Edit Project: Reproducible Patent Data

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<onlyinclude>The [[Reproducible Patent Data]] project is a continuation of the [[Redesigning Patent Database]] 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> == 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 <code>src/db/schemas/</code> in your new database # Modify the constant <code>DATABASE_NAME</code> in <code>E:\McNair\Projects\SimplerPatentData\src\main\java\org\bakerinstitute\mcnair\postgres\DatabaseHelper.java</code> # Run the Driver scripts in IntelliJ with the correct value for <code>DATA_DIRECTORY</code> (or run <code>RunInitialImport.java</code> which will do all of the data directories for that patent item type) # [Take a really, really long lunch...in total should take no more than five hours to load data on RDP] # Run scripts in <code>src/db/constraints</code> to check data assumptions # That's it! ===Troubleshooting=== If you're new to IntelliJ (and even if you're not) you might run into problems with importing the project. '''Setting Up Project as a Maven project''' It should be clear if the project is not set up as a Maven project - when you right click on RunInitialImport.java, for example, 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, 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 (there will be several options with check boxes next to them) make sure "import Maven projects automatically" is selected * On the "Please select project SDK" window, make sure it says "1.8" in the "Name" slot. * On the next window, 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''' 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, 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 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'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 == === Where is the Data? === ==== Directories ==== All of the information for this project is located at <code>E:\McNair\Projects\SimplerPatentData</code> There are several interesting directories: * <code>data/downloads/</code> is USPTO bulkdata, unmodified straight from the scraper * <code>data/extracts/</code> is a directory of a strict subset of the information stored in <code>data/downloads/</code>. It is the result of running a bulk 7-zip job on that directory to get everything unzipped in a flat data structure. Note that these files have the USPTO modified-by time since that metadata is stored in the zipfiles. To extract files in this nice format, select all of the zipfiles and setup an extraction job like in this [[media:7zip-params.png|screenshot]] * <code>data/backups/</code> is a 7zip'd backup of the corresponding directory in extracts * <code>src/</code> is the main code repository for the java project ==== Input Files ==== All of the text-only Red Book files for '''granted patents''' from 1976 to 2016, inclusive. To find a specific year's XML file, find it in <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 <code>E:\McNair\Projects\SimplerPatentData\data\extracts\granted\</code> '''To find maintenance fee data''', look in <code>E:\McNair\Projects\SimplerPatentData\data\downloads\maintenance\</code> === Where is the Code? === The code has the same parent directory as the data, so it is at <code>E:\McNair\Projects\SimplerPatentData\src</code>. You might notice a lot of single-entry directories; this is an idiomatic Java pattern that is used for package separation. If using IntelliJ or some other IDE, these directories are a bit less annoying. The development environment is Java 8 JDK, IntelliJ Ultimate IDE, Maven build tools, and git VCS. The git repository can be found at http://rdp.mcnaircenter.org/codebase/Repository/ReproduciblePatent ==== Prior Art ==== This tool is not so concerned with adding new functionality; rather, it aims to take a bunch of spread out Perl scripts and create a faster system that is easier to work with. As such, its functionality is largely stolen from those scripts: * Downloader: <code>E:\McNair\Software\Scripts\Patent\USPTO_Parser.pl</code> * XML Splitter: <code>E:\McNair\PatentData\splitter.pl</code> * XML Parsing: <code>E:\McNair\PatentData\Processed\xmlparser_4.5_4.4_4.3.pl</code> and <code>E:\McNair\PatentData\Processed\*.pm</code> In addition, I used several non-standard Java libraries listed below: * [https://github.com/mashape/unirest-java/ Unirest] for easy HTTP requests (MIT License) * [https://github.com/google/guava Google Guava] for immutable collections and Stream utilities (Apache v2.0 License) * [https://github.com/jhy/jsoup/ jsoup] for HTML parsing (MIT License) * [http://commons.apache.org/proper/commons-codec/ Apache Commons Codec] (Apache v2.0 License) * [http://commons.apache.org/proper/commons-lang/ Apache Commons Lang v3] (Apache v2.0 License) * [https://mvnrepository.com/artifact/org.jetbrains/annotations/15.0 Jetbrains Annotations] for enhanced null checks (Apache v2.0 License) * [http://search.maven.org/#artifactdetails%7Corg.postgresql%7Cpostgresql%7C42.1.1.jre7%7Cbundle PostgreSQL JDBC] (BSD 3-clause per https://github.com/pgjdbc/pgjdbc-jre7/blob/master/LICENSE) If using maven, these dependencies are listed and should automatically be setup. ==== Using Code ==== Any 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. The 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=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> to include all of the runtime dependencies and it's just not worth it. ==== Altering Code ==== * 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? !! 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: green; color: white;" | Yes |✓ |~ |~ |~ |- |<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: green; color: white;" | Yes |✓ |~ |~ |~ |- |January 2005 to December 2005 |XML Version 4.0 ICE |<code>data/extracts/granted/modern</code> |style="background: green; color: white;" | Yes |✓ |~ |~ |~ |- |January 2006 to December 2006 |XML Version 4.1 ICE |<code>data/extracts/granted/modern</code> |style="background: green; color: white;" | Yes |✓ |~ |~ |~ |- |January 2007 to December 2012 |XML Version 4.2 ICE |<code>data/extracts/granted/modern</code> |style="background: green; color: white;" | Yes |✓ |~ |~ |~ |- |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 == Because there isn't a compelling reason not to, I used the existing PostgreSQL infrastructure on the RDP. The "Java Way" of interacting with databases is the Java Database Connectivity API (JDBC), an implementation-agnostic API for interacting with databases. This project uses the stock [https://jdbc.postgresql.org/ Postgres JDBC], version 42.1.1 === Create an empty database on RDP === To create an empty database, run this command: <code>$ createdb --username=postgres database-name-goes-here # password is tabspaceenter</code> === 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\main\java\org\bakerinstitute\mcnair\models\GrantedPatent.java</code> for '''an example of how to extend''' the abstraction layer to deal with more complex scenarios. === New Table Checklist === * Create schema DDL SQL code for the new table in <code>E:\McNair\Projects\SimplerPatentData\src\db</code> * Run the schema creation * Create an enum with the same names for attributes as in the DDL (case-insensitive! prefer all-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 Patent 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]] * [[Patent_Data_Cleanup_(June_2016)|Patent Data Cleanup, June 2016 by Marcela]] * [[Patent_Data|Patent Data, Spring 2016 by Marcela]] * [[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]]* [[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] * [http://rdp.mcnaircenter.org/codebase/Repository/ReproduciblePatent Git Repository]

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