RST formatting fixes

intermine · Jul 31, 2019 · 54a08d1 · 54a08d1
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diff --git a/docs/data-model/model.rst b/docs/data-model/model.rst
@@ -100,17 +100,16 @@ One to one relationship
 
 One to many relationship
   a collection has a reverse-relationship that is a reference. In this case you should always fill in the reference and leave the collection empty (it will be ignored). 
-  ::
-   e.g. Gene has a collection Transcripts and Transcript references one Gene, fill in Transcript.gene only.
 
+  e.g. Gene has a collection Transcripts and Transcript references one Gene, fill in Transcript.gene only.
 
 Many to many relationship
   this is where a collection has a reverse-relationship that is a collection, or where a collection does not have a reverse-relationship. This type of collection can be altered from either side, and the changes will be observed in both sides.
 
   In practice if one side is very large and the other smaller it is faster to populate the smaller collection.
-  ::
-   e.g. Gene has a collection of Pathways and Pathway has a collection of Genes, fill in either Gene.pathways or Pathway.genes but not both.  
-   If Pathway.genes contains e.g. 20,000 items and Gene.pathways typically 100 items then it is faster to populate Gene.pathways.
+
+  e.g. Gene has a collection of Pathways and Pathway has a collection of Genes, fill in either Gene.pathways or Pathway.genes but not both.  
+  If Pathway.genes contains e.g. 20,000 items and Gene.pathways typically 100 items then it is faster to populate Gene.pathways.
 
 Ontologies
 -----------------------

diff --git a/docs/database/data-sources/library/index.rst b/docs/database/data-sources/library/index.rst
@@ -2,7 +2,7 @@ Data Source Library
 ================================
 
 
-This page lists the current sources available for use in InterMine. All the sources here are found as ready-to-use JARs in the central repository, `JCenter <https://jcenter.bintray.com/org/intermine/>`_. Look at `FlyMine <https://github.com/intermine/flymine/blob/master/project.xml>`_ for examples of how to use these sources.  
+This page lists the current sources available for use in InterMine. All the sources here are found as ready-to-use JARs in the central repository, `JCenter <https://jcenter.bintray.com/org/intermine/>`_. 
 
 You can also add your own sources to load custom file formats, see :doc:`/database/data-sources/custom/index` for more information.  In addition, the :doc:`/get-started/tutorial/index` contains detailed steps on creating sources for a variety of different data formats.
 
@@ -64,7 +64,7 @@ These are sources that load Drosophila specific data sets into FlyMine, we don't
 * redfly
 * rnai
 
-See `FlyMine <http://www.flymine.org>`_ for more information about these datasets. Look at `FlyMine <https://github.com/intermine/flymine/blob/master/project.xml>`_ for examples of how to use these sources.
+See `FlyMine <http://www.flymine.org>`_ for more information about these datasets. Look at FlyMine's `project.xml <https://github.com/intermine/flymine/blob/master/project.xml>`_ for examples of how to use these sources.
 
 HumanMine Specific sources
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -84,4 +84,4 @@ HumanMine Specific sources
 * orphanet
 * protein-atlas
 
-See `HumanMine <http://www.humanmine.org>`_ for more information about these datasets. Look at `HumanMine <https://github.com/intermine/humanmine/blob/master/project.xml>`_ for examples of how to use these sources.
+See `HumanMine <http://www.humanmine.org>`_ for more information about these datasets. Look at HumanMine's `project.xml <https://github.com/intermine/humanmine/blob/master/project.xml>`_ for examples of how to use these sources.
diff --git a/docs/database/database-building/build-script.rst b/docs/database/database-building/build-script.rst
@@ -1,7 +1,7 @@
 project_build script
 ========================
 
-To run a full build of InterMine, you must use the  `project_build` script.  This is a Perl program that reads a project.xml file and loads each source in turn.  This makes multiple calls to ant to avoid memory problems encountered when running many Java task sequentially from ant.  It also has the option of dumping the production database during the build and recovering from these dumps in case of problems.
+To run a full build of InterMine, you must use the  `project_build` script. This is a Perl program that reads a project.xml file and loads each source in turn. This makes multiple calls to Gradle to avoid memory problems encountered when running many Java task sequentially from Gradle. It also has the option of dumping the production database during the build and recovering from these dumps in case of problems.
 
