https://github.com/sfu-cl-lab/FactorBase

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e0833fd Merge pull request #239 from sfu-cl-lab/2023_project_test removed the second jar file 17 March 2024, 20:57:34 UTC
0e44db7 removed the second jar file 17 March 2024, 20:56:52 UTC
0889d3e Update README.md adding description of bif file for inspection 14 March 2024, 20:39:03 UTC
f626a4e Add files via upload 14 March 2024, 20:23:32 UTC
4b1cceb Update README.md 11 March 2024, 22:05:47 UTC
502cd99 Update README.md 11 March 2024, 22:03:46 UTC
b156889 Update README.md 11 March 2024, 22:01:34 UTC
c1767a5 Merge pull request #238 from sfu-cl-lab/2023_project_test Merge pull request #237 from sfu-cl-lab/master 11 March 2024, 21:25:47 UTC
b07d52e Merge pull request #237 from sfu-cl-lab/master merge Mingyi's version to the master 11 March 2024, 21:23:01 UTC
caffa88 Merge branch '2023_project_test' into master 11 March 2024, 21:22:41 UTC
3b4aa5e Parmis final commit 11 March 2024, 21:20:00 UTC
4c4441e setting local_mult = mult 05 December 2023, 23:16:35 UTC
4658e1c adding new jar file after changin CP.java 05 December 2023, 23:15:04 UTC
f6cc9ab adding jar file for mingyi's code 05 December 2023, 18:32:49 UTC
b1ccb32 removed the previous commit 04 December 2023, 22:41:22 UTC
5a46529 Update CP.java 25 November 2023, 10:47:56 UTC
76e1ef6 commit modify the sql 15 November 2023, 22:27:12 UTC
7a38d15 Add files via upload 15 November 2023, 19:37:57 UTC
cc594b4 Add make_xml_sum_to_one.py 15 November 2023, 18:39:24 UTC
e7179a9 change cp table schema 19 October 2023, 18:05:09 UTC
4ed070f remove target file 16 October 2023, 17:37:53 UTC
73657ff Update CP.java 27 September 2023, 16:52:38 UTC
36d6ca0 change file 27 September 2023, 16:46:33 UTC
c63bbf6 Merge pull request #235 from sfu-cl-lab/collation-configuration Use configuration file to set database collation. 25 September 2023, 21:54:44 UTC
444eb3d Setting the database collation via the configuration file. - The executable comments found in the SQL files were being removed due to the logic in the prepareFile() method. - Updated areas in the codebase that set the collation to set the collation via a value drawn from the configuration file passed to FactorBase. 25 September 2023, 05:09:47 UTC
79b2c1e Removed trailing white-space. 25 September 2023, 02:40:32 UTC
326972f Update README.md 14 September 2023, 17:47:30 UTC
2b68872 update the example Mutagenesis_std 14 September 2023, 17:46:20 UTC
b191a55 Merge branch 'master' of https://github.com/sfu-cl-lab/FactorBase 14 September 2023, 07:22:46 UTC
bfc52f1 add the travis sql files 14 September 2023, 07:22:42 UTC
28fe1f6 Update README.md 14 September 2023, 07:19:34 UTC
677bd56 Update README.md 14 September 2023, 07:14:10 UTC
d829f40 Update config.cfg 14 September 2023, 07:10:05 UTC
e43c77b Update README.md 14 September 2023, 07:08:30 UTC
aff252e modify database dump storage 14 September 2023, 07:02:17 UTC
6eaffcc Merge pull request #234 from sfu-cl-lab/revert-sql-table-changes Revert SQL script table creation changes. 05 July 2023, 18:11:48 UTC
5007d50 Update metadata.sql Resolve the case of pair of Rnodes are same 04 July 2023, 19:27:56 UTC
3dd9cec Revert SQL script table creation changes. - Reverting SQL script changes that seem to only be needed if a specific version of MariaDB/MySQL is not used. The version that has been shown to work is: MariaDB 10.4.17 - Revert character set and collation changes. - Revert storage type change. 04 July 2023, 19:20:12 UTC
8916550 new version of metadata.sql. Adds extra copies of pvariables 29 June 2023, 22:43:45 UTC
49b692e ignoring backup files 29 June 2023, 22:03:58 UTC
0509be2 Add files via upload upload the new flow documentation 28 June 2023, 15:43:56 UTC
e9343e6 Merge pull request #233 from sfu-cl-lab/use-local-jar-file Use local copy of Tetrad JAR file. 26 June 2023, 17:06:01 UTC
