)q¸}q¹(h"XE���A scientist with R on their system can easily install d1r from CRAN_
h$h±h%h&h'U	list_itemqºh)}q»(h+]h,]h-]h.]h0]uh2Nh3hh]q¼hN)q½}q¾(h"XD���A scientist with R on their system can easily install d1r from CRAN_h$h¸h%h&h'hQh)}q¿(h+]h,]h-]h.]h0]uh2K"h]qÀ(h<X?���A scientist with R on their system can easily install d1r from qÁ…qÂ}qÃ(h"X?���A scientist with R on their system can easily install d1r from h$h½ubhW)qÄ}qÅ(h"X���CRAN_hZKh$h½h'h[h)}qÆ(UnameX���CRANh]h{h.]h-]h+]h,]h0]uh]qÇh<X���CRANqÈ…qÉ}qÊ(h"U�h$hÄubaubeubaubh·)qË}qÌ(h"X(��A scientist can load a data object using its DataONE identifier from the
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h$h±h%h&h'hºh)}qÍ(h+]h,]h-]h.]h0]uh2Nh3hh]qÎ(hN)qÏ}qÐ(h"XÀ���A scientist can load a data object using its DataONE identifier from the
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data objects supported should minimally include:qÑh$hËh%h&h'hQh)}qÒ(h+]h,]h-]h.]h0]uh2K$h]qÓh<XÀ���A scientist can load a data object using its DataONE identifier from the
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q×)qØ}qÙ(h"U�h)}qÚ(h+]h,]h-]h.]h0]uh$hËh]qÛh°)qÜ}qÝ(h"U�h)}qÞ(hµX���*h.]h-]h+]h,]h0]uh$hØh]qß(h·)qà}qá(h"X.���Data Tables in CSV and other delimited formatsqâh)}qã(h+]h,]h-]h.]h0]uh$hÜh]qähN)qå}qæ(h"hâh$hàh%h&h'hQh)}qç(h+]h,]h-]h.]h0]uh2K(h]qèh<X.���Data Tables in CSV and other delimited formatsq酁qê}që(h"hâh$håubaubah'hºubh·)qì}qí(h"X���NetCDF filesqîh)}qï(h+]h,]h-]h.]h0]uh$hÜh]qðhN)qñ}qò(h"hîh$hìh%h&h'hQh)}qó(h+]h,]h-]h.]h0]uh2K)h]qôh<X���NetCDF filesqõ…qö}q÷(h"hîh$hñubaubah'hºubh·)qø}qù(h"X!���Raster images in various formats
h)}qú(h+]h,]h-]h.]h0]uh$hÜh]qûhN)qü}qý(h"X ���Raster images in various formatsqþh$høh%h&h'hQh)}qÿ(h+]h,]h-]h.]h0]uh2K*h]r���h<X ���Raster images in various formatsr��…r��}r��(h"hþh$hüubaubah'hºubeh'h³ubah'Ublock_quoter��ubeubh·)r��}r��(h"XÈ���A scientist can use d1r to search for data based on critical metadata,
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identifiers for individual data objectsr��…r��}r��(h"j��h$j��ubaubaubh·)r��}r��(h"X��Given a data object loaded from DataONE into R, a scientist can display
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h$h±h%h&h'hºh)}r��(h+]h,]h-]h.]h0]uh2Nh3hh]r ��hN)r!��}r"��(h"X��Given a data object loaded from DataONE into R, a scientist can display
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h$h±h%h&h'hºh)}r+��(h+]h,]h-]h.]h0]uh2Nh3hh]r,��hN)r-��}r.��(h"Xƒ���A scientist can authenticate with the DataONE system in order to establish
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parameter of the method call. So, all signatures below need to have an
added parameter for this object to be passed in.h$jO��h%h&h'Unoter`��h)}ra��(h+]h,]h-]h.]h0]uh2Nh3hh]rb��hN)rc��}rd��(h"XE��All of the classes and methods in R are inverted (ie, classes don't
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parameter of the method call. So, all signatures below need to have an
added parameter for this object to be passed in.re��h$j^��h%h&h'hQh)}rf��(h+]h,]h-]h.]h0]uh2KFh]rg��h<XE��All of the classes and methods in R are inverted (ie, classes don't
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particular classes, and the class is generally passed in as the first
parameter of the method call. So, all signatures below need to have an
added parameter for this object to be passed in.rh��…ri��}rj��(h"je��h$jc��ubaubaubj]��)rk��}rl��(h"X��This design is out of date, and instead follows the design in DataPackage.
