Changeset 5784
- Timestamp:
- Oct 5, 2011, 2:52:42 PM (11 years ago)
- Location:
- trunk/doc/src/docbook/user
- Files:
-
- 2 edited
-
export_data.xml (modified) (4 diffs)
-
import_data.xml (modified) (18 diffs)
Legend:
- Unmodified
- Added
- Removed
-
trunk/doc/src/docbook/user/export_data.xml
r5738 r5784 38 38 --> 39 39 <chapter id="export_data" chunked="0"> 40 40 41 <title>Export of data</title> 41 42 <para> … … 59 60 <menuchoice> 60 61 <guimenu>Administrate</guimenu> 61 <guimenuitem>Plug ins</guimenuitem>62 <guisubmenu> Definitions</guisubmenu>62 <guimenuitem>Plug-ins & extensions</guimenuitem> 63 <guisubmenu>Plug-in definitions</guisubmenu> 63 64 </menuchoice> 64 65 to check which plug-ins are installed on your BASE server. When … … 68 69 </para> 69 70 <note> 70 <title> Missing/unavailable button</title>71 <title>No "Export" button?</title> 71 72 <para> 72 73 If the export button is missing from a page were you would expect … … 369 370 <varlistentry> 370 371 <term> 372 <guilabel>Units</guilabel> 373 </term> 374 <listitem> 375 <para> 376 If the export includes annotation with units, the exporter normally 377 uses the same unit that was used when annotating each item. This can be 378 different from item to item. Select this option to force all annotation 379 values to use the same unit (=the default unit for the annotation type). 380 </para> 381 </listitem> 382 </varlistentry> 383 <varlistentry> 384 <term> 385 <guilabel>Column prefix</guilabel> 386 </term> 387 <listitem> 388 <para> 389 Adds a prefix to each column header. This is useful for keeping 390 column names unique when combining multiple files outside of 391 BASE. 392 </para> 393 </listitem> 394 </varlistentry> 395 <varlistentry> 396 <term> 371 397 <guilabel>Save as</guilabel> 372 398 </term> -
trunk/doc/src/docbook/user/import_data.xml
r5738 r5784 45 45 to enter by hand due to the large number of data items. There is 46 46 also convenience batch importers for importing other items such as 47 biosources, samples, and extracts. The batch importers are47 biosources, samples, and annotations. The batch importers are 48 48 described later in this chapter after the general import 49 49 description. … … 53 53 configuration, for example, the import plug-ins need some 54 54 information about how to find headers and data lines in 55 files. BASE ships with a number of export plug-ins as a part of55 files. BASE ships with a number of import plug-ins as a part of 56 56 the core plug-ins package, cf. <xref linkend="coreplugins.import" 57 57 />. The core plug-in section links to configuration examples for … … 59 59 <menuchoice> 60 60 <guimenu>Administrate</guimenu> 61 <guimenuitem>Plug ins</guimenuitem>62 <guisubmenu> Definitions</guisubmenu>61 <guimenuitem>Plug-ins & extensions</guimenuitem> 62 <guisubmenu>Plug-in definitions</guisubmenu> 63 63 </menuchoice> 64 64 to check which plug-ins are installed on your BASE server. When … … 68 68 </para> 69 69 <note> 70 <title> Missing/unavailable button</title>70 <title>No "Import" button?</title> 71 71 <para> 72 72 If the import button is missing from a page were you would expect … … 170 170 <menuchoice> 171 171 <guimenu>Administrate</guimenu> 172 <guimenuitem>Plug ins</guimenuitem>173 <guisubmenu> Definitions</guisubmenu>172 <guimenuitem>Plug-ins & extensions</guimenuitem> 173 <guisubmenu>Plug-in definitions</guisubmenu> 174 174 </menuchoice> 175 175 and 176 176 <menuchoice> 177 177 <guimenu>Administrate</guimenu> 178 <guimenuitem>Plug ins</guimenuitem>179 <guisubmenu> Configurations</guisubmenu>180 </menuchoice> .178 <guimenuitem>Plug-ins & extensions</guimenuitem> 179 <guisubmenu>Plug-in configuration</guisubmenu> 180 </menuchoice> 181 181 </para> 182 182 <note> … … 302 302 <para> 303 303 Click on the &gbNext; button 304 to start the auto detection. 304 to start the auto detection. There are three possible outcomes: 305 305 </para> 306 306 307 <para> 308 If the auto detection finds a exactly one plug-in and file format 309 the next step is to configure any additional parameters needed 310 by the plug-in. This is the same step as if you had selected 311 the same plug-in and file format in the first step. 312 If no plug-in can be found an error message is displayed. 