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specify_cli 0.0.5

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checksums.yaml +7 -0
data/.gitignore +4 -0
data/.rspec +1 -0
data/Gemfile +17 -0
data/Gemfile.lock +117 -0
data/LICENSE.txt +21 -0
data/README.rdoc +43 -0
data/Rakefile +15 -0
data/bin/specify_cli +248 -0
data/lib/specify.rb +45 -0
data/lib/specify/branch_parser.rb +85 -0
data/lib/specify/cli.rb +11 -0
data/lib/specify/cli/database_setup.rb +46 -0
data/lib/specify/cli/stubs.rb +63 -0
data/lib/specify/cli/viewset.rb +21 -0
data/lib/specify/configuration.rb +12 -0
data/lib/specify/configuration/config.rb +120 -0
data/lib/specify/configuration/db_config.rb +162 -0
data/lib/specify/configuration/host_config.rb +37 -0
data/lib/specify/database.rb +140 -0
data/lib/specify/models.rb +43 -0
data/lib/specify/models/accession.rb +33 -0
data/lib/specify/models/agent.rb +138 -0
data/lib/specify/models/app_resource_data.rb +32 -0
data/lib/specify/models/app_resource_dir.rb +43 -0
data/lib/specify/models/auto_numbering_scheme.rb +94 -0
data/lib/specify/models/collecting_event.rb +38 -0
data/lib/specify/models/collection.rb +67 -0
data/lib/specify/models/collection_object.rb +127 -0
data/lib/specify/models/createable.rb +21 -0
data/lib/specify/models/determination.rb +63 -0
data/lib/specify/models/discipline.rb +61 -0
data/lib/specify/models/division.rb +26 -0
data/lib/specify/models/geography.rb +5 -0
data/lib/specify/models/geography/administrative_division.rb +32 -0
data/lib/specify/models/geography/geographic_name.rb +66 -0
data/lib/specify/models/geography/geography.rb +23 -0
data/lib/specify/models/institution.rb +13 -0
data/lib/specify/models/locality.rb +50 -0
data/lib/specify/models/preparation.rb +53 -0
data/lib/specify/models/preparation_type.rb +30 -0
data/lib/specify/models/record_set.rb +55 -0
data/lib/specify/models/record_set_item.rb +29 -0
data/lib/specify/models/taxonomy.rb +6 -0
data/lib/specify/models/taxonomy/common_name.rb +14 -0
data/lib/specify/models/taxonomy/rank.rb +31 -0
data/lib/specify/models/taxonomy/taxon.rb +54 -0
data/lib/specify/models/taxonomy/taxonomy.rb +21 -0
data/lib/specify/models/tree_queryable.rb +55 -0
data/lib/specify/models/updateable.rb +20 -0
data/lib/specify/models/user.rb +104 -0
data/lib/specify/models/view_set_object.rb +32 -0
data/lib/specify/number_format.rb +60 -0
data/lib/specify/services.rb +18 -0
data/lib/specify/services/service.rb +51 -0
data/lib/specify/services/stub_generator.rb +291 -0
data/lib/specify/services/view_loader.rb +177 -0
data/lib/specify/session.rb +77 -0
data/lib/specify/user_type.rb +61 -0
data/lib/specify/version.rb +19 -0
data/man/specify_cli-database.1 +60 -0
data/man/specify_cli-database.1.html +137 -0
data/man/specify_cli-database.1.ronn +53 -0
data/man/specify_cli-repository.1 +55 -0
data/man/specify_cli-repository.1.html +128 -0
data/man/specify_cli-repository.1.ronn +42 -0
data/man/specify_cli-stubs.1 +177 -0
data/man/specify_cli-stubs.1.html +239 -0
data/man/specify_cli-stubs.1.ronn +147 -0
data/man/specify_cli-viewset.1 +92 -0
data/man/specify_cli-viewset.1.html +154 -0
data/man/specify_cli-viewset.1.ronn +72 -0
data/man/specify_cli.1 +213 -0
data/man/specify_cli.1.html +252 -0
data/man/specify_cli.1.ronn +157 -0
data/spec/branch_parser_spec.rb +94 -0
data/spec/cli/stubs_spec.rb +44 -0
data/spec/configuration/config_spec.rb +269 -0
data/spec/configuration/db_config_spec.rb +299 -0
data/spec/configuration/host_config_spec.rb +64 -0
