With this import routines, you can import data from text files (as tab-separated lists) into the database. For a comprehensive real-life example that shows many features of the import wizard take a look at the import wizard tutorial.
Choose Data ->
Import ->
Import wizard and then the type of data that should be imported, e.g.
Import descriptors ... from the menu. If you did not use the import
wizard before, the following window is shown to create a new import session.
In section Session project the projects with write access are listed for selection. In section Session description you should enter a detailled text description. If already an import session is present in the database, the window below will be shown where you may select the session. You may select one of the offered sessions or create a new one by selecting Create new import session.
After selecting or creating an import session a window as shown below will open that will lead you through the import of the data. The window is separated in 3 areas. On the left side you see a list of possible data related import steps according to the type of data you choosed for the import. On the right side you see the list of currently selected import steps. In the middle part the details of the selected import steps are shown.
As a first step, choose the
File from where the data should
be imported. The currently supported format is tab-separated text.
Then choose the Encoding of the file, e.g. Unicode. The Start line
and End line will automatically be set according to your data. You may change
these to restrict the data lines that should be imported. The not imported parts in the file are indicated
as shown below with a gray background. If the
First line contains the column definition this line will not be imported
as well. If your data contains e.g. date information or floating point values, where
notations differ between countries (e.g. 3.14 - 3,14), choose the Language / Country
to ensure a correct interpretation of your data. Finally you can select a prepared
Schema (see chapter Schema below) for the import.
In the selection list on the left side of the window (see below) all possible import steps for the data are listed according to the type of data you want to import.
Certain tables can be imported in parallel. To add parallels
click on the
button (see below). To remove parallels, use the
button. Only selected ranges will appear in the list of the steps on the right (see
below).
To import information of logging columns like who created
and changed the data, click on
button in the header line. This will include an additional substeps for every step
containing the logging columns (see below). If you do not import these data, they
will be automatically filled by default values like the current time and user.
You can either import your data as new data or
Attach
them to data in the database. Select the import step
Attachment
from the list. All tables that are selected and contain columns at which you can
attach data are listed (see below). Either choose the first option
Import as new data or one of the columns the attachment columns offered like
"id" in the table "Descriptor" in the example below.
If you select a column for attachment, this column will be marked with a blue backgroud (see below and chapter Table data).
You can either import your data as new data or
Merge them wih data in the database. Select the import step
Merge from the list. For every table you can choose between
Insert,
Merge,
Update and
Attach (see below).
The
Insert option will import the data from the file independent of existing data
in the database.
The
Merge option will compare the data from the file with those in the database
according to the
Key columns (see below). If no matching data are found in the database, the
data from the file will be imported, otherwise the data will be updated..
The
Update option will compare the data from the file with those in the database
according to the
Key columns. Only matching data found in the database will be updated.
The
Attach option will compare the data from the file with those in the database
according to the
Key columns. The found data will not be changed, but used as a reference
data in depending tables.
To set the source for the columns in the file, select
the step of a table listed underneath the Merge step. Some columns may be grouped
below the table name as shown for the
Descriptor table.
Click on one of the subordinated column groups and in the central part of the window the data columns avaialble for importing will be listed in the central part of the window. In the example shown below the column is used to attach the new data to data in the database.
All columns that have not been grouped beneath the table
may be accessed by selecting the table ste itself. In the example shown below table
Descriptor was selected to supply the "data_entry_note" column
for import.
A reminder in the header line will show you what actions are still needed to import the data into the table:
The handling of the columns in described in the chapter columns.
To test if all requirements for the import are met use
the
Testing step. You can use a certain line in the file for you test and than click
on the Test data in line: button. If there are still unmet requirements,
these will be listed in a window as shown below.
If finally all requirements are met, the testing function will try to write the data into the database and display you any errors that occurred as shown below. All datasets marked with a red backgroud, produced some error.
To see the list of all errors, double click in the error list window in the header line (see below).
If finally no errors are left, your data are ready for import. The colors in the table nodes in the tree indicate the handling of the datasets: INSERT, MERGE, UPDATE, No difference. Attach, No data. The colors of the table colums indicate whether a colums is decisive , a key column or an attachment column.
If you suspect, that the import file contains data allready
present in the database, you may test this an extract only the missing lines in
a new file. Choose the attachment column (see chapter Attaching data) and click
on the button Check for allready present data. The data allready present
in the database will be marked red
(see below). Click on the button Save missing data a text file
to store the data not present in the database in a new file for the import.
If you happen to get a file with a content as shown below, you may have seleted the wrong encoding or the encoding is incompatible. Please try to save the original file as UTF8 and select this encoding for the import.
With the last step you can finally start to import the data into the database. If you want to repeat the import with the same settings and data of the same structure, you can save a schema of the current settings (see below).
