Changes

{{Project|Has project output=Data,Tool,Content,How-to,Guide|Has sponsor=McNair ProjectsCenter

A <onlyinclude>The [[Reproducible Patent Data]] project is a continuation of the [[Redesigning Patent Database]] that project. It aims to write faster, more centralized code to deal with data from the United States Patent and Trademark Office (USPTO). By having an end-to-end pipeline we can easily reproduce or update data without worrying about unintentional side effects or missing data.See also the [[Patent Data]] umbrella project. </onlyinclude>

== Progress Quickstart ==

To get up and running with the code, do the following: # Clone the git project (link at end of page) to your user directory# Launch IntelliJ with >= Java 8 and Maven configured (default version installed on the RDP is setup to do this)# Open project in IntelliJ# Create an empty database (see [[#Database]])# Run the table creation scripts in <delcode>Downloadersrc/db/schemas/</delcode> ''done''in your new database# Modify the constant <delcode>SplitterDATABASE_NAME</delcode> ''done''# in <delcode>ParserE:\McNair\Projects\SimplerPatentData\src\main\java\org\bakerinstitute\mcnair\postgres\DatabaseHelper.java</delcode> ''done''# Run the Driver scripts in IntelliJ with the correct value for <delcode>Setup PostgreSQL JDBCDATA_DIRECTORY</delcode> ''done''# (or run <delcode>Create naive schema based on previous approachesRunInitialImport.java</delcode> ''done''which will do all of the data directories for that patent item type)# <del>Create new [Take a really, really long lunch...in total should take no more than five hours to load data structures</del> ''done''on RDP]# <del>Database Insert (modify Run scripts in <code>modelssrc/db/constraints</code> files with some mapping to database fields)</del> check data assumptions# That's it! ===Troubleshooting=== If you're new to IntelliJ (and even if you'donere not) you might run into problems with importing the project.  ''# <del>Create tooling for minions</del> 'Setting Up Project as a Maven project'skipped''# Create XPath queries It should be clear if the project is not set up as a Maven project - when you right click on RunInitialImport.java, for reissueexample, design patents (only utility right now)you won't see an option with a green triangle next to it that says "Run 'RunInitialImport.java'", and the green triangle in the top toolbar will be grayed out. If the project is not set up as a Maven project, you will not be able to run any of the code. To set up the project as a Maven project, when you import the project, follow the instructions at the following [https://www.jetbrains.com/help/idea/maven.html# maven_import_project_start link]. * Note that when you click "Import Project", you should select the "Simpler Patent Data" folder, not the "src" folder within Simpler Patent Data Cleanup , otherwise you won't get the pom.xml file that you need to let IntelliJ know that this is a Maven project.* On the second window (reference [[Patent_Assignment_Data_Restructure|Marcela and Sonia's work]]there will be several options with check boxes next to them)make sure "import Maven projects automatically" is selected# Investigate parallel speedup (e* On the "Please select project SDK" window, make sure it says "1.g8" in the "Name" slot. multithread* On the next window, mmap)enter a name for the project and enter a folder location. This should ensure that the project is set up as a Maven project.  # '''Setting Up Your Data Source Merger (''only USPTO granted' If you run into a message across the top that says something along the lines of "Configure Data Source", maintfeethen you have not connected IntelliJ to a database. You will not be able to run the code located under src/db until you configure one. Start by clicking on the link in the message, assignmentor if it doesn'' not USPTO applications or Harvard Dataverse or Lex Machina currently)t appear, follow the instructions [https://www.jetbrains.com/help/idea/connecting-to-a-database.html here] to open up the "Data Sources and Drivers" pop-up to add a PostgreSQL database. When you get to the dialogue asking about the host, database, user, and password, do the following to connect to the database on the RDP:  host: localhost database: whatever the constant DATABASE_NAME is set to - the default is patentsj user: postgres password: tabspaceenter # Setup pipeline script Make sure to test the connection by clicking "Test Connection". Now you should be able to complete all run the scripts under src/db. If you're seeing issues such as "column [something] of these steps relation [something] doesn't exist" but you've run the schema scripts, you probably have different database name under the data source than the one the constant DATABASE_NAME is set to. To change this, right click on the data source in seriesthe Database tab and select "Properties".