data/spec/database_spec.rb +83 -0
data/spec/examples.txt +217 -0
data/spec/helpers.rb +15 -0
data/spec/models/app_resource_data_spec.rb +38 -0
data/spec/models/app_resource_dir_spec.rb +8 -0
data/spec/models/auto_numbering_scheme_spec.rb +78 -0
data/spec/models/collection_object_spec.rb +92 -0
data/spec/models/collection_spec.rb +32 -0
data/spec/models/discipline_spec.rb +31 -0
data/spec/models/record_set_spec.rb +18 -0
data/spec/models/user_spec.rb +182 -0
data/spec/models/view_set_object_spec.rb +70 -0
data/spec/number_format_spec.rb +43 -0
data/spec/services/stub_generator_spec.rb +635 -0
data/spec/services/view_loader_spec.rb +436 -0
data/spec/session_spec.rb +105 -0
data/spec/spec_helper.rb +116 -0
data/spec/support/db.yml +12 -0
data/spec/support/stub.yaml +17 -0
data/spec/support/stub_locality.yaml +19 -0
data/spec/support/viewsets/paleo.views.xml +30 -0
data/spec/support/viewsets/paleo.xml +30 -0
data/spec/user_type_spec.rb +79 -0
data/specify_cli.gemspec +27 -0
data/specify_cli.rdoc +1 -0
metadata +246 -0

data/man/specify_cli-stubs.1.html ADDED Viewed

@@ -0,0 +1,239 @@
+<!DOCTYPE html>
+<html>
+<head>
+  <meta http-equiv='content-type' value='text/html;charset=utf8'>
+  <meta name='generator' value='Ronn/v0.7.3 (http://github.com/rtomayko/ronn/tree/0.7.3)'>
+  <title>specify_cli-stubsy(1) - A command line interface for Specify</title>
+  <style type='text/css' media='all'>
+  /* style: man */
+  body#manpage {margin:0}
+  .mp {max-width:100ex;padding:0 9ex 1ex 4ex}
+  .mp p,.mp pre,.mp ul,.mp ol,.mp dl {margin:0 0 20px 0}
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+  ol.man-decor li.tc {text-align:center;letter-spacing:4px}
+  ol.man-decor li.tr {text-align:right;float:right}
+  </style>
+</head>
+<!--
+  The following styles are deprecated and will be removed at some point:
+  div#man, div#man ol.man, div#man ol.head, div#man ol.man.
+  The .man-page, .man-decor, .man-head, .man-foot, .man-title, and
+  .man-navigation should be used instead.
+-->
+<body id='manpage'>
+  <div class='mp' id='man'>
+  <div class='man-navigation' style='display:none'>
+    <a href="#NAME">NAME</a>
+    <a href="#SYNOPSIS">SYNOPSIS</a>
+    <a href="#DESCRIPTION">DESCRIPTION</a>
+    <a href="#FILES">FILES</a>
+    <a href="#OPTIONS">OPTIONS</a>
+    <a href="#EXAMPLES">EXAMPLES</a>
+    <a href="#SPECIFY_CLI">SPECIFY_CLI</a>
+  </div>
+  <ol class='man-decor man-head man head'>
+    <li class='tl'>specify_cli-stubsy(1)</li>
+    <li class='tc'></li>
+    <li class='tr'>specify_cli-stubsy(1)</li>
+  </ol>
+  <h2 id="NAME">NAME</h2>
+<p class="man-name">
+  <code>specify_cli-stubsy</code> - <span class="man-whatis">A command line interface for Specify</span>
+</p>
+<h2 id="SYNOPSIS">SYNOPSIS</h2>
+<p><code>specify_cli</code> [<var>global options</var>] <code>stubs</code> [<var>options</var>] <var>collection</var> <var>count</var>
+<code>specify_cli</code> <code>stubs</code> <code>--file</code> <var>count</var></p>
+<h2 id="DESCRIPTION">DESCRIPTION</h2>
+<p>The stubs command creates stub records in a collection, so that catalog
+numbers can be printed to labels e.g. prior to mass digitizaton. The command
+currently only works for collection objects, and will currently only work for
+collections using the numeric catalog numbering scheme.</p>
+<p>Generated catalog numbers are printed to stdout.</p>
+<p>The number of stub records created is specified with the <em>count</em> argument.