Schedule for import of tab-separated text files into DiversityCollection | |||
Target within DiversityCollection: Specimen | |||
Schedule version: | 1 | Database version: | 02.05.41 |
Lines: | 2 - 3215 | First line contains column definition: | ? |
Encoding: | Unicode | Language: | de |
Column in table | ? | Key | Copy | Pre | Post | File pos. | Transformations | Value | Source | Table |
---|---|---|---|---|---|---|---|---|---|---|
CollectionSpecimenID | Database | |||||||||
AccessionNumber | ? | ? | 0 | File |
Column in table | ? | Key | Copy | Pre | Post | File pos. | Transformations | Value | Source | Table |
---|---|---|---|---|---|---|---|---|---|---|
CollectionSpecimenID | Database | |||||||||
IdentificationUnitID | Database | |||||||||
LastIdentificationCache | ? | 2 | File | |||||||
+ | 3 | File | ||||||||
+ | 4 | File | ||||||||
+ | 5 | File | ||||||||
TaxonomicGroup | ? | fish | Interface |
Column in table | ? | Key | Copy | Pre | Post | File pos. | Transformations | Value | Source | Table |
---|---|---|---|---|---|---|---|---|---|---|
CollectionSpecimenID | Database | |||||||||
IdentificationUnitID | Database | |||||||||
AnalysisID | 94 | Interface | ||||||||
AnalysisNumber | 1 | Interface | ||||||||
AnalysisResult | ? | ? | 39 | File |
Lines that could not be imported will be marked with a red background while imported lines are marked green (see below).
If you want to save lines that produce errors during the import in a separate file, use the Save failed lines option. The protocol of the import will contain all settings acording to the used schema and an overview containing the number of inserted, updated, unchanged and failed lines (see below).
A description of the schema may be included in the schema
itself or with a click on the
button generated as a separate file.
This file will be located in a separate directory Description to avoid confusion
with import schemas. An example for a description file is shown below, containing
common settings, the treatment of the file columns and interface settings as defined
in the schema.
Schedule for import of tab-separated text files into DiversityCollection | |||
Target within DiversityCollection: Specimen | |||
Schedule version: | 1 | Database version: | 02.05.52 |
Lines: | 2 - 5 | First line contains column definition: | ? |
Encoding: | Unicode | Language: | de |
Description: | Import Schema fuer Literaturdaten (Bayernflora) aus Dörr & Lippert mit MTB Daten und max. 4 Sammlern |
Merge handling of table | Column usage | |||||||
---|---|---|---|---|---|---|---|---|
Insert | Merge | Update | Attach | Decisive | Key |
Pos. | Name | Table | Column | Example | Transformed | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | ID | |||||||||||||||||||||||||
CollectionSpecimen. | ExternalIdentifier | 1 | ||||||||||||||||||||||||
1 | originalname | |||||||||||||||||||||||||
Identification_1_2. | TaxonomicName | Ophioglossum vulgatum | ||||||||||||||||||||||||
2 | nameautor | |||||||||||||||||||||||||
Identification_1_1. | TaxonomicName | Ophioglossum vulgatum L. | ||||||||||||||||||||||||
3 | taxnr | |||||||||||||||||||||||||
Identification_1_1. | NameURI | 3949 | ||||||||||||||||||||||||
Prefix: | http://tnt.diversityworkbench.de/TaxonNames_Plants/ | |||||||||||||||||||||||||
4 | mtb | |||||||||||||||||||||||||
CollectionEventLocalisation_6. | Location1 | 8423 | ||||||||||||||||||||||||
5 | qu | |||||||||||||||||||||||||
CollectionEventLocalisation_6. | Location2 | 2 | ||||||||||||||||||||||||
6 | unschärfe | |||||||||||||||||||||||||
CollectionEventLocalisation_6. | LocationAccuracy | |||||||||||||||||||||||||
7 | jahr_von | |||||||||||||||||||||||||
CollectionEvent. | CollectionYear | 1902 | ||||||||||||||||||||||||
8 | jahr_bis | |||||||||||||||||||||||||
CollectionEvent. | CollectionDateSupplement | |||||||||||||||||||||||||
Prefix: | bis? | |||||||||||||||||||||||||
9 | status | |||||||||||||||||||||||||
IdentificationUnitAnalysis_1_1. | AnalysisResult | |||||||||||||||||||||||||
10 | verwaltungseinheit | not imported | ||||||||||||||||||||||||
