Opened 13 years ago

Closed 13 years ago

Last modified 13 years ago

#600 closed (fixed)

Alternative 3D server URL when downloading protein 3D structure data

Reported by: olle Owned by: olle
Milestone: Proteios SE 2.9 Keywords:
Cc:

Description

When web pages are parsed to find a web link to downloadable PDB (Protein Data Bank) data as a RasMol script file, the server URL obtained sometimes refer to a web page containing an error message, which when parsed for coordinate data will result in an empty coordinate file. However, the desired data can often be found using the default CATH server URL "http://www.cathdb.info/". If the first download attempt results in an empty coordinate file, a new attempt should therefore be made using the default CATH server URL "http://www.cathdb.info/" instead.

Change History (9)

comment:1 Changed 13 years ago by olle

Status: newassigned

Ticket accepted.

comment:2 Changed 13 years ago by olle

Traceability note:

  • Display of protein 3D structure data was introduced in Ticket #541 (Easter Egg - Protein 3D Structure as View Action for Proteins in Hits Table).

comment:3 Changed 13 years ago by olle

Reference note:

  • CATH represents "Class (C), Architecture (A), Topology (T) and Homologous superfamily (H)".

comment:4 Changed 13 years ago by olle

(In [3374]) Refs #600. Refs #541. Class/file action/hit/ShowPDBFileStructure.java in client/servlet/ updated:

  1. Public method void runMe() updated to check if downloaded

protein coordinate file is empty, in which case a new download attempt is made using default CATH server URL "http://www.cathdb.info/".

comment:5 Changed 13 years ago by olle

(In [3375]) Refs #600. Refs #541. Class/file action/hit/ViewActiveHitPDBFile.java in client/servlet/ updated in private method <E extends ProteiosAction> void addTableRow(Table table, ...) by removing extra white spaces that were unintentionally added when removing compile warnings in changeset [3260].

comment:6 Changed 13 years ago by olle

(In [3376]) Refs #600. Refs #541. Class/file action/hit/ShowPDBFileStructure.java in client/servlet/ updated to store default protein 3D server URL as a string constant DEFAULT_PROTEIN_3D_SERVER_URL, in order for it to be easier to change, if necessary:

  1. Public method void runMe() updated to use string constant

DEFAULT_PROTEIN_3D_SERVER_URL for the default protein 3D server URL.

comment:7 Changed 13 years ago by olle

severity: 162

Severity set to 2 since no new design elements were needed.

comment:8 Changed 13 years ago by olle

Resolution: fixed
Status: assignedclosed

Ticket closed as the desired functionality has been added.

comment:9 Changed 13 years ago by olle

(In [3435]) Refs #600. Refs #541. Class/file action/hit/ViewActiveHitPDBFile.java in client/servlet/ updated to try alternative parsing to obtain protein 3D server url and title strings, if first attempt fails:

  1. Public method void runMe() updated to try alternative parsing

to obtain protein 3D server url and title strings, if first attempt fails. The alternative parsing is based on server url and title strings being separated by string "cathnode/".

  1. Private method List<String> fetchGene3DURLStringList(String fileURLStr)

updated by addition of comment with examples of input strings and parsed result.

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