313 </para> 314 315 <note> 316 <title>More then one compatible plug-in/file format</title> 317 <para> 318 If more than one matching plug-in or file format is used 307 <itemizedlist> 308 <listitem> 309 <para> 310 Exactly one matching plug-in and file format is found. The next step is 311 to configure any additional parameters needed 312 by the plug-in. This is the same step as if you had selected 313 the same plug-in and file format in the first step. 314 </para> 315 </listitem> 316 <listitem> 317 <para> 318 If no matching plug-in and file format is found an error message 319 is displayed. If logged in with enough permissions to do so there 320 is an option to create a new file format/configuration. 321 </para> 322 </listitem> 323 <listitem> 324 <para> 325 If multiple matching plug-ins and file formats are found 319 326 you will be taken back to the first step. This time 320 327 the lists will only include the matching plug-ins/file formats 321 328 and the auto detect option is not present. 322 </para> 323 </note> 329 </para> 330 </listitem> 331 </itemizedlist> 324 332 325 333 <seeother> … … 383 391 A section which contains different options how to 384 392 handle errors when parsing the file. Normally you can 385 select if the import should fail as a wh ile or if386 the line with the error should be skipped.393 select if the import should fail as a whole or if 394 only the line with the error should be skipped. 387 395 </para> 388 396 </listitem> … … 506 514 <para> 507 515 Multi-item references are references to several other 508 items of the same type. The labeledextracts of a509 hybridizationor pooled samples are two examples of510 items that refer to several other items; a hybridization511 may contain several labeledextracts and a sample may be516 items of the same type. The extracts of a 517 physical bioassay or pooled samples are two examples of 518 items that refer to several other items; a physical bioassay 519 may contain several extracts and a sample may be 512 520 a pool of several samples. In some cases a multi-item 513 521 reference is bundled with simple 514 522 values, <emphasis>eg.</emphasis>, used quantity of a 515 source biomaterial, the array index a labeledextract is523 source biomaterial, the position an extract is 516 524 used on, etc. Multi-item references are never removed by 517 525 the importer, only added or updated. Removing an item … … 522 530 </itemizedlist> 523 531 The batch importers do not set values for annotations since 524 this is handled by the a lready existing annotation importer532 this is handled by the annotation importer 525 533 plug-in (<xref linkend="annotations.massimport" />). However, 526 534 the annotation importer and batch item importers have similar … … 530 538 531 539 <para> 532 The importer only works one item typeat each use and can be540 The importer only works with one type of items at each use and can be 533 541 used in a <emphasis>dry-run</emphasis> mode where everything 534 542 is performed as if a real import is taking place, but the work … … 547 555 For proper and efficient use of the batch importers users 548 556 need to understand how the files to be imported should be 549 formatted. For users who wishes to get a hands-on 550 experience there is 551 an <ulink url="http://base.thep.lu.se/attachment/wiki/DocBookSupport/batchimport_sample.ods?format=raw">OpenOffice 552 spreadsheet with sample sheets that work with the batch 553 importers</ulink> available for download. This file can be 554 used to import a set of data from the biosource level down 555 to hybridizations with proper associations and properties 556 simply by using the batch importers. 557 </para> 558 559 <para> 560 The input file must be organised into columns separated by a 557 formatted. The input file must be organised into columns separated by a 561 558 specified character such as a tab or comma character. The 562 559 data header line contains the column headers which defines … … 650 647 parameters. The list below comments on some of the 651 648 parameters available. 649 </para> 650 652 651 <variablelist> 653 652 <varlistentry> … … 672 671 <varlistentry> 673 672 <term> 673 <guilabel>Data directory</guilabel> 674 </term> 675 <listitem> 676 <para> 677 This option is only available for items that has support for 678 attaching files (eg. array design, derived bioassay, etc.). 679 This setting is used to resolve file references that doesn't 680 include a complete absolute path. 681 </para> 682 </listitem> 683 </varlistentry> 684 <varlistentry> 685 <term> 674 686 <guilabel>Identification method</guilabel> 675 687 </term> … … 682 694 the user must be mapped to a column in the file. If 683 695 it is not set there is obviously no way for the 684 plug-in to identify if an item already exists . 