Metadata-Version: 1.1
Name: medic
Version: 2.2.0
Summary: A command line tool to manage a PubMed DB mirror.
Home-page: https://github.com/fnl/medic
Author: Florian Leitner
Author-email: florian.leitner@gmail.com
License: GNU GPL v3
Description: =====
        medic
        =====
        -------------------------------------------------
        a command-line tool to manage a mirror of MEDLINE
        -------------------------------------------------
        
        The Swiss Army knife to parse MEDLINE_ XML files or
        download eUtils' PubMed_ XML records,
        bootstrapping a local MEDLINE/PubMed database,
        updating and/or deleting the records, and
        writing the contents of selected PMIDs into flat-files.
        A more in-depth tutorial for this tool is part of my blog_.
        
        .. image:: https://zenodo.org/badge/4016/fnl/medic.png
           :target: https://zenodo.org/record/9968
           :alt: DOI:10.5281/zendo.9968
        
        DOI:10.5281/zendo.9968
        
        Synopsis
        ========
        
        ::
        
          medic [options] CMD FILE|PMID...
        
          man medic
          medic --help
          medic --output /tmp parse baseline/medline*.xml.gz
          medic --update parse update/medline*.xml.gz
          medic --info delete delete.txt
          medic --url sqlite:///tmp.db insert pubmed.xml
          medic --pmid-lists update pmids_to_fetch_online.txt
          medic --all update medline13n1000.xml
          medic --format html write 1028734 1298474 > out.html
          medic --logfile log.txt write pmid_list.txt
        
        Setup
        =====
        
        If you are **not** using ``pip install medic``, install all
        dependencies/requirements::
        
          pip install sqlalchemy
          # only if using python3 < 3.2:
          pip install argparse 
        
        Install the **DB driver** you prefer to use (supported are PostgreSQL
        and SQLite, with the latter part of the Python StdLib)::
        
          pip install psycopg2 
        
        Create the PostgreSQL database::
        
          createdb medline 
        
        If you are fine working with SQLite, you only need to use the path to the
        SQLite DB file in the URL option (that will implicitly "create" the DB)::
        
          medic insert --url sqlite:///tmp.db 123456
        
        To create the tables in the DB, you can "try" to fetch a record: As the DB
        is empty, this will not write anything, but SQL Alchemy will create the tables
        for you in the DB::
        
          medic write 123 # for PostgreSQL
          medic --url sqlite:///tmp.db write 123 # for SQLite
        
        Description
        ===========
        
        ``medic [options] COMMAND PMID|FILE...``
        
        The ``--url URL`` option represents the DSN of the database and might
        be needed (default: ``postgresql://localhost/medline``); For example:
        
        PostgreSQL
          ``postgresql://host//dbname``
        SQLite DB
          ``sqlite:////absolute/path/to/foo.db`` or
          ``sqlite:///relative/path/to/foo.db``
        
        The five **COMMAND** arguments:
        
        ``insert``
          Create records in the DB by parsing MEDLINE XML files or
          by downloading PubMed XML from NCBI eUtils for a list of PMIDs.
          The insert fails if the record already exists in the DB.
        ``write`` *
          Write records as MEDLINE_ files to a directory, each file named as
          "<pmid>.txt". Alternatively, just the TIAB (title and abstract) plain-text
          can be output, and finally, a single file in TSV or HTML format can be
          generated (see option ``--format``).
          If the requested PMID does not exist in the DB, the command does not fail,
          but the relevant file, row, or element will not have been written.
        ``update``
          Insert or update records in the DB (instead of creating them); note that
          if a record exists, but is added with ``create``, this would throw an
          `IntegrityError`. If you are not sure if the records are in the DB or
          not, use ``update`` (N.B. that ``update`` is slower).
        ``delete`` *
          Delete records from the DB for a list of PMIDs (using ``--pmid-lists``)
        ``parse``
          Does not interact with the DB, but rather creates ".tab" files for each
          table that later can be used to load a database, particularly useful when
          bootstrapping a large collection.
        
        \* Note that ``write`` and ``delete`` can only use PMID lists (option
        ``--pmid-lists``), so for these two commands, that option is always active
        (implicitly).
        
