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{{Project|Has project output=Data,Tool,Content,How-to,Guide|Has sponsor=McNair ProjectsCenter
|Has Image=Uspto web logo.jpg
|Has title=Reproducible Patent Data
}}
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. Currently, it succeeds in bulk downloading from See also the USPTO; streaming file splitting, that is, splitting large concatenated files into their component parts in-memory; and parsing of XML to Java objects, APS to Java Maps, and maintenance fee data to Java objects[[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 fieldscheck data assumptions# That's it! ===Troubleshooting=== If you're new to IntelliJ (and even if you're not)</del> you might run into problems with importing the project.  '''Setting Up Project as a Maven project'done''# Create tooling It should be clear if the project is not set up as a Maven project - when you right click on RunInitialImport.java, for minionsexample, 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# Create XPath queries for reissuemaven_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, design patents (only utility right now)otherwise you won't get the pom.xml file that you need to let IntelliJ know that this is a Maven project.# Data Cleanup * 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# Setup pipeline script to complete all of these steps * On the "Please select project SDK" window, make sure it says "1.8" in seriesthe "Name" slot. # Investigate parallel speedup (e* On the next window, enter a name for the project and enter a folder location.g This should ensure that the project is set up as a Maven project. multithread, mmap)# '''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", then 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, or if it doesn't appear, maintfeefollow 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, assignmentdo 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 Make sure to test the connection by clicking "Test Connection". Now you should be able to run the scripts under src/db. If you're seeing issues such as "column [something] of relation [something] doesn't exist" but you' not USPTO applications or Harvard Dataverse or Lex Machina currently)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 the Database tab and select "Properties".
== Directory Layout ==
<code>E:\McNair\Projects\SimplerPatentData\data\extracts\granted\</code>
 
'''To find application data''' from 2001 to 2016, inclusive, look in
 
<code>E:\McNair\Projects\SimplerPatentData\data\extracts\applications\</code>
'''To find assignment data''', look in
'''To find maintenance fee data''', look in
<code>E:\McNair\Projects\SimplerPatentData\data\downloads\maintenance\</code>
=== Where is the Code? ===
The development environment is Java 8 JDK, IntelliJ Ultimate IDE, Maven build tools, and git VCS.
The git repository can be found at httpshttp://rdp.mcnaircenter.org/codebase/Repository/ReproduciblePatent
==== Prior Art ====
If using maven, these dependencies are listed and should automatically be setup.
==== Design Using Code ====
E:\McNair\Projects\Market for IdeasE:\McNair\Projects\Little Guy Academic PaperAny file with a line that says <code>public static void main(String[] args) {</code> can be run as a standalone file. The easiest way to do this is to load the project and then the file in IntelliJ and click the little green play arrow next to this bit of code.
TODOThe code can also be run via the standard <code>javac</code> and <code>java</code> commands but since this project has a complicated structure you end up having to run commands like
<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=== Using Code ====UTF-8 -classpath "[...contents truncated...];C:\Users\OliverC\.m2\repository\org\postgresql\postgresql\42.1.1\postgresql-42.1.1.jar" org.bakerinstitute.mcnair.uspto_assignments.XmlDriver</code>
TODOto include all of the runtime dependencies and it's just not worth it.
==== Altering Code ====
TODO* Use the IntelliJ command Reformat code (found in the menus at <code>Code > Reformat Code</code>* Use the optimize imports function found under the same menu* Use spaces for indentation* Loosely try to keep lines below 120 characters* Commit changes to the Git remote repository "bonobo"
== Schema Reconciliation ==
 
For the work by Joe, see the [[Patent Schema Reconciliation]] page
 
=== Patents (Granted) ===
 
See <code>E:\McNair\Projects\SimplerPatentData\data\examples\granted</code> for extracted examples of what specific data is available for a sample of the data.
{| class="wikitable"
|+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
|-
|January 1976 to December 2001
|APS
|<code>data/extracts/granted/vintage</code>|style="background: redgreen; color: white;" | Only syntaxYes|✓|~|~|~
|-
|<del>January 2001 to December 2001</del>
|<del>SGML</del>
|Ignored; use concurrently recorded APS data
|No|N/A|N/A|N/A|N/A
|-
|January 2002 to December 2004
|XML Version 2.5
|<code>data/extracts/granted/blunderyears</code>|style="background: redgreen; color: white;" | Only syntaxYes|✓|~|~|~
|-
|January 2005 to December 2005
|XML Version 4.0 ICE
|<code>data/extracts/granted/modern</code>|style="background: yellowgreen; color: white;" | MaybeYes|✓|~|~|~
|-
|January 2006 to December 2006
|XML Version 4.1 ICE
|<code>data/extracts/granted/modern</code>|style="background: yellowgreen; color: white;" | MaybeYes|✓|~|~|~
|-
|January 2007 to December 2012
|XML Version 4.2 ICE
|<code>data/extracts/granted/modern</code>|style="background: yellowgreen; color: white;" | MaybeYes|✓|~|~|~
|-
|January 2013 to September 24, 2013
|XML Version 4.3 ICE
|<code>data/extracts/granted/modern</code>
|style="background: green; color: white;" | Yes
|✓
|~|~|~
|-
|October 8, 2013 to December 2014
|XML Version 4.4 ICE
|<code>data/extracts/granted/modern</code>
|style="background: green; color: white;" | Yes
|✓
|~|~|~
|-
|January 2015 to December 2016
|XML Version 4.5 ICE
|<code>data/extracts/granted/modern</code>
|style="background: green; color: white;" | Yes
|✓
|~|~|~
|}
=== APS Rosetta Stone ===
 