+The target collection is provided as the <em>collection</em> argument. <em>Host</em> and
+<em>database</em> are provided using the global options <code>--host</code> and <code>--database</code>
+respectively.
+The command will generate a record set with all generated collection objects.
+The record set will be owned by either the <em>Specify user</em> (as provided via the
+global option <code>--specify_user</code> or in the database configuration file), or the
+<em>Specify user</em> provided with the <code>--cataloger</code> option. If no dataset name is
+provided using the <code>--dataset</code> option, the default name will be <code>stub record set
+&lt;TIMESTAMP></code>.</p>
+<p>Records can be created with the following basic information (provided using
+command options - see below): cataloger, accession, geography/locality, taxon,
+preparation.</p>
+<p>Only existing accessions and preparation types can be assigned at present.
+Unknown items will raise an error.</p>
+<p>If geographic information is provided, but no locality name, the
+default locality name will be <code>not cataloged, see label</code>. This can be changed
+using the <code>--locality</code> option. Geographic information should be passed in the
+format <code>Geographic Rank: Name; Geographic Subrank: Name; locality: name</code> where
+<em>locality</em> is optional (if not given, the default locality name will be used).
+Only geographic names/ranks and locality names that exist in the database will
+can be used (unknown item will raise an error).</p>
+<p>Taxon information is assigned as a determination. Only one determination can
+be given to a stub records using the command. Taxon information is provided
+in the format <code>Taxon Rank: Name; Taxon Subrank: Name</code>. Only taxonomic names that exist in the database will be accepted. Unknown items will raise an error.</p>
+<p>Alternatively to using the options, a YAML file with all required information
+can be passed with the <code>--file option</code>. In that case, the <em>database</em> and
+<em>collection</em> arguments can be ommitted.</p>
+<h2 id="FILES">FILES</h2>
+<p>YAML files with stub record information provided using the <code>--file</code> option
+should have the general structure:</p>
+<pre><code>---
+:stub_generator:
+  :host: &lt;hostname>
+  :database: &lt;database name>
+  :collection: &lt;collection name>
+  :config: &lt;database configuration file>
+dataset_name: &lt;record set name>
+accession: &lt;accession number>
+cataloger: &lt;specify user name>
+collecting_data:
+  &lt;1st rank>: &lt;name>
+  &lt;2nd rank>: &lt;name>
+  &lt;3rd rank>: &lt;name>
+  :locality: &lt;name>
+default_locality_name: &lt;name>
+determination:
+  &lt;rank>: &lt;name>
+preparation:
+  :type: &lt;preparation type>
+  :count: &lt;preparation count>
+</code></pre>
+<p>Items prefixed with <code>:</code> in the YAML will be deserialized as Ruby symbols and
+need to be prefixed with <code>:</code> in your file. Leave any unnecessary items out.
+The first section <code>:stub_generator</code> contains connection information. When
+<code>:config</code> is left out, <em>stubs</em> will use the config file provided with the global
+option <code>--db_config</code> or the default file <code>~/.specify_dbs.rc.yaml</code> if none
+provided. Likewise, <code>:host</code>, and <code>:database</code> can be provided using the global
+options <code>--host</code> and <code>--database</code> respectively.</p>
+<p>If you provide the <code>:locality</code> under <code>collecting data:</code>, this will have
+precedence over the <code>default_locality_name</code>, so the latter is redundant.</p>
+<h2 id="OPTIONS">OPTIONS</h2>
+<ul>
+<li><code>-f</code>, <code>--file</code> <var>file</var>:
+  Load stub record information from a YAML file.</li>
+<li><code>-c</code>, <code>--cataloger</code> <var>name</var>:
+  Specify user appearing as cataloger and owner of the record set.</li>
+<li><code>-d</code>, <code>--dataset</code> <var>name</var>:
+  Name of the datas set (record set) generated.</li>
+<li><code>-a</code>, <code>--accession</code> <var>accession_number</var>
+  Accession number for the accession to which the stub records belong.</li>