fc5d5c7 Use local copy of Tetrad JAR file. - The URL that we were retrieving the JAR file from for Tetrad does not appear to be valid anymore so using a local copy of the JAR file instead. - The file tetrad-6.5.3.pom is my local copy from before the URL issue. - The new thirdparty module can be used to hold and transfer other third party dependencies in the future if necessary. 25 June 2023, 08:46:21 UTC
0c1e75a Update README.md 21 June 2023, 17:39:52 UTC
f93ae82 Merge pull request #232 from sfu-cl-lab/build-status-text Minor adjustment to the status badge text. 15 June 2023, 23:02:43 UTC
4804f77 upload example jar file 15 June 2023, 20:03:44 UTC
dfe41b6 Add example jar file 15 June 2023, 20:02:09 UTC
ff0fe34 Update initialize_databases.sql 15 June 2023, 19:48:39 UTC
0e5a1c0 Modify mysql script files 15 June 2023, 00:47:52 UTC
fe8edcb Revert "Modify the sql script files," This reverts commit b6810022ca183b35901eb8a02fac771ab389ad6e. 15 June 2023, 00:42:18 UTC
7b626cd Update README.md 14 June 2023, 21:48:44 UTC
b681002 Modify the sql script files, Modify the sql script files, solve long key issue 14 June 2023, 21:33:45 UTC
89fd6d8 Update README.md simplifying the instructions 13 June 2023, 23:20:11 UTC
7b259d8 Minor adjustment to the status badge text. - Changed the text for the status badge so that it is the same as the value used for the Travis version of the build. - Added a newline in README.md so that the status badge is on a separate line. 05 April 2023, 18:07:54 UTC
9718fa8 Merge pull request #230 from sfu-cl-lab/ci-pipeline Use GitHub Actions to run the tests. 04 April 2023, 17:51:00 UTC
4bde501 Updated the status badge. - Replaced the Travis status badge with the GitHub Actions version. 14 March 2023, 21:41:14 UTC
cbbde6a Revert "Bump mysql-connector-java from 8.0.19 to 8.0.28 in /code/common" This reverts commit 3c8f87c7350cefc34f79d1421912b1dcf2cd65e1. - This commit needs to be reverted otherwise there is an issue when connecting to a database. 14 March 2023, 21:36:16 UTC
6287a86 Use GitHub Actions with MariaDB service to run the tests. - Use a MariaDB service to run the tests instead of the MySQL installed on the GitHub Actions runner machine. - Added a "-h 127.0.0.1" option to the mysql commands so that the connection will go through TCP instead of a socket file. - Updated the dbdump.sh script to allow the hostname for the database to be specified. 14 March 2023, 21:36:16 UTC
5357eb3 Use GitHub Actions to run the tests. - Travis changed their service so switching to use GitHub actions, which will hopefully be longer lasting than Travis. - Created a GitHub Actions YAML file that is equivalent to the Travis one. - Updated the dbdump.sh script so that the sort command ignores the casing for the text to try and make the sort order more consistent. - Updated pom.xml to include a required class definition. - Updated the expected output for the Bif_unielwin.xml and mysql-extraction.txt files so that they match the output of the GitHub action run. - Moved the .travis.yml into the obsolete directory for easy reference. 14 March 2023, 21:36:12 UTC
1454ac3 Merge pull request #231 from sfu-cl-lab/dependabot/maven/code/common/mysql-mysql-connector-java-8.0.28 Bump mysql-connector-java from 8.0.19 to 8.0.28 in /code/common 12 March 2023, 01:07:22 UTC
3c8f87c Bump mysql-connector-java from 8.0.19 to 8.0.28 in /code/common Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 8.0.19 to 8.0.28. - [Release notes](https://github.com/mysql/mysql-connector-j/releases) - [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES) - [Commits](https://github.com/mysql/mysql-connector-j/compare/8.0.19...8.0.28) --- updated-dependencies: - dependency-name: mysql:mysql-connector-java dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> 20 June 2022, 23:31:48 UTC
8490851 Merge pull request #229 from sfu-cl-lab/fix-for-ubc-tool Fixed precision for conditional probabilities for the UBC tool. 19 November 2021, 17:14:24 UTC