The Advanced Patent System (APS) is a fixed-width text format used to store historical patent grant data. The documentation for this sucks; there are pages missing at random. Luckily, we only care about the content contained here: [[File:PatentFullTextAPSDoc_GreenBook_pgs13-22.pdf]].
 
It's worth mentioning that the APS contains an advanced text markup system for chemical formulae, basic text markup, tables, etc. that can lead to seemingly garbled text that is perfectly well-formed.
 
==== APS Gotchas ====
 
* PATN.WKU is the granted patent number. It is 7 digits while the spec promises 6 digits. The rightmost digit is a check digit modulus 11. See [[File:Aps-wku-modulus11.pdf]] for the words from the horse's mouth.
 
=== Patents (Applications) ===
 
{| class="wikitable"
|+Patent Application Data Formats
|-
! scope="col" | Dates Used !! scope="col" | Format !! scope="col" | Location !! scope="col" | Supported by Parser?
|-
|March 15, 2001 to December 2001
|XML Version 1.5
|<code>data/extracts/applications/vintage</code>
|style="background: yellow;" | Yes, for basic information, inventors, and correspondents
|-
|January 2002 to December 2004
|XML Version 1.6
|<code>data/extracts/applications/vintage</code>
|style="background: yellow;" | Ditto
|-
|January 2005 to December 2005
|XML Version 4.0 ICE
|<code>data/extracts/applications/modern</code>
|style="background: yellow;" | Ditto
|-
|January 2006 to December 2006
|XML Version 4.1 ICE
|<code>data/extracts/applications/modern</code>
|style="background: yellow;" | Ditto
|-
|January 2007 to December 2012
|XML Version 4.2 ICE
|<code>data/extracts/applications/modern</code>
|style="background: yellow;" | Ditto
|-
|January 2013 to December 2014
|XML Version 4.3 ICE
|<code>data/extracts/applications/modern</code>
|style="background: yellow;" | Ditto
|-
|January 2015 to ''Present''
|XML Version 4.4 ICE
|<code>data/extracts/applications/modern</code>
|style="background: yellow;" | Ditto
|}
== Database ==
This project uses the stock [https://jdbc.postgresql.org/ Postgres JDBC], version 42.1.1
# === 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.
== Related Pages ==
* [[Redesign_Assignment_and_Patent_Database|Redesign Assignment and Patent Database, Fall 2017 by Shelby]]
* [[Equivalent_XPath_and_APS_Queries|Equivalent XPath and APS Queries, Summer 2017 by Oliver & Joe]]
* [[US_Address_Verification|US Address Verification, Summer 2017 based on tables from Assignment Data Restructure]]
* [[Patent_Assignment_Data_Restructure|Assignment Data Restructure, Spring 2017 by Marcela and Sonia]]
* [[Redesigning_Patent_Database|Redesigning Patent Database, Spring 2017 by Shelby]]
* [[Lex_Machina|Lex Machina]]
* [[USPTO_Patent_Litigation_Data|USPTO Patent Litigation Research Dataset by Ed]]
* [[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]]
* [[Oliver_Chang_(Work_Log)|My Work Log]]
== External Links ==
* Understanding Assignment Data: [https://www.uspto.gov/sites/default/files/documents/USPTO_Patents_Assignment_Dataset_WP.pdf USPTO Documentation on their cleanup of this data]
* [https://bulkdata.uspto.gov/data2/patent/grant/redbook/fulltext/1976/PatentFullTextAPSDoc_GreenBook.pdf USPTO Green Book (APS) Documentation]
* [https://bulkdata.uspto.gov/ USPTO Bulk Data Storage System (BDSS)]
* [https://en.wikipedia.org/wiki/Builder_pattern Builder Pattern in Object-Oriented Programming]
* [httpshttp://rdp.mcnaircenter.org/codebase/Repository/ReproduciblePatent Git Repository]

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