696 plug-in to identify if an item already exists. 697 </para> 698 </listitem> 699 </varlistentry> 700 <varlistentry> 701 <term> 702 <guilabel>Item subtypes</guilabel> 703 </term> 704 <listitem> 705 <para> 706 Only look for existing items among the selected subtypes. If no subtype 707 is selected all items are searched. If exactly one subtype is selected 708 new items are automatically created with this subtype (unless it is overridden 709 by specific subtype values in the import file). 685 710 </para> 686 711 </listitem> … … 722 747 </para> 723 748 <para> 724 When creating pooled items, 725 the <property>pooled</property> property is used to 726 tell the plug-in that an item is pooled. Pooled in 727 BASE language really means that the item parent is 728 of the same type as the item itself. If an item is 729 not pooled then the parent is of another type 730 following a predefined hierarchy in BASE. In 731 ascending order the BASE ordering 749 When working with biomaterial items, the 750 <guilabel>Parent type</guilabel> property is used to 751 tell the plug-in how to find parent items. This only 752 has to be set if the parent item is of the same type 753 as the biomaterial being imported since the default 754 is to look for the nearest parent type in the predefined hierarchy. 755 In ascending order the BASE ordering 732 756 of <emphasis>parent - child - grandchild - 733 757 ...</emphasis> item relation is <emphasis>biosource 734 - sample - extract - labeled extract</emphasis>. 735 </para> 736 <para> 737 The values accepted for <property>pooled</property> 738 are <constant>empty (' ')</constant>, 739 <constant>0</constant>, <constant>1</constant>, 740 <constant>no</constant>, <constant>yes</constant>, 741 <constant>false</constant>, 742 and <constant>true</constant>. Any other string is 743 interpreted as the item is pooled. Sometimes all 744 items in a file to be imported are pooled but there 745 is no column that marks the pooled status. This can 758 - sample - extract</emphasis>. 759 </para> 760 <para> 761 The values accepted for <guilabel>Parent type</guilabel> 762 are <constant>BIOSOURCE</constant>, 763 <constant>SAMPLE</constant> or <constant>EXTRACT</constant>. 764 Sometimes all items in a file to be imported have the same parent 765 type but there is no column with this information. This can 746 766 be resolved by setting 747 the <property>pooled</property> mapping to a 748 constant string 749 <constant>'1'</constant> which make all items to be 750 treated as pooled in the import (no backslash '\' 751 character, compare with column header mapping 752 strings that contain backslash characters 753 like <constant>'\pool column\'</constant>). 767 the <guilabel>Parent type</guilabel> mapping to a 768 constant string (eg. no backslash '\' character). 769 </para> 770 </listitem> 771 </varlistentry> 772 <varlistentry> 773 <term> 774 <guilabel>Permissions</guilabel> 775 </term> 776 <listitem> 777 <para> 778 This is a column mapping that can be used to update the permissions 779 set on items. Normally, new items are only shared to the active project 780 (if any). By naming a permission template, new items are shared using 781 the permissions from that template instead. Permissions on already existing 782 items are merged with the permission from the template. 754 783 </para> 755 784 </listitem> 756 785 </varlistentry> 757 786 </variablelist> 787 788 <para> 758 789 After setting the parameters, 759 790 select <guilabel>Next</guilabel>. Another parameter dialog 760 791 will appear where error handling options can be set among 761 792 with 793 </para> 794 762 795 <variablelist> 763 796 <varlistentry> … … 792 825 </varlistentry> 793 826 </variablelist> 794 </para> 827 795 828 796 829 <para> … … 798 831 referenced on each line. There are three outcomes of this 799 832 item search 833 </para> 834 800 835 <itemizedlist> 801 836 <listitem> … … 816 851 More than one item is found. Depending on parameter 817 852 settings this may abort the plug-in or the plug-in may 818 ignore dthe line.853 ignore the line. 819 854 </para> 820 855 </listitem> 821 856 </itemizedlist> 822 </para>823 857 824 858 </sect2>
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