3e66347 Fixed precision for conditional probabilities for the UBC tool. - The conditional probabilities weren't adding up to 1 exactly, which caused the UBC tool to complain (the Bayes net couldn't be visualized with the tool). - Restricting the decimal places to 6 digits for the CP column fixes the issue and seems to be due to how precision is returned from a division operation and then stored in the database. - Updated the expected output files (BIF and database content files). 18 November 2021, 00:48:27 UTC
07b906f Merge pull request #228 from sfu-cl-lab/dependabot/maven/code/factorbase/org.mybatis-mybatis-3.5.6 Bump mybatis from 3.5.2 to 3.5.6 in /code/factorbase 22 April 2021, 19:08:22 UTC
f93bc25 Bump mybatis from 3.5.2 to 3.5.6 in /code/factorbase Bumps [mybatis](https://github.com/mybatis/mybatis-3) from 3.5.2 to 3.5.6. - [Release notes](https://github.com/mybatis/mybatis-3/releases) - [Commits](https://github.com/mybatis/mybatis-3/compare/mybatis-3.5.2...mybatis-3.5.6) Signed-off-by: dependabot[bot] <support@github.com> 22 April 2021, 18:34:36 UTC
acac95c Merge pull request #227 from sfu-cl-lab/join-pdp PDPs for Table JOINs 06 January 2021, 21:51:51 UTC
89561c1 Generate the PDP information for an extra case. - The partial dependency plot (PDP) information is now also generated for the JOINs to generate the "_counts" tables for RNodes when the Ondemand method is used. - Updated the generateCountsTableAndPDPInfo() method to return the name of the "_counts" table generated so that it could be used in place of the generateCountsTable() method. - Updated associated Javadoc. 06 January 2021, 21:16:33 UTC
d4fef5d Updated the PDP information for table joins. - Updated the partial dependency plot (PDP) information for table JOINs to include the number of relationship tables involved in the JOIN. - Created a new variable "tableAlias" to make the code more clear. 01 January 2021, 01:06:47 UTC
509524a Generation of partial depenency plot (PDP) data for table JOINs. - Completed the changes from this commit: 5dc11c468ae68377f747c7e3c7df7d0353c5eb07 - Created *_SEPARATOR variables to make sure that the separator used to generate the query Strings and then parse the Strings to extract the PDP information are consistent. - The PDP information for table JOINs consists of the max degree, average degree, and the max number of rows of the entity tables involved in the table JOIN. 31 December 2020, 10:24:55 UTC
22cf2ad Made alias keyword more specific when extracting the aliases for SELECT columns. - Made the "AS" keyword more specific by including a space prefix when extracting the aliases for SELECT columns. 31 December 2020, 07:17:19 UTC
5dc11c4 Initial commit to enable the generation of PDP data for table JOINs. - Initial changes required to enable the generation of partial dependency plot (PDP) data for doing database table JOINs. - Created a new generateCountsTableQueryDetails() method to help return the query to execute to generate an "_counts" table as well as the tables that are involved in the JOIN. - Created some helper methods (createCountsTable*String) to reduce the duplication of code. - Added a stub method generateCountsTableAndPDPInfo() which will have the code needed to generate the PDP information for database table JOINs. - Changed the variable name "st2" to "statement" since we no longer have multiple Statement objects referenced in one given scope. 31 December 2020, 01:57:31 UTC
af67f4a Merge pull request #223 from sfu-cl-lab/dependabot/maven/code/factorbase/junit-junit-4.13.1 Bump junit from 4.12 to 4.13.1 in /code/factorbase 23 December 2020, 23:25:51 UTC
c9760f6 Merge pull request #226 from sfu-cl-lab/pdps-aggregated-intermediates Intermediate CT table build times are aggregated. 23 December 2020, 23:18:30 UTC
41cb83e Intermediate CT table build times are aggregated. - Prior to this change, the build times for intermediate CT tables were logged separately. They are now aggregated together to capture the total time it takes to build the target CT table. - The name of the last CT table built had to be passed around so that we would know which table to extract metadata from. 08 December 2020, 02:18:05 UTC