        For example, to download two PubMed records by PMID and update them in
        the DB::
        
          medic update 100000 123456
        
        Add a single MEDLINE or PubMed XML file to the database::
        
          medic insert pudmed.xml
        
        Export a few records from the database as HTML (to STDOUT)::
        
          medic write --format html 292837491 128374 213487
        
        Note that if the suffix ".gz" is present, the parser automatically
        decompresses the XML file(s) first. This feature *only* works with
        GNU-zipped files and the ".gz" suffix must be present.
        
        Therefore, command line arguments are treated as follows:
        
        integer values
          are always treated as PMIDs to download PubMed XML data
        all other values
          are always treated as MEDLINE XML files to parse
          **unless** you use the option ``--pmid-lists``
        files ending in ".gz"
          are treated as gzipped MEDLINE XML files
        
        Requirements
        ============
        
        - Python 3.2+
        - SQL Alchemy 0.8+
        - PostgreSQL 8.4+ or SQLite 3.7+
        
        *Note* that while any DB supported by SQL Alchemy should work, all other DBs
        are **untested**.
        
        Loading MEDLINE
        ===============
        
        Please be aware that the MEDLINE distribution **is not unique**, meaning that
        it contains a few records multiple times (see the section about
        **Version IDs**).
        
        Parsing and loading the baseline into a PostgreSQL DB on the same machine::
        
          medic parse baseline/medline14n*.xml.gz
        
          for table in citations abstracts authors chemicals databases \
          descriptors identifiers keywords publication_types qualifiers sections; 
            do psql medline -c "COPY $table FROM '`pwd`/${table}.tab';";
          done
        
        For the update files, you need to go *one-by-one*, adding each one *in order*,
        and using the flag ``--update`` when parsing the XML. After parsing an XML file
        and *before* loading the dump, run ``medic delete delete.txt`` to get rid of
        all entities that will be updated or should be removed (PMIDs listed as
        ``DeleteCitation``\ s)::
        
          # parse a MEDLINE update file:
          medic --update parse medline14n1234.xml.gz
        
          # delete its updated and DeleteCitation records:
          medic delete delete.txt
        
          # load (COPY) all tables for that MEDLINE file:
          for table in citations abstracts authors chemicals databases \
          descriptors identifiers keywords publication_types qualifiers sections; 
            do psql medline -c "COPY $table FROM '`pwd`/${table}.tab';";
          done
        
        Alternatively - simpler but slower - you can just ``update`` from the XML
        directly::
        
          medic update medline14n1234.xml.gz
        
        Version IDs
        ===========
        
        MEDLINE has began to use versions to allow publishers to add multiple citations
        for the same PMID. This only occurs with 71 articles from one journal,
        "PLOS Curr", in the 2013 baseline, creating a total of 149 non-unique records.
        
        As this is the only journal and as there may only be one record per PMID in the
        database, alternative versions are currently being ignored. In other words, if
        a MedlineCitation has a VersionID value other than "1", those records can be
        skipped to avoid DB errors from non-unique records.
        
        For example, in the 2013 baseline, PMID 20029614 is present ten times in the
        baseline, each version at a different stage of revision. Because it is the
        first entry (in the order they appear in the baseline files) without a
        ``VersionID`` or a version of "1" that is the relevant record, ``medic`` by
        default filters citations with other versions than "1". If you do want to
        process other versions of a citation, use the option ``--all``.
        
        To summarize, *medic* by default **removes** alternate citations.
        
        Database Tables
        ===============
        
        Citation (citations)
          **pmid**:BIGINT, *status*:ENUM(state), *title*:TEXT, *journal*:VARCHAR(256),
          *pub_date*:VARCHAR(256), issue:VARCHAR(256), pagination:VARCHAR(256),
          *created*:DATE, completed:DATE, revised:DATE, modified:DATE
        
        Abstract (abstracts)
          **pmid**:FK(Citation), **source**:ENUM(type), copyright:TEXT
        
        Section (sections)
          **pmid**:FK(Citation), **source**:ENUM(type), **seq**:SMALLINT,
          *name*:ENUM(section), label:VARCHAR(256), *content*:TEXT, *truncated*:BOOLEAN
        
        Author (authors)
          **pmid**:FK(Citation), **pos**:SMALLINT, *name*:TEXT,
          initials:VARCHAR(128), forename:VARCHAR(128), suffix:VARCHAR(128),
        
        PublicationType (publication_types)
          **pmid**:FK(Citation), **value**:VARCHAR(256)
        
        Descriptor (descriptors)
          **pmid**:FK(Citation), **num**:SMALLINT, major:BOOL, *name*:TEXT
        