+<li><code>-g</code>, <code>--geography</code> <var>geography</var>
+  Geographic and locality information for the stub records. Format of
+  <var>geography</var>: <code>'Rank1: Name; Rank2: Name; locality: name'</code></li>
+<li><code>-l</code>, <code>--locality</code> <var>name</var>:
+  Default locality name if geographic information has no locality.</li>
+<li><code>-t</code>, <code>--taxon</code> <var>taxon</var>:
+  Taxon to which stub records are determined.  Format of <var>taxon</var>:
+  <code>'Rank1: Name; Rank2: Name; locality: name'</code></li>
+<li><code>-p</code>, <code>--preptype</code> <var>name</var>:
+  Preparation type for the stub records, if they have preparations.</li>
+<li><code>-n</code>, <code>--prepcount</code> <var>number</var>:
+  Number of preparation items (requires --preptype to be set).</li>
+</ul>
+<h2 id="EXAMPLES">EXAMPLES</h2>
+<p>Create 10 blank stub records in the collection <code>Triloites</code> in the database
+<code>Specify</code> on localhost:</p>
+<pre><code>$ specify_cli -D Specify stubs Trilobites 10
+</code></pre>
+<p>Create 10 stub records determined to <code>Asaphidae</code> in the collection <code>Triloites</code>
+in the database<code>Specify</code> on localhost:</p>
+<pre><code>$ specify_cli -D Specify stubs\n
+    --taxon='Class: Trilobita; Order: Asaphida; Family: Asaphidae'\n
+    Trilobites 10
+</code></pre>
+<p>Create 10 stub records for herbarium sheets in the collection <code>Orchids</code> in the
+database <code>Specify</code> on localhost, determined to taxon <code>Orchidaceae</code>:</p>
+<pre><code>$ specify_cli -D Specify stubs --taxon='Family: Orchidaceae'\n
+    --preptype=Sheet --perpcount=1 Orchids 10
+</code></pre>
+<p>Create 10 stub records for herbarium sheets in the collection <code>Orchids</code> in the
+database <code>Specify</code> on localhost, determined to taxon <code>Orchidaceae</code>, collected
+in <code>Downtown Lawrence</code>:</p>
+<pre><code>$ specify_cli -D Specify stubs --taxon='Family: Orchidaceae'\n
+    --geography='Country: United States, State: Kansas,\n
+    County: Douglas County; locality: Downtown Lawrence'
+    --preptype=Sheet --perpcount=1 Orchids 10
+</code></pre>
+<p>Create 10 stub records from a YAML file <code>stub_details.yaml</code>:</p>
+<pre><code>$ specify_cli stubs --file=stub_details.yaml 10
+</code></pre>
+<h2 id="SPECIFY_CLI">SPECIFY_CLI</h2>
+<p>Part of the <span class="man-ref">specify_cli<span class="s">(1)</span></span> suite</p>
+  <ol class='man-decor man-foot man foot'>
+    <li class='tl'></li>
+    <li class='tc'>August 2018</li>
+    <li class='tr'>specify_cli-stubsy(1)</li>
+  </ol>
+  </div>
+</body>
+</html>

data/man/specify_cli-stubs.1.ronn ADDED Viewed

@@ -0,0 +1,147 @@
+specify_cli-stubsy(1) -- A command line interface for Specify
+===============================================================================
+## SYNOPSIS
+`specify_cli` [<global options>] `stubs` [<options>] <collection> <count>
+`specify_cli` `stubs` `--file` <count>
+## DESCRIPTION
+The stubs command creates stub records in a collection, so that catalog
+numbers can be printed to labels e.g. prior to mass digitizaton. The command
+currently only works for collection objects, and will currently only work for
+collections using the numeric catalog numbering scheme.
+Generated catalog numbers are printed to stdout.
+The number of stub records created is specified with the *count* argument.
+The target collection is provided as the *collection* argument. *Host* and
+*database* are provided using the global options `--host` and `--database`
+respectively.
+The command will generate a record set with all generated collection objects.
+The record set will be owned by either the *Specify user* (as provided via the
+global option `--specify_user` or in the database configuration file), or the
+*Specify user* provided with the `--cataloger` option. If no dataset name is
+provided using the `--dataset` option, the default name will be `stub record set
+<TIMESTAMP>`.
+Records can be created with the following basic information (provided using
+command options - see below): cataloger, accession, geography/locality, taxon,
+preparation.
+Only existing accessions and preparation types can be assigned at present.