f8eb1c9 Merge pull request #225 from sfu-cl-lab/partial-dependency-plots-rchains Partial dependency plots for RChains 30 November 2020, 17:08:34 UTC
e5bed5b Output to generate PDPs for the CT tables of RChains. - Added new logging code to output the information necessary to generate the partial dependency plots (PDPs) for the creation of "_CT" tables for RChains. 28 November 2020, 00:23:02 UTC
791a0af Updated the warning message in CountsManager.java. - Updated the warning message in CountsManager.java that is output if a problem occurs when attempting to extract information necessary to generate partial dependency plots (PDPs) by making the message more helpful for debugging. 28 November 2020, 00:12:52 UTC
c8fc9e5 Updated counts extraction query in CountsManager.java. - Updated the query for retrieving the counts information from a CT table in CountsManager.java so that it matches the one used in MySQLFactorBaseDataBase.java. - Improved the query by adding surrounding backticks to the table name to ensure that the name is read properly. 28 November 2020, 00:00:32 UTC
e1ec240 Updated counts extraction query in MySQLFactorBaseDataBase.java. - Updated the query for retrieving the counts information from a CT table in MySQLFactorBaseDataBase.java so that it uses a FactorBaseDataBaseInfo object to retrieve the counts column name. This should make it easier to change the name of the column if we need to in the future. 27 November 2020, 23:42:15 UTC
57089ec Merge pull request #224 from sfu-cl-lab/partial-dependency-plots Partial Dependency Plots for RNode CT Tables 26 November 2020, 17:47:06 UTC
4f84b35 PDP output now includes whether or not the CT table was created from the cache. - The output for the partial dependency plots (PDPs) contains a new component "cachedT" or "cachedF", which indicates whether or not the "_CT" table was created using the cached version. - Updated the BuildRNodesCTMethod functional interface to reflect this change. 25 November 2020, 22:35:00 UTC
31fdbee Output to generate PDPs for the CT tables of RNodes. - Added new logging code to output the information necessary to generate the partial dependency plots (PDPs) for the creation of "_CT" tables. - Had to update some variables to prevent name collisions. - Note: This output is produced when the logging level is set to "runtimeDetails" or "debug". 25 November 2020, 22:34:09 UTC
cf76987 CountsManager uses a FactorBaseDataBaseInfo object to retrieve information. - CountsManager uses a FactorBaseDataBaseInfo object to retrieve database information specific to FactorBase. - Updated FactorBaseDataBaseInfo to generate and store the name of the CT cache database and the global counts database. - Replaced some variables in CountsManager with a FactorBaseDataBaseInfo object. 25 November 2020, 10:26:34 UTC
1c4406d Bump junit from 4.12 to 4.13.1 in /code/factorbase Bumps [junit](https://github.com/junit-team/junit4) from 4.12 to 4.13.1. - [Release notes](https://github.com/junit-team/junit4/releases) - [Changelog](https://github.com/junit-team/junit4/blob/main/doc/ReleaseNotes4.12.md) - [Commits](https://github.com/junit-team/junit4/compare/r4.12...r4.13.1) Signed-off-by: dependabot[bot] <support@github.com> 13 October 2020, 07:46:26 UTC
9f40f1d Merge pull request #222 from sfu-cl-lab/improved-bifchecker Updated the bifchecker script to support the XML file in the res directory. 24 September 2020, 17:19:42 UTC
f03cd6b Updated the bifchecker script to support the XML file in the res directory. - In the case when there are issues with generating the BIF file via FactorBase, the bifchecker.py script has been updated to support extracting metrics from the XML file that is produced in the "res" directory created by FactorBase. 24 September 2020, 01:01:51 UTC
e4bdc8b Merge pull request #221 from sfu-cl-lab/improved-metadata Improved metadata 16 September 2020, 22:07:14 UTC