        Qualifier (qualifiers)
          **pmid**:FK(Descriptor), **num**:FK(Descriptor), **sub**:SMALLINT, major:BOOL, *name*:TEXT
        
        Identifier (identifiers)
          **pmid**:FK(Citation), **namespace**:VARCHAR(32), *value*:VARCHAR(256)
        
        Database (databases)
          **pmid**:FK(Citation), **name**:VARCHAR(32), **accession**:VARCHAR(256)
        
        Chemical (chemicals)
          **pmid**:FK(Citation), **idx**:VARCHAR(32), uid:VARCHAR(256), *name*:VARCHAR(256)
        
        Keyword (keywords)
          **pmid**:FK(Citation), **owner**:ENUM(owner), **cnt**:SMALLINT, major:BOOL, *value*:TEXT
        
        - **bold** (Composite) Primary Key
        - *italic* NOT NULL (Strings that may not be NULL are also never empty.)
        
        Supported XML Elements
        ======================
        
        Entities
        --------
        
        - MedlineCitation and ArticleTitle (``Citation`` and ``Identifier``)
        - Abstract and OtherAbstract (``Abstract`` and ``Section``)
        - Author (``Author``)
        - Chemical (``Chemical``)
        - DataBank (``Database``)
        - Keyword (``Keyword``)
        - MeshHeading (``Descriptor`` and ``Qualifier``)
        - PublicationType (``PublicationType``)
        - DeleteCitation (for deleting records when parsing updates)
        
        Fields/Values
        -------------
        
        - Abstract (with "NLM" as ``Abstract.source``)
        - AbstractText (``Section.name`` "Abstract" or the *NlmCategory*, ``Section.content`` with *Label* as ``Section.label``)
        - AccessionNumber (``Database.accession``)
        - ArticleId (``Identifier.value`` with *IdType* as ``Identifier.namesapce``; only available in online PubMed XML)
        - ArticleTitle (``Citation.title``; if empty, use the VernacularTitle or set to "UNKNOWN")
        - CollectiveName (``Author.name``)
        - CopyrightInformation (``Abstract.copyright``)
        - DataBankName (``Database.name``)
        - DateCompleted (``Citation.completed``)
        - DateCreated (``Citation.created``)
        - DateRevised (``Citation.revised``)
        - DescriptorName (``Descriptor.name`` with *MajorTopicYN* as ``Descriptor.major``)
        - ELocationID (``Identifier.value`` with *EIdType* as ``Identifier.namespace``)
        - ForeName (``Author.forename``)
        - Initials (``Author.initials``)
        - Issue (``Citation.issue``)
        - Keyword (``Keyword.value`` with *Owner* as ``Keyword.owner`` and *MajorTopicYN* as ``Keyword.major``)
        - LastName (``Author.name``)
        - MedlineCitation (with *Status* as ``Citation.status``)
        - MedlineTA (``Citation.journal``)
        - NameOfSubstance (``Chemical.name``)
        - MedlinePgn (``Citation.pagination``)
        - OtherAbstract (with *Type* as ``Abstract.source``)
        - OtherID (``Identifier.value`` iff *Source* is "PMC" with ``Identifier.namespace`` as "pmc")
        - PMID (``Citation.pmid``)
        - PubDate (``Citation.pub_date``)
        - PublicationType (``PublicationType.value``)
        - QualifierName (``Qualifier.name`` with *MajorTopicYN* as ``Qualifier.major``)
        - RegistryNumber (``Chemical.uid``)
        - Suffix (``Author.suffix``)
        - VernacularTitle (``Citation.title`` if AbstractTitle is empty)
        - Volume (``Citation.issue``)
        
        Version History
        ===============
        
        2.2.0
          - Ensured compatibility with the MEDLINE DTD updates for 2015 and cleaned some code pieces.
            Includes a fix for the bad (long) keyword in PMID 25114415 (with a carriage return).
          - A column was added to the ORM, resulting in backwards incompatible change: From this version
            on, the trailing string "``(ABSTRACT TRUNCATED AT xxx WORDS)``" is stripped from AbstractText
            and instead the flag ``truncated`` has be added to table ``sections`` and is set if the string
            was present (but has been removed); To migrate your Postgres database, please run::
        
                ALTER TABLE sections ADD "truncated" boolean NOT NULL DEFAULT 'false';
        
