[Bio] / Sprout / LoadSproutTables.pl Repository:
ViewVC logotype

Diff of /Sprout/LoadSproutTables.pl

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.26, Sun Apr 2 17:33:52 2006 UTC revision 1.27, Thu Apr 13 18:01:22 2006 UTC
# Line 20  Line 20 
20  commands.  commands.
21    
22      LoadSproutTables -dbLoad -dbCreate "*"      LoadSproutTables -dbLoad -dbCreate "*"
23      TestSproutLoad      TestSproutLoad [genomeID] ...
24      index_sprout      index_sprout_lucene
25    
26    where I<[genomeID]> is one or more genome IDs. These genomes will be tested more
27    thoroughly than the others.
28    
29  All three commands send output to the console. In addition, C<LoadSproutTables> and  All three commands send output to the console. In addition, C<LoadSproutTables> and
30  C<TestSproutLoad> write tracing information to C<trace.log> in the FIG temporary  C<TestSproutLoad> write tracing information to a trace log in the FIG temporary
31  directory (B<$FIG_Config::Tmp>). At the bottom of the log file will be a complete  directory (B<$FIG_Config::Tmp>). At the bottom of the log file will be a complete
32  list of errors. If errors occur in C<LoadSproutTables>, then the data must be corrected  list of errors. If errors occur in C<LoadSproutTables>, then the data must be corrected
33  and the offending table group reloaded. So, for example, if there are errors in the  and the offending table group reloaded. So, for example, if there are errors in the
# Line 46  Line 49 
49  to give you an idea of the progress.  to give you an idea of the progress.
50    
51  Once the Sprout database is loaded, B<TestSproutLoad> can be used to verify the load  Once the Sprout database is loaded, B<TestSproutLoad> can be used to verify the load
52  against the FIG data. Again, the end of the C<trace.log> file will contain a summary  against the FIG data. The end of the trace log file will contain statistics on
53  of the errors found. Like C<LoadSproutTables>, C<TestSproutLoad> is a time-consuming  the errors found. Like C<LoadSproutTables>, C<TestSproutLoad> is a time-consuming
54  script, so you may want to set the trace level to 3 to see visible progress.  script, so you may want to set the trace level to 3 to see visible progress.
55    
56      TestSproutLoad -trace=3      TestSproutLoad -trace=3 [genomeID] ...
57    
58    The I<[genomeID]> specifies zero or more IDs of genomes to receive more thorough
59    testing. So, for example,
60    
61        TestSproutLoad -trace=3 100226.1 83333.1
62    
63    would do thorough testing of I<Streptomyces coelicolor A3-2> (100226.1) and
64    I<Escherichia coli K12> (83333.1).
65    
66  Unlike C<LoadSproutTables>, in C<TestSproutLoad>, the individual errors found are  Unlike C<LoadSproutTables>, in C<TestSproutLoad>, the individual errors found are
67  mixed in with the trace messages. They are all, however, marked with a trace type  mixed in with the trace messages. They are all, however, marked with a trace type
# Line 68  Line 79 
79  The test may reveal that some tables need to be reloaded, or that a software  The test may reveal that some tables need to be reloaded, or that a software
80  problem has crept into the Sprout.  problem has crept into the Sprout.
81    
82  Once all the tables have the correct data, C<index_sprout> can be run to create the  Once all the tables have the correct data, C<index_sprout_lucene> can be run to create the
83  Glimpse indexes.  Lucene search indexes. Lucene is a web site search engine produced by the Apache project.
84    It is written in Java, and in order to run it you must have the B<LuceneSearch> and
85    B<NmpdrConfigs> projects checked out from CVS and made.
86    
87  =head2 Procedure For Loading Sprout  =head2 Procedure For Loading Sprout
88    
89    In order to load the Sprout, you need to have the B<Sprout>, B<NmpdrConfigs>, and
90    B<LuceneSearch> projects checked out from CVS in addition to the standard FIG
91    projects. You must also set up the following B<FIG_Config.pm> variables in addition
92    to the normal ones.
93    
94    =over 4
95    
96    =item sproutData
97    
98    Name of the data directory for the Sprout load files.
99    
100    =item var
101    
102    Name of the directory to contain cached NMPDR pages. The most important file in
103    this directory is C<nmpdr_page_template.html>, which contains a skeleton page
104    from the main NMPDR web site. This skeleton page is used to generate output
105    pages that look like the other NMPDR pages.
106    
107    =item java
108    
109    Path to the Java runtime environment.
110    
111    =item sproutDB
112    
113    Name of the Sprout database
114    
115    =item dbuser
116    
117    User name for logging into the Sprout database.
118    
119    =item dbpass
120    
121    Password for logging into the Sprout database.
122    
123    =item nmpdr_site_url
124    
125    URL for the NMPDR cover pages. The NMPDR cover pages are informational and text
126    pages that serve as the entry point to the NMPDR web site. They are generated by
127    a Content Management tool, and some Sprout scripts need to know where to find
128    them.
129    
130    =item nmpdr_site_template_id
131    
132    Page number for the template page used to generate results that look like they're
133    part of the NMPDR web site.
134    
135    =back
136    
137  =over 4  =over 4
138    
139    The procedure for loading Sprout is as follows.
140    
141  =item 1  =item 1
142    
143  Type  Type
# Line 99  Line 162 
162    
163  =item 2  =item 2
164    
165  Type C<TestSproutLoad 100226.1 83333.1> and press ENTER. This will validate  Type
166  the Sprout database against the SEED data.  
167        nohup TestSproutLoad -user=you -background >null &100226.1 83333.1>
168    
169    and press ENTER. This will validate the Sprout database against the SEED data.
170    
171  =item 3  =item 3
172    
# Line 110  Line 176 
176    
177  =item 4  =item 4
178    
179  Type C<index_sprout> and press ENTER. This will create the Glimpse indexes  Type
180  for the Sprout data. (The Windows version of SEED does not support Glimpse,  
181  so only do this for the Unix version.)      index_sprout_lucene
182    
183     and press ENTER. This will create the Lucene indexes for the Sprout data.
184    
185    =item 5
186    
187    Change to the B<SproutData/Indexes> directory under B<FIGdisk> and look for the
188    directory created by C<index_sprout_lucene>. The directory name will be
189    something like C<Lucene.20060412-154112>. The numbers indicate the date and time
190    the index was created. In this case it was 04/12/2006 03:41:12pm. Type
191    
192        ln -sf directory Lucene
193    
194    where C<directory> is the new directory name, to point the C<Lucene> directory to the
195    new search index.
196    
197  =back  =back
198    

Legend:
Removed from v.1.26  
changed lines
  Added in v.1.27

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3