The R package mainly follows and uses the Java implementation, so does not
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* D1Client(CN_URI)h$jï��h%h&h'j‡��h)}rõ��(h+]h,]h-]h.]h0]uh2KXh]rö��(jŠ��)r÷��}rø��(h"X���Constructorsrù��h$jó��h%h&h'jŽ��h)}rú��(h+]h,]h-]h.]h0]uh2KXh]rû��h<X���Constructorsrü��…rý��}rþ��(h"jù��h$j÷��ubaubj”��)rÿ��}r���(h"U�h)}r��(h+]h,]h-]h.]h0]uh$jó��h]r��h°)r��}r��(h"U�h)}r��(hµX���*h.]h-]h+]h,]h0]uh$jÿ��h]r��h·)r��}r��(h"X���D1Client(CN_URI)r	��h)}r
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  * login(username, password): AuthToken
  * logout()
  * getEndpoint(): String
  * getPackage(pid): DataPackage
  * getUsername(): String
  * getToken(): AuthToken
  * search(): ResultSet
  * resolve(pid): [MemberNodeURI]
h)}r��(h+]h,]h-]h.]h0]uh$j™��h]r��j��)r��}r��(h"U�h)}r��(h+]h,]h-]h.]h0]uh$j��h]r��j„��)r��}r��(h"X×���Methods
* login(username, password): AuthToken
* logout()
* getEndpoint(): String
* getPackage(pid): DataPackage
* getUsername(): String
* getToken(): AuthToken
* search(): ResultSet
* resolve(pid): [MemberNodeURI]
h$j��h%h&h'j‡��h)}r��(h+]h,]h-]h.]h0]uh2Kbh]r��(jŠ��)r��}r ��(h"X���Methodsr!��h$j��h%h&h'jŽ��h)}r"��(h+]h,]h-]h.]h0]uh2Kbh]r#��h<X���Methodsr$��…r%��}r&��(h"j!��h$j��ubaubj”��)r'��}r(��(h"U�h)}r)��(h+]h,]h-]h.]h0]uh$j��h]r*��h°)r+��}r,��(h"U�h)}r-��(hµX���*h.]h-]h+]h,]h0]uh$j'��h]r.��(h·)r/��}r0��(h"X$���login(username, password): AuthTokenr1��h)}r2��(h+]h,]h-]h.]h0]uh$j+��h]r3��hN)r4��}r5��(h"j1��h$j/��h%h&h'hQh)}r6��(h+]h,]h-]h.]h0]uh2K[h]r7��h<X$���login(username, password): AuthTokenr8��…r9��}r:��(h"j1��h$j4��ubaubah'hºubh·)r;��}r<��(h"X���logout()r=��h)}r>��(h+]h,]h-]h.]h0]uh$j+��h]r?��hN)r@��}rA��(h"j=��h$j;��h%h&h'hQh)}rB��(h+]h,]h-]h.]h0]uh2K\h]rC��h<X���logout()rD��…rE��}rF��(h"j=��h$j@��ubaubah'hºubh·)rG��}rH��(h"X���getEndpoint(): StringrI��h)}rJ��(h+]h,]h-]h.]h0]uh$j+��h]rK��hN)rL��}rM��(h"jI��h$jG��h%h&h'hQh)}rN��(h+]h,]h-]h.]h0]uh2K]h]rO��h<X���getEndpoint(): StringrP��…rQ��}rR��(h"jI��h$jL��ubaubah'hºubh·)rS��}rT��(h"X���getPackage(pid): DataPackagerU��h)}rV��(h+]h,]h-]h.]h0]uh$j+��h]rW��hN)rX��}rY��(h"jU��h$jS��h%h&h'hQh)}rZ��(h+]h,]h-]h.]h0]uh2K^h]r[��h<X���getPackage(pid): DataPackager\��…r]��}r^��(h"jU��h$jX��ubaubah'hºubh·)r_��}r`��(h"X���getUsername(): Stringra��h)}rb��(h+]h,]h-]h.]h0]uh$j+��h]rc��hN)rd��}re��(h"ja��h$j_��h%h&h'hQh)}rf��(h+]h,]h-]h.]h0]uh2K_h]rg��h<X���getUsername(): Stringrh��…ri��}rj��(h"ja��h$jd��ubaubah'hºubh·)rk��}rl��(h"X���getToken(): AuthTokenrm��h)}rn��(h+]h,]h-]h.]h0]uh$j+��h]ro��hN)rp��}rq��(h"jm��h$jk��h%h&h'hQh)}rr��(h+]h,]h-]h.]h0]uh2K`h]rs��h<X���getToken(): AuthTokenrt��…ru��}rv��(h"jm��h$jp��ubaubah'hºubh·)rw��}rx��(h"X���search(): ResultSetry��h)}rz��(h+]h,]h-]h.]h0]uh$j+��h]r{��hN)r|��}r}��(h"jy��h$jw��h%h&h'hQh)}r~��(h+]h,]h-]h.]h0]uh2Kah]r��h<X���search(): ResultSetr€��…r��}r‚��(h"jy��h$j|��ubaubah'hºubh·)rƒ��}r„��(h"X���resolve(pid): [MemberNodeURI]
h)}r…��(h+]h,]h-]h.]h0]uh$j+��h]r†��hN)r‡��}rˆ��(h"X���resolve(pid): [MemberNodeURI]r‰��h$jƒ��h%h&h'hQh)}rŠ��(h+]h,]h-]h.]h0]uh2Kbh]r‹��h<X���resolve(pid): [MemberNodeURI]rŒ��…r��}rŽ��(h"j‰��h$j‡��ubaubah'hºubeh'h³ubah'jé��ubeubah'jê��ubah'hºubeh'h³ubah'jé��ubeubah'jê��ubaubh·)r��}r��(h"Xl��DataPackage
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     * identifier
     * scimeta
     * sysmeta
     * [dataObject]
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     * DataPackage(identifier, scimeta, sysmeta)
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     * getDataObjectCount(): int
     * getDataObject(index): DataObject
     * getTitle(): String
     * getCreator(): String
     * getDisplayURL(): String
h$jw��h%Nh'hºh)}r‘��(h+]h,]h-]h.]h0]uh2Nh3hh]r’��j��)r“��}r”��(h"U�h)}r•��(h+]h,]h-]h.]h0]uh$j��h]r–��j„��)r—��}r˜��(h"X^��DataPackage
* Fields
    * identifier
    * scimeta
    * sysmeta
    * [dataObject]
* Constructors
    * DataPackage(identifier, scimeta, sysmeta)
* Methods
    * addData(DataObject): DataPackage
    * getDataObjectCount(): int
    * getDataObject(index): DataObject
    * getTitle(): String
    * getCreator(): String
    * getDisplayURL(): String