11 | fundort | not imported | ||||||||||||||||||||||||
12 | finder | not imported | ||||||||||||||||||||||||
13 | ID_collector1 | |||||||||||||||||||||||||
CollectionAgent_1. | CollectorsAgentURI | 43708 | ||||||||||||||||||||||||
Prefix: | http://snsb.diversityworkbench.de/Agents_BayernFlora/ | |||||||||||||||||||||||||
14 | ID_collector2 | |||||||||||||||||||||||||
CollectionAgent_2. | CollectorsAgentURI | |||||||||||||||||||||||||
Prefix: | http://snsb.diversityworkbench.de/Agents_BayernFlora/ | |||||||||||||||||||||||||
15 | ID_collector3 | |||||||||||||||||||||||||
CollectionAgent_3. | CollectorsAgentURI | |||||||||||||||||||||||||
Prefix: | http://snsb.diversityworkbench.de/Agents_BayernFlora/ | |||||||||||||||||||||||||
16 | ID_collector4 | |||||||||||||||||||||||||
CollectionAgent_4. | CollectorsAgentURI | |||||||||||||||||||||||||
Prefix: | http://snsb.diversityworkbench.de/Agents_BayernFlora/ | |||||||||||||||||||||||||
17 | primärquelle | not imported | ||||||||||||||||||||||||
18 | ID_primärquelle | |||||||||||||||||||||||||
Annotation_1. | ReferenceURI | |||||||||||||||||||||||||
Prefix: | http://id.snsb.info/references/ | |||||||||||||||||||||||||
19 | primärquelle_seiten | not imported | ||||||||||||||||||||||||
20 | bestand | |||||||||||||||||||||||||
IdentificationUnitAnalysis_1_2. | AnalysisResult | |||||||||||||||||||||||||
21 | sonstiges | |||||||||||||||||||||||||
CollectionSpecimen. | OriginalNotes | |||||||||||||||||||||||||
22 | höhe | |||||||||||||||||||||||||
CollectionEventLocalisation_7. | Location1 | |||||||||||||||||||||||||
23 | herbar1 | not imported | ||||||||||||||||||||||||
24 | herbar2 | not imported | ||||||||||||||||||||||||
25 | herbar3 | not imported | ||||||||||||||||||||||||
26 | ID_herbar1 | |||||||||||||||||||||||||
CollectionSpecimenRelation_1. | RelatedSpecimenCollectionID | |||||||||||||||||||||||||
27 | ID_herbar2 | not imported | ||||||||||||||||||||||||
28 | ID_herbar3 | not imported | ||||||||||||||||||||||||
29 | det | not imported | ||||||||||||||||||||||||
30 | ID_det | not imported | ||||||||||||||||||||||||
31 | rev | not imported | ||||||||||||||||||||||||
32 | ID_rev | not imported | ||||||||||||||||||||||||
33 | datenquelle | not imported | ||||||||||||||||||||||||
34 | ID_datenquelle | |||||||||||||||||||||||||
CollectionSpecimen. | ReferenceURI | 135 | ||||||||||||||||||||||||
Prefix: | http://id.snsb.info/references/ | |||||||||||||||||||||||||
35 | project1 | not imported | ||||||||||||||||||||||||
36 | project2 | |||||||||||||||||||||||||
CollectionSpecimen. | AdditionalNotes | O | Beobachtung | |||||||||||||||||||||||
Transformations: |
|
Table | Table alias | Column | Value |
---|---|---|---|
Annotation | Annotation_1 | AnnotationType | Reference |
Annotation_1 | Annotation | Literaturauswertung: nach Dörr & Lippert (2004) | |
Annotation_1 | ReferenceDisplayText | Annotation | |
CollectionAgent | CollectionAgent_1 | CollectorsName | Collector1 |
CollectionAgent_2 | CollectorsName | Collector2 | |
CollectionAgent_3 | CollectorsName | Collector3 | |
CollectionAgent_4 | CollectorsName | Collector4 | |
CollectionEvent | CountryCache | Germany | |
CollectionProject | CollectionProject_1 | ProjectID | 37 |
CollectionProject_2 | ProjectID | 149 | |
CollectionSpecimen | ReferenceTitle | Reference | |
CollectionSpecimenRelation | CollectionSpecimenRelation_1 | RelatedSpecimenURI | |
CollectionSpecimenRelation_1 | RelatedSpecimenDisplayText | ||
CollectionSpecimenRelation_1 | Notes | Herbarauswertung: nach Dörr & Lippert (2004) | |
Identification | Identification_1_1 | IdentificationSequence | 2 |
Identification_1_2 | IdentificationSequence | 1 | |
Identification_1_2 | Notes | Originalname aus Dörr & Lippert (2004) | |
IdentificationUnit | IdentificationUnit_1 | LastIdentificationCache | plant |
IdentificationUnit_1 | TaxonomicGroup | plant | |
IdentificationUnitAnalysis | IdentificationUnitAnalysis_1_1 | AnalysisID | 2 |
IdentificationUnitAnalysis_1_1 | AnalysisNumber | 1 | |
IdentificationUnitAnalysis_1_2 | AnalysisID | 4 | |
IdentificationUnitAnalysis_1_2 | AnalysisNumber | 2 |