<code>E:\McNair\Projects\SimplerPatentData\data\downloads\maintenance\</code>

The git repository can be found at httpshttp://rdp.mcnaircenter.org/codebase/Repository/ReproduciblePatent

<code>"C:\Program Files\Java\jdk1.8.0_131\bin\java" "-javaagent:C:\Users\OliverC\IntelliJ IDEA 2017.1.3\lib\idea_rt.jar=62364:C:\Users\OliverC\IntelliJ IDEA 2017.1.3\bin" -Dfile.encoding=UTF-8 -classpath "C:\Program Files\Java\jdk1[.8.0_131\jre\lib\charsets.jar;C:\Program Files\Java\jdk1contents truncated.8.0_131\jre\lib\deploy.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\ext\access-bridge-64.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\ext\cldrdata.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\ext\dnsns.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\ext\jaccess.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\ext\jfxrt.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\ext\localedata.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\ext\nashorn.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\ext\sunec.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\ext\sunjce_provider.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\ext\sunmscapi.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\ext\sunpkcs11.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\ext\zipfs.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\javaws.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\jce.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\jfr.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\jfxswt.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\jsse.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\management-agent.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\plugin.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\resources.jar;C:\Program Files\Java\jdk1.8.0_131\jre\lib\rt.jar;E:\McNair\Projects\SimplerPatentData\target\classes;C:\Users\OliverC\.m2\repository\com\mashape\unirest\unirest-java\1.4.9\unirest-java-1.4.9.jar;C:\Users\OliverC\.m2\repository\org\apache\httpcomponents\httpclient\4.5.2\httpclient-4.5.2.jar;C:\Users\OliverC\.m2\repository\org\apache\httpcomponents\httpcore\4.4.4\httpcore-4.4.4.jar;C:\Users\OliverC\.m2\repository\commons-logging\commons-logging\1.2\commons-logging-1.2.jar;C:\Users\OliverC\.m2\repository\org\apache\httpcomponents\httpasyncclient\4.1.1\httpasyncclient-4.1.1.jar;C:\Users\OliverC\.m2\repository\org\apache\httpcomponents\httpcore-nio\4.4.4\httpcore-nio-4.4.4.jar;C:\Users\OliverC\.m2\repository\org\apache\httpcomponents\httpmime\4.5.2\httpmime-4.5.2.jar;C:\Users\OliverC\.m2\repository\org\json\json\20160212\json-20160212.jar;C:\Users\OliverC\.m2\repository\com\google\guava\guava\21.0\guava-21.0.jar;C:\Users\OliverC\.m2\repository\org\jsoup\jsoup\1.10.2\jsoup-1.10.2.jar;C:\Users\OliverC\.m2\repository\commons-codec\commons-codec\1.10\commons-codec-1.10.jar;C:\Users\OliverC\.m2\repository\org\jetbrains\annotations\15.0\annotations-15.0.jar;C:\Users\OliverC\.m2\repository\org\apache\commons\commons-lang3\3.5\commons-lang3-3.5.jar];C:\Users\OliverC\.m2\repository\org\postgresql\postgresql\42.1.1\postgresql-42.1.1.jar" org.bakerinstitute.mcnair.uspto_assignments.XmlDriver</code>

As it turns outFor the work by Joe, since many of the fields we care about are date and author data the schemas are see the same ("universal")[[Patent Schema Reconciliation]] page

<code>select count=== Patents (*Granted), patent_type from patents group by patent_type;725;"design"18;"plant"14;"reissue"28187;"utility"</code>===

where "plant" literally refers to floraSee <code>E:\McNair\Projects\SimplerPatentData\data\examples\granted</code> for extracted examples of what specific data is available for a sample of the data.