h$j“��h%h&h'j‡��h)}r™��(h+]h,]h-]h.]h0]uh2Krh]rš��(jŠ��)r›��}rœ��(h"X���DataPackager��h$j—��h%h&h'jŽ��h)}rž��(h+]h,]h-]h.]h0]uh2Krh]rŸ��h<X���DataPackager ��…r¡��}r¢��(h"j��h$j›��ubaubj”��)r£��}r¤��(h"U�h)}r¥��(h+]h,]h-]h.]h0]uh$j—��h]r¦��h°)r§��}r¨��(h"U�h)}r©��(hµX���*h.]h-]h+]h,]h0]uh$j£��h]rª��(h·)r«��}r¬��(h"X>���Fields
  * identifier
  * scimeta
  * sysmeta
  * [dataObject]h)}r­��(h+]h,]h-]h.]h0]uh$j§��h]r®��j��)r¯��}r°��(h"U�h)}r±��(h+]h,]h-]h.]h0]uh$j«��h]r²��j„��)r³��}r´��(h"X6���Fields
* identifier
* scimeta
* sysmeta
* [dataObject]h$j¯��h%h&h'j‡��h)}rµ��(h+]h,]h-]h.]h0]uh2Khh]r¶��(jŠ��)r·��}r¸��(h"X���Fieldsr¹��h$j³��h%h&h'jŽ��h)}rº��(h+]h,]h-]h.]h0]uh2Khh]r»��h<X���Fieldsr¼��…r½��}r¾��(h"j¹��h$j·��ubaubj”��)r¿��}rÀ��(h"U�h)}rÁ��(h+]h,]h-]h.]h0]uh$j³��h]rÂ��h°)rÃ��}rÄ��(h"U�h)}rÅ��(hµX���*h.]h-]h+]h,]h0]uh$j¿��h]rÆ��(h·)rÇ��}rÈ��(h"X
���identifierrÉ��h)}rÊ��(h+]h,]h-]h.]h0]uh$jÃ��h]rË��hN)rÌ��}rÍ��(h"jÉ��h$jÇ��h%h&h'hQh)}rÎ��(h+]h,]h-]h.]h0]uh2Kfh]rÏ��h<X
���identifierrÐ��…rÑ��}rÒ��(h"jÉ��h$jÌ��ubaubah'hºubh·)rÓ��}rÔ��(h"X���scimetarÕ��h)}rÖ��(h+]h,]h-]h.]h0]uh$jÃ��h]r×��hN)rØ��}rÙ��(h"jÕ��h$jÓ��h%h&h'hQh)}rÚ��(h+]h,]h-]h.]h0]uh2Kgh]rÛ��h<X���scimetarÜ��…rÝ��}rÞ��(h"jÕ��h$jØ��ubaubah'hºubh·)rß��}rà��(h"X���sysmetará��h)}râ��(h+]h,]h-]h.]h0]uh$jÃ��h]rã��hN)rä��}rå��(h"já��h$jß��h%h&h'hQh)}ræ��(h+]h,]h-]h.]h0]uh2Khh]rç��h<X���sysmetarè��…ré��}rê��(h"já��h$jä��ubaubah'hºubh·)rë��}rì��(h"X���[dataObject]rí��h)}rî��(h+]h,]h-]h.]h0]uh$jÃ��h]rï��hN)rð��}rñ��(h"jí��h$jë��h%h&h'hQh)}rò��(h+]h,]h-]h.]h0]uh2Kih]ró��h<X���[dataObject]rô��…rõ��}rö��(h"jí��h$jð��ubaubah'hºubeh'h³ubah'jé��ubeubah'jê��ubah'hºubh·)r÷��}rø��(h"X:���Constructors
  * DataPackage(identifier, scimeta, sysmeta)h)}rù��(h+]h,]h-]h.]h0]uh$j§��h]rú��j��)rû��}rü��(h"U�h)}rý��(h+]h,]h-]h.]h0]uh$j÷��h]rþ��j„��)rÿ��}r���(h"X8���Constructors
* DataPackage(identifier, scimeta, sysmeta)h$jû��h%h&h'j‡��h)}r��(h+]h,]h-]h.]h0]uh2Kjh]r��(jŠ��)r��}r��(h"X���Constructorsr��h$jÿ��h%h&h'jŽ��h)}r��(h+]h,]h-]h.]h0]uh2Kjh]r��h<X���Constructorsr��…r	��}r
