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 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''# <del>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 minions</del> example, you won't see an option with a green triangle next to it that says "Run 'skippedRunInitialImport.java''# <del>Investigate parallel speedup (e", and the green triangle in the top toolbar will be grayed out.gIf the project is not set up as a Maven project, you will not be able to run any of the code. multithreadTo set up the project as a Maven project, when you import the project, mmap)<follow the instructions at the following [https://www.jetbrains.com/help/idea/del> ''done'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.# Create XPath queries for reissue, design patents * On the second window (only utility right nowthere will be several options with check boxes next to them)make sure "import Maven projects automatically" is selected# Create semantic parser * 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 APS filesthe project and enter a folder location. This should ensure that the project is set up as a Maven project.  # '''Setting Up Your Data Cleanup (reference [[Patent_Assignment_Data_Restructure|Marcela and SoniaSource'''s work]])# If you run into a message across the top that says something along the lines of "Configure Data Source Merger (''only USPTO granted", maintfee, assignment'' then you have not connected IntelliJ to a database. You will not USPTO applications or Harvard Dataverse or Lex Machina currently)# Setup pipeline script be able to complete all of these steps run the code located under src/db until you configure one. Start by clicking on the link in series# Add constraints the message, or if it doesn't appear, follow the instructions [https://www.jetbrains.com/help/idea/connecting-to -a-database tables, e.ghtml here] to open up the "Data Sources and Drivers" pop-up to add a PostgreSQL database. correct typesWhen you get to the dialogue asking about the host, database, foreign keysuser, not nulland password, lookup tablesdo the following to connect to the database on the RDP:# Add deduplication 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".

<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") <code>select count(*), patent_type from patents group by patent_type;</code> {| class="wikitable"|+Results|-! scope="col" | count(*) !! scope="col" | patent_type|- | 725 | design|- | 18 | plant|-| 14 | reissue|- | 28187 | utility|}[[Patent Schema Reconciliation]] page

However, it uses parts of the base schema that are unused in the granted patent data. From a short, cursory glance it seems like the meat of the join data appears in the See <code><us-related-documents>E:\McNair\Projects\SimplerPatentData\data\examples\granted</code> tagfor 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|✓|~|~|~

|<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|✓|~|~|~

|✓~|✓~|~

|✓~|✓~|~

|✓~|✓~|~|} === 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

# === Create an empty database: <code>$ createdb --usernameon RDP ===postgres patents_june_2017 # password is tabspaceenter</code># Create tables via script at <code>E:\McNair\Projects\SimplerPatentData\src\db\NaiveSchema.sql</code>#* Prior Example <code>E:\McNair\Software\Scripts\Patent\createTables.sql</code>#* Aim to create a completely naive schema with as few constraints as possible--iteratively add more constraints in the future

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>. For a concrete example, see See <code>E:\McNair\Projects\SimplerPatentData\src\main\java\org\bakerinstitute\mcnair\uspto_assignmentsmodels\GeonamesZipsGrantedPatent.java</code> for a simple, self-contained '''an example or 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\main\java\org\bakerinstitute\mcnair\models\GrantedPatent.javadb</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 an example of how 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 extend the abstraction layer to deal with more complex scenarios.table (see DatabaseHelper for the pattern I use)

* Question: "In which zipcodes are 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.* Zipcode granularity--if possibleThis 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, finer detail wantedthe data generated here should be superset of the data present in the Patent Assignment Data Restructure project.* Filter non-USNote that as of the beginning of August 2017, null addressesthis part '''has not been completed.'''  === Intuition === * Need Use <code>assignments_longform.last_update_date</code> to cleanup addresses* Extract zipcode find current/latest (or reverse locate first/earliest) date of assignment. Then match with <code>properties.docid</code> on <code>reelno, frameno</code> to find zippatent 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]