|+Granted Patent Data Formats

! scope="col" | Dates Used !! scope="col" | Format !! scope="col" | Location !! scope="col" | Supported by Parser? !! scope="col" | Utility !! scope="col" | Reissue !! scope="col" | Design !! scope="col" | Plant

|<code>data/extracts/granted/vintage</code>|style="background: redgreen; color: white;" | Only syntaxYes|✓|~|~|~

|✗No|✗N/A|✗N/A|N/A|N/A

|<code>data/extracts/granted/blunderyears</code>|style="background: redgreen; color: white;" | Only syntaxYes|✓|~|~|~

|<code>data/extracts/granted/modern</code>|style="background: yellowgreen; color: white;" | MaybeYes|✓|~|~|~

|<code>data/extracts/granted/modern</code>|style="background: yellowgreen; color: white;" | MaybeYes|✓|~|~|~

|<code>data/extracts/granted/modern</code>|style="background: yellowgreen; color: white;" | MaybeYes|✓|~|~|~

|✓~|✓~|~

|✓~|✓~|~

|✓~|✓~|~

# === Create an empty databaseon RDP === To create an empty database, run this command: <code>$ createdb --username=postgres patents_june_2017 database-name-goes-here # password is tabspaceenter</code># Create tables via script at === Abstraction Layer === Since writing raw SQL is a bit cumbersome and error-prone, I have added some abstraction layers that make it much easier to quickly add bulk data. By using Postgres's <code>CopyManager</code> class, we buffer SQL copy commands in memory (as many as possible) and then flush these rows. To understand how the abstraction layers work, see the code in <code>E:\McNair\Projects\SimplerPatentData\src\main\java\org\bakerinstitute\mcnair\postgres</code>. See <code>E:\McNair\Projects\SimplerPatentData\src\dbmain\java\org\bakerinstitute\mcnair\models\NaiveSchemaGrantedPatent.sqljava</code>for '''an example of how to extend''' the abstraction layer to deal with more complex scenarios. === New Table Checklist === #* Prior Example Create schema DDL SQL code for the new table in <code>E:\McNair\SoftwareProjects\ScriptsSimplerPatentData\Patentsrc\createTables.sqldb</code>#* Aim to create a completely naive Run the schema creation* Create an enum with the same names for attributes as few constraints as possiblein the DDL (case-insensitive! prefer all-iteratively add more constraints caps screaming snake case)* Create a class which subclasses <code>AbstractInsertableData</code>* Inside that class, create a static class which subclasses <code>AbstractTableMetadata</code> and has the proper values for getTableName(), getStringColumns(), getIntColumns()* (Optional) Implement builder pattern* (Optional) Create a custom databasehelper for complex extras (see PatentApplication and GrantedPatent for examples)* Write the data to the table (see DatabaseHelper for the pattern I use) == Address Data == To get the most granular address data (street level, or at least postcode level) about who owns patents, the path is not so straightforward because off the complicated mapping of ownership to a granted patent.This is the final part of this project that I am working on and it is all at the level of SQL.See <code>E:\McNair\Projects\SimplerPatentData\src\db\joins</code> for my attempts to create a clean mapping.Optimistically speaking, the data generated here should be superset of the data present in the futurePatent Assignment Data Restructure project. Note that as of the beginning of August 2017, this part '''has not been completed.'''  === Intuition === Use <code>assignments_longform.last_update_date</code> to find current/latest (or first/earliest) date of assignment. Then match with <code>properties.docid</code> on <code>reelno, frameno</code> to find patent application id. With this mapping to granted patents, we can discover the details of the original granted patent. And with the right date and reelno and frameno, we can match to the <code>assignees</code> table and get fine granularity addresses.

* [[Patent_Litigation_and_Review|Patent Litigation and Review by Marcela]]* [[Bag_of_Words_Analysis_of_Patent_Data|Bag of Words Analysis]]* [[Patent|Existing Database Schema]]

* [httpshttp://rdp.mcnaircenter.org/codebase/Repository/ReproduciblePatent Git Repository]