setupguide:upgrade2v1_0
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setupguide:upgrade2v1_0 [2015/07/10 14:46] 132.168.72.225 [Upgrading-Installing Sequence Repository] |
setupguide:upgrade2v1_0 [2016/06/13 12:58] (current) 193.48.0.3 |
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| ==== From graphical interface ProlineAdmin GUI ==== | ==== From graphical interface ProlineAdmin GUI ==== | ||
| - | Open the graphical interface by running ''start.bat'' (or ''start.sh'' on linux system). | + | Open the graphical interface by running ''start.bat'' (or ''start.sh'' on linux system). |
| + | If you used the Windows installer, a shortcut "Proline Admin" is available in the Windows Start Menu, under the Proline folder. | ||
| - | If you don't have a valid configuration file, you can edit it. | + | If you don't have a valid configuration file, you can change it or edit it (see [[setupguide:setup_with_prolineadmin_gui|how to]]). |
| - | Click the "Upgrade databases" button. | + | Click the button named //Upgrade Proline databases//. |
| + | |||
| + | **Note:** This functionnality will be disable if the configuration is invalid or if Proline is not set up (see how to [[setupguide:firstinstall|configure and set up Proline]], or [[setupguide:setup_with_prolineadmin_gui#setup with prolineadmin gui|using ProlineAdmin GUI]]) | ||
| + | |||
| + | {{ :setupguide:upgrade_proline_databases.png?nolink&800 |}} | ||
| - | **Note:** This functionality is not available if Proline is not set up (see how to [[setupguide:firstinstall|set up Proline]]). | ||
| - | {{ :setupguide:upgrade_dbs.png?nolink&600 |}} | ||
| ==== ==== | ==== ==== | ||
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| Configuration files didn't change, you can copy them from previous version to new one. They are located under the "<your_folder>/config". | Configuration files didn't change, you can copy them from previous version to new one. They are located under the "<your_folder>/config". | ||
| - | Here is a description of these files, for new Sequence Reposiroty's user : | + | Here is a description of these files, for new Sequence Reposiroty's user: |
| **Datastore description ** | **Datastore description ** | ||
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| </code> | </code> | ||
| - | __note__ : | + | __note__: |
| * If you didn't change the default naming scheme of databases the <uds_db>= 'uds_db' so <code>javax.persistence.jdbc.url=jdbc:postgresql://<host>:5432/uds_db</code> | * If you didn't change the default naming scheme of databases the <uds_db>= 'uds_db' so <code>javax.persistence.jdbc.url=jdbc:postgresql://<host>:5432/uds_db</code> | ||
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| As this module is used to extract Protein Sequence, description from a fasta file for a specific protein accession, it is necessary to configure the rule used to parse the protein ACC, from fasta description line. This is similar to the rules specified in Mascot Server. | As this module is used to extract Protein Sequence, description from a fasta file for a specific protein accession, it is necessary to configure the rule used to parse the protein ACC, from fasta description line. This is similar to the rules specified in Mascot Server. | ||
| - | To do this, //retrieve-service.properties// file should be edited. In this file it is necessary to escape (this means prefix with '\') some characters : '\' , ':' and '=' | + | To do this, //retrieve-service.properties// file should be edited. In this file it is necessary to escape (this means prefix with '\') some characters: '\' , ':' and '=' |
| <code> | <code> | ||
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| _Note_: | _Note_: | ||
| - | * fr.proline.module.seq.localFASTAPaths : only one instance should be defined. For linux system, fr.proline.module.seq.localFASTAPaths=/local/data/fasta;/local/mascot/sequence | + | * fr.proline.module.seq.localFASTAPaths: only one instance should be defined. For linux system, fr.proline.module.seq.localFASTAPaths=/local/data/fasta;/local/mascot/sequence |
| - | * fr.proline.module.seq.defaultReleaseRegex : Regular expression to extract release version (CASE_INSENSITIVE) from the fasta files. | + | * fr.proline.module.seq.defaultReleaseRegex: Regular expression to extract release version (CASE_INSENSITIVE) from the fasta files. |
| - | * fr.proline.module.seq.uniProtSEDbNames : Regular expression to identify Uniprot like fasta. The entry of theses files will be parse using specific rule (fr.proline.module.seq.uniProtSEDbIdentifierRegex) to extract protein accession. | + | * fr.proline.module.seq.uniProtSEDbNames: Regular expression to identify Uniprot like fasta. The entry of these files will be parse using specific rule (fr.proline.module.seq.uniProtSEDbIdentifierRegex) to extract protein accession. |
| - | For other fasta file the protein accssion will be extract by using string before first blank. | + | For other fasta file the protein accession will be extract by using string before first blank. |
setupguide/upgrade2v1_0.1436532375.txt.gz · Last modified: 2015/07/10 14:46 by 132.168.72.225
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