��(h"j��h$j��ubaubj”��)r��}r��(h"U�h)}r
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  * addData(DataObject): DataPackage
  * getDataObjectCount(): int
  * getDataObject(index): DataObject
  * getTitle(): String
  * getCreator(): String
  * getDisplayURL(): String
h)}r!��(h+]h,]h-]h.]h0]uh$j§��h]r"��j��)r#��}r$��(h"U�h)}r%��(h+]h,]h-]h.]h0]uh$j��h]r&��j„��)r'��}r(��(h"X°���Methods
* addData(DataObject): DataPackage
* getDataObjectCount(): int
* getDataObject(index): DataObject
* getTitle(): String
* getCreator(): String
* getDisplayURL(): String
h$j#��h%h&h'j‡��h)}r)��(h+]h,]h-]h.]h0]uh2Krh]r*��(jŠ��)r+��}r,��(h"X���Methodsr-��h$j'��h%h&h'jŽ��h)}r.��(h+]h,]h-]h.]h0]uh2Krh]r/��h<X���Methodsr0��…r1��}r2��(h"j-��h$j+��ubaubj”��)r3��}r4��(h"U�h)}r5��(h+]h,]h-]h.]h0]uh$j'��h]r6��h°)r7��}r8��(h"U�h)}r9��(hµX���*h.]h-]h+]h,]h0]uh$j3��h]r:��(h·)r;��}r<��(h"X ���addData(DataObject): DataPackager=��h)}r>��(h+]h,]h-]h.]h0]uh$j7��h]r?��hN)r@��}rA��(h"j=��h$j;��h%h&h'hQh)}rB��(h+]h,]h-]h.]h0]uh2Kmh]rC��h<X ���addData(DataObject): DataPackagerD��…rE��}rF��(h"j=��h$j@��ubaubah'hºubh·)rG��}rH��(h"X���getDataObjectCount(): intrI��h)}rJ��(h+]h,]h-]h.]h0]uh$j7��h]rK��hN)rL��}rM��(h"jI��h$jG��h%h&h'hQh)}rN��(h+]h,]h-]h.]h0]uh2Knh]rO��h<X���getDataObjectCount(): intrP��…rQ��}rR��(h"jI��h$jL��ubaubah'hºubh·)rS��}rT��(h"X ���getDataObject(index): DataObjectrU��h)}rV��(h+]h,]h-]h.]h0]uh$j7��h]rW��hN)rX��}rY��(h"jU��h$jS��h%h&h'hQh)}rZ��(h+]h,]h-]h.]h0]uh2Koh]r[��h<X ���getDataObject(index): DataObjectr\��…r]��}r^��(h"jU��h$jX��ubaubah'hºubh·)r_��}r`��(h"X���getTitle(): Stringra��h)}rb��(h+]h,]h-]h.]h0]uh$j7��h]rc��hN)rd��}re��(h"ja��h$j_��h%h&h'hQh)}rf��(h+]h,]h-]h.]h0]uh2Kph]rg��h<X���getTitle(): Stringrh��…ri��}rj��(h"ja��h$jd��ubaubah'hºubh·)rk��}rl��(h"X���getCreator(): Stringrm��h)}rn��(h+]h,]h-]h.]h0]uh$j7��h]ro��hN)rp��}rq��(h"jm��h$jk��h%h&h'hQh)}rr��(h+]h,]h-]h.]h0]uh2Kqh]rs��h<X���getCreator(): Stringrt��…ru��}rv��(h"jm��h$jp��ubaubah'hºubh·)rw��}rx��(h"X���getDisplayURL(): String
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