9b1b137 Replaced the local lattice_mapping table with a view. - Replaced the local lattice_mapping table with a view that retrieves all the mappings instead of pre-filtering out the results. 11 September 2020, 23:19:02 UTC
cb8dfd7 Changed local FNodes table into a view. - The local FNodes table is only referenced once in the code so it should be more efficient to use a view instead of a table. - Have to convert the FNodes view into a table so that UPDATE calls in CP.java work. 11 September 2020, 23:18:56 UTC
6bd3099 Removed unnecessary table JOIN in the metaqueries. - When adding some entries to the MetaQueries table we JOINed the RNodes_2Nodes with the 2Nodes table to get the 2Nodes associated with the RNodes of the current family, but this isn't necessary as RNodes_2Nodes already only contains the 2Nodes associated with the RNodes of the current family. 11 September 2020, 09:35:19 UTC
e8b6298 Merge pull request #220 from sfu-cl-lab/console-output "_counts" and "_CT" Table Runtimes Written to the Console Output. 22 July 2020, 17:59:31 UTC
e60f069 Improved the logic for creating the "_counts" tables for RChains. - Improved the logic for determining when/if the "_counts" tables for RChains should be created. - When building the "_counts" tables for the global counts or precount we should start from an RChain length of 1 since we need to build all the tables. - When building the "_counts" tables for ondemand or hybrid we should start from an RChain length of 2 since we cache the CT tables meaning that we might not need to construct the "_counts" table for some RNodes. Also, for hybrid we use subqueries instead of materializing the tables for RNodes, so creating the tables is unnecessary for RNodes. - Updated the buildRChainCounts() method to take in a starting height since it's easier to determine this value outside the method. 19 July 2020, 23:45:05 UTC
e87d2fc Executed queries are only displayed when logging set to debug level. - Most of the SQL queries that are executed are only written to the console when the log level is set to "debug" now. - Created a new method logExecutedQuery() to help write the executed SQL query out to the console in a consistent format. 19 July 2020, 14:02:03 UTC
4ac1e62 Removed additional unnecessary logging statements. - Removed logging statements that printed unnecessary runtimes. - Removed logging statements that printed information that wasn't too helpful. - Removed logging statements that printed duplicate information. 19 July 2020, 14:02:03 UTC
896e452 Console output logging for "_counts" and "_CT" table creation. - Added a new logging level, "runtimeDetails," to enable console logging of the runtime for creating the "_counts" and "_CT" tables. - Created the method logRunTimeDetails() to help write the console output of the runtimes consistently. - Also output the build time for the "_counts" tables for PVars so that the times add up to the value found on the line that looks like: Building Time(ms) for ALL CT tables: 448 ms. 19 July 2020, 14:01:59 UTC
4386785 Removed more unnecessary logging statements. - Removed logging statements that didn't provide much information. 15 July 2020, 22:50:44 UTC
9416326 Removed unnecessary logging statements. - There were logging statements that printed out components of queries to the console; however, this shouldn't be necessary as we can just print out the final query which contains all the components. 15 July 2020, 21:08:11 UTC
4ad0b2c Removed duplicate code for printing the Structure Learning time. - Removed the duplicate code for printing the Structure Learning time. 15 July 2020, 19:08:02 UTC
c5b75fe Merge pull request #219 from sfu-cl-lab/ondemand-improvement Ondemand improvement 14 July 2020, 23:41:32 UTC
018766a Merge pull request #217 from sfu-cl-lab/large-database-support Changes required for large DBs like VisualGenome. 14 July 2020, 23:41:12 UTC
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