+Unknown items will raise an error.
+If geographic information is provided, but no locality name, the
+default locality name will be `not cataloged, see label`. This can be changed
+using the `--locality` option. Geographic information should be passed in the
+format `Geographic Rank: Name; Geographic Subrank: Name; locality: name` where
+*locality* is optional (if not given, the default locality name will be used).
+Only geographic names/ranks and locality names that exist in the database will
+can be used (unknown item will raise an error).
+Taxon information is assigned as a determination. Only one determination can
+be given to a stub records using the command. Taxon information is provided
+in the format `Taxon Rank: Name; Taxon Subrank: Name`. Only taxonomic names that exist in the database will be accepted. Unknown items will raise an error.
+Alternatively to using the options, a YAML file with all required information
+can be passed with the `--file option`. In that case, the *database* and
+*collection* arguments can be ommitted.
+## FILES
+YAML files with stub record information provided using the `--file` option
+should have the general structure:
+    ---
+    :stub_generator:
+      :host: <hostname>
+      :database: <database name>
+      :collection: <collection name>
+      :config: <database configuration file>
+    dataset_name: <record set name>
+    accession: <accession number>
+    cataloger: <specify user name>
+    collecting_data:
+      <1st rank>: <name>
+      <2nd rank>: <name>
+      <3rd rank>: <name>
+      :locality: <name>
+    default_locality_name: <name>
+    determination:
+      <rank>: <name>
+    preparation:
+      :type: <preparation type>
+      :count: <preparation count>
+Items prefixed with `:` in the YAML will be deserialized as Ruby symbols and
+need to be prefixed with `:` in your file. Leave any unnecessary items out.
+The first section `:stub_generator` contains connection information. When
+`:config` is left out, *stubs* will use the config file provided with the global
+option `--db_config` or the default file `~/.specify_dbs.rc.yaml` if none
+provided. Likewise, `:host`, and `:database` can be provided using the global
+options `--host` and `--database` respectively.
+If you provide the `:locality` under `collecting data:`, this will have
+precedence over the `default_locality_name`, so the latter is redundant.
+## OPTIONS
+* `-f`, `--file` <file>:
+    Load stub record information from a YAML file.
+* `-c`, `--cataloger` <name>:
+    Specify user appearing as cataloger and owner of the record set.
+* `-d`, `--dataset` <name>:
+    Name of the datas set (record set) generated.
+* `-a`, `--accession` <accession_number>
+    Accession number for the accession to which the stub records belong.
+* `-g`, `--geography` <geography>
+    Geographic and locality information for the stub records. Format of
+    <geography>: `'Rank1: Name; Rank2: Name; locality: name'`
+* `-l`, `--locality` <name>:
+    Default locality name if geographic information has no locality.
+* `-t`, `--taxon` <taxon>:
+    Taxon to which stub records are determined.  Format of <taxon>:
+    `'Rank1: Name; Rank2: Name; locality: name'`
+* `-p`, `--preptype` <name>:
+    Preparation type for the stub records, if they have preparations.
+* `-n`, `--prepcount` <number>:
+    Number of preparation items (requires --preptype to be set).
+## EXAMPLES
+Create 10 blank stub records in the collection `Triloites` in the database
+`Specify` on localhost:
+    $ specify_cli -D Specify stubs Trilobites 10
+Create 10 stub records determined to `Asaphidae` in the collection `Triloites`
+in the database`Specify` on localhost:
+    $ specify_cli -D Specify stubs\n
+        --taxon='Class: Trilobita; Order: Asaphida; Family: Asaphidae'\n
+        Trilobites 10
+Create 10 stub records for herbarium sheets in the collection `Orchids` in the
+database `Specify` on localhost, determined to taxon `Orchidaceae`:
+    $ specify_cli -D Specify stubs --taxon='Family: Orchidaceae'\n
+        --preptype=Sheet --perpcount=1 Orchids 10
+Create 10 stub records for herbarium sheets in the collection `Orchids` in the
+database `Specify` on localhost, determined to taxon `Orchidaceae`, collected
+in `Downtown Lawrence`:
+    $ specify_cli -D Specify stubs --taxon='Family: Orchidaceae'\n
+        --geography='Country: United States, State: Kansas,\n
+        County: Douglas County; locality: Downtown Lawrence'
+        --preptype=Sheet --perpcount=1 Orchids 10
+Create 10 stub records from a YAML file `stub_details.yaml`:
+    $ specify_cli stubs --file=stub_details.yaml 10
+## SPECIFY_CLI
+Part of the specify_cli(1) suite

data/man/specify_cli-viewset.1 ADDED Viewed

@@ -0,0 +1,92 @@
+.\" generated with Ronn/v0.7.3
+.\" http://github.com/rtomayko/ronn/tree/0.7.3
+.