            Note that for one case this produces a Section with just one whitespace character, because
            the original content was only the "ABSTRACT TRUNCATED..." message.
          - MEDLINE formatted output is now written to STDOUT or a single file, because it makes selecting
            specific fields with grep very easy. Records are separated with an empty line.
        2.1.7
          - Work-around for the limit of SQLite that only lets you use 999 variables per query.
          - Corrected the outdated VernacularTitle documentation in this document.
        2.1.6
          - Work-around for parsing citations that have an empty ArticleTitle element (which they
            shouldn't, according to the DTD): Either use the VernacularTitle (e.g., PMID 22536004), or
            otherwise set the title to "UNKNOWN" (the empty string is not a valid title) and log a
            warning.
          - Work-around for non-unique PublicationType entries (e.g., PMID 10500000): drop non-unique
            PublicationTypes (with the same PMID and value).
          - Corrected left-over "Medline" entity names in this document to "Citation".
        2.1.5
          - Added page_size=MAX and synchronous=OFF pragmas for SQLite DBs (hat-tip to Jason)
        2.1.4
          - A MEDLINE issue found by Jason: PMID 24073073 has an empty keyword and keyword
            list that should not be there; Medic prevents adding improper data to the DB
            by raising an AssertionError.
            To deal with such cases, medic now ensures each keyword is non-empty before
            attempting to generate a database entry and drops empty (i.e., whitespace-only)
            keyword data.
        2.1.3
          - Jason Hennessey changed the (absolute) path of medic's man-page, set to
            ``/usr/local/share/man`` in the setup script, to a relative location
            (``share/man``) to avoid issues when installing medic in a virtualenv
        2.1.2
          - fixed a bug where SQLite did not find the implicit FK->PK reference
            (thanks to Jason Hennessey for reporting the issue)
        2.1.1
          - added SQLite temporary DB example URL to help output
          - refactored HTML output code
        2.1.0
          - DB schema change from: ``records() -> sections(content)``
            to: ``citations(title) -> abstracts(copyright) -> sections(content)``
          - name change: the entity/table Medline/records is now called Citation/citations
          - title and copyright text is no longer stored in Section/sections
          - added a new Abstract/abstracts entity/table with a ``copyright`` attribute
            (formerly stored in ``sections.content`` with ``name`` = 'Copyright') 
          - added a new ``citations.title`` attribute
            (formerly stored in ``sections.content`` with ``name`` = 'Title') 
          - added a new ``source`` primary-key attribute to Section and Abstract
            (set to either 'NLM' for regular Abstract elements or to
            the value of the OtherAbstract Type attribute for other abstracts)
          - skipping "Abstract available from the publisher."-only abstracts
        2.0.2
          - made the use of ``--pmid-lists`` for ``delete`` and ``write`` implicit
          - added instructions to bootstrap the tables in a PostgreSQL DB
          - minor improvements to this manual
          - fixed a bug when inserting/updating from MEDLINE XML files
        2.0.1
          - fixed a bug that lead to skipping of abstracts
            (thanks to Chris Roeder for detecting the issue)
        2.0.0
          - added Keywords and PublicationTypes
          - added MEDLINE publication date, volume, issue, and pagination support
          - added MEDLINE output format and made it the default
          - DB structure change: descriptors.major and qualifiers.major columns swapped
          - DB structure change: section.name is now an untyped varchar (OtherAbstract separation)
          - cleaned up the ORM test cases
        1.1.1
          - code cleanup (PEP8, PyFlake)
          - fixed an issue where the parser would not leave the skipping state
        1.1.0
          - ``--update parse`` now writes a file to use with ``--pmid-lists delete``
          - fixed a bug with CRUD manager
          - added a man page
        1.0.2
          - fixes to make the PyPi version and ``pip install medic`` work
        1.0.1
          - updates to the setup.py and README.rst files
        1.0.0
          - initial release
        
        Copyright and License
        =====================
        
        License: `GNU GPL v3`_\ .
        Copyright 2012-2014 Florian Leitner. All rights reserved.
        
        .. _GNU GPL v3: http://www.gnu.org/licenses/gpl-3.0.html
        .. _MEDLINE: http://www.nlm.nih.gov/bsd/mms/medlineelements.html
        .. _PubMed: http://www.ncbi.nlm.nih.gov/pubmed
        .. _blog: http://fnl.es/medline-kung-fu.html
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: GNU Affero General Public License v3
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Text Processing
Classifier: Topic :: Text Processing :: Linguistic