+.TH "SPECIFY_CLI\-STUBSY" "1" "August 2018" "" ""
+.
+.SH "NAME"
+\fBspecify_cli\-stubsy\fR \- A command line interface for Specify
+.
+.SH "SYNOPSIS"
+\fBspecify_cli\fR [\fIglobal options\fR] \fBviewset\fR [\fIoptions\fR] \fIcollection\fR \fIfile\fR \fBspecify_cli\fR \fBviewset\fR \fB\-\-branch=\fR\fIname\fR \fIfile\fR \fBspecify_cli\fR \fBviewset\fR \fB\-b\fR \fIfile\fR
+.
+.SH "DESCRIPTION"
+The viewset command uploads a view definition file (\fI\.views\.xml\fR) to the database\. Viewsets can be uploaded to either of the following levels: \fIdiscipline\fR, \fIcollection\fR, \fIuser type\fR, or \fIuser\fR\.
+.
+.P
+Use the \fB`\-c\fR or \fB\-d\fR switches to upload to collection or discipline level respectively\.
+.
+.P
+To upload for a specific user type in a collection, use the \fB\-\-user_type\fR option and provide the user type name (\fImanager\fR, \fIfullaccess\fR, \fIlimitedaccess\fR, or \fIguest\fR)\.
+.
+.P
+To upload for a specific user level, use the \fB\-\-user\fR option and provide the Specify user name\.
+.
+.P
+The \fIcollection\fR argument is required unless the \fB\-b\fR or \fB\-B\fR options are used (the collection is needed to register a login session)\.
+.
+.P
+Provide information about the host, database, MySQL/MariaDB user and Specify user with the global options\.
+.
+.P
+The \fB\-\-branch\fR option allows to provide a Git branch name, from which all necessary information about the target (host, database, collection, level) can be parsed\. This requires that the directory containing the \fI\.views\.xml\fR file is mapped to a host, and that the branch name follows the naming convention \fBrepository_name/database_name/collection_name/level\fR\.
+.
+.P
+If your present working directory is mapped to a host and contains a Git repository and the current branch conforms to the naming convention, use the \fB\-b\fR switch to use the current branch instead of specifying the branch name with \fB\-\-branch\fR\.
+.
+.SH "FILES"
+The command requires a \fI\.views\.xml\fR as an argument\.
+.
+.SH "OPTIONS"
+.
+.TP
+\fB\-b\fR
+Use current branch to resolve target\.
+.
+.TP
+\fB\-B\fR, \fB\-\-branch\fR \fIname\fR
+Resolve target from branch name\.
+.
+.TP
+\fB\-c\fR
+Upload to collection level\.
+.
+.TP
+\fB\-d\fR
+Upload to discipline level\.
+.
+.TP
+\fB\-t\fR, \fB\-\-user_type\fR \fIname\fR
+Upload to specific user type [name] in the collection\.
+.
+.TP
+\fB\-u\fR, \fB\-\-user\fR \fIname\fR
+Upload to specify user \fIname\fR in the collection\.
+.
+.SH "EXAMPLES"
+Upload \fBinvertpaleo\.views\.xml\fR to discipline level for collection \fBTrilobites\fR in the database \fBSpecify\fR on localhost:
+.
+.IP "" 4
+.
+.nf
+$ specify_cli \-D Specify viewset \-d Trilobites invertpaleo\.views\.xml
+.
+.fi
+.
+.IP "" 0
+.
+.P
+Upload \fBinvertpaleo\.views\.xml\fR auto\-resolving target from current Git branch:
+.
+.IP "" 4
+.
+.nf
+$ specify_cli viewset \-b invertpaleo\.views\.xml
+.
+.fi
+.
+.IP "" 0
+.
+.SH "SPECIFY_CLI"
+Part of the specify_cli(1) suite