 .. note::
 
@@ -52,7 +52,7 @@ The `project_build` script accepts the following flags:
   run build-db before starting build and drop any existing backup databases  (created when using the -t flag)
 
 -V
-  set the release number to pass to ant (as -Drelease=release_number) [1]_.
+  set the release number to pass to gradle (as -Prelease=release_number)
 
 Dump files take the name `dump_file_prefix`.final.  
 

diff --git a/docs/database/database-building/primary-keys.rst b/docs/database/database-building/primary-keys.rst
@@ -35,7 +35,7 @@ It is still possible to use a legacy method of configuring keys, where keys are
 
 
 Global primary key configuration file [DEPRECATED]
----------------------------------------------
+---------------------------------------------------------
 
 .. warning::
 

diff --git a/docs/database/performance/precomputing.rst b/docs/database/performance/precomputing.rst
@@ -146,6 +146,7 @@ The LOG records three queries:
 .. topic:: optimised sql
 
 	optimised sql: SELECT DISTINCT P98.a1_id AS a7_id, P98.a3_id AS a2_id, P96.id AS a3_id, a8_.id AS a8_id, a5_.id AS a5_id, a6_.id AS a6_id, P98.a1_symbol AS orderbyfield1, P98.a3_symbol AS orderbyfield2, P96.name AS orderbyfield3, P96.role1 AS orderbyfield4, P96.role2 AS orderbyfield5, P96.type AS orderbyfield6, a8_.name AS orderbyfield7, a5_.name AS orderbyfield8, a6_.pubMedId AS orderbyfield9 FROM precomp_45503 AS P98, InteractionDetail AS P96, InteractionExperiment AS P97, InteractionTerm AS a5_, Publication AS a6_, InteractionTerm AS a8_, InteractionDetectionMethodsInteractionExperiment AS indirect0 WHERE P98.a2_id = P96.interactionId AND P96.experimentId = P97.id AND P96.relationshipTypeId = a5_.id AND P97.publicationId = a6_.id AND P97.id = indirect0.InteractionExperiment AND indirect0.InteractionDetectionMethods = a8_.id AND P98.a1_id IN (1007850) AND P98.a3_id IN (2848406) ORDER BY P98.a1_symbol, P98.a3_symbol, P96.name, P96.role1, P96.role2, P96.type, a8_.name, a5_.name, a6_.pubMedId, P98.a1_id, P98.a3_id, P96.id, a8_.id, a5_.id, a6_.id LIMIT 5000
+
 bag tables: 0 ms, generate: 1 ms, optimise: 0 ms,  ms,  estimate: 14 ms, execute: 11 ms, convert results: 0 ms, extra queries: 27 ms, total: 53 ms, rows: 1
 
 Note the `FROM` clause now includes `precomp_45503`. You can query for this name in the database:

diff --git a/docs/embedding/list-widgets/enrichment-widgets.rst b/docs/embedding/list-widgets/enrichment-widgets.rst
@@ -23,7 +23,7 @@ k
 M
     the number of objects annotated with item in the reference population
 
-Apache library - `Hypergeometric Distribution <https://commons.apache.org/proper/commons-math/javadocs/api-2.2/org/apache/commons/math/distribution/HypergeometricDistributionImpl.html>`_
+`Apache library - Hypergeometric Distribution <https://commons.apache.org/proper/commons-math/javadocs/api-2.2/org/apache/commons/math/distribution/HypergeometricDistributionImpl.html>`_
 
 Multiple Test Correction
 ------------------------

diff --git a/docs/embedding/list-widgets/index.rst b/docs/embedding/list-widgets/index.rst
@@ -179,7 +179,7 @@ See other mines' config files for more examples, eg:
 * `HumanMine's webconfig-model.xml <https://github.com/intermine/humanmine/blob/master/webapp/src/main/webapp/WEB-INF/webconfig-model.xml>`_
 
 Background population
-~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~
 In the enrichement widgets, you can change the reference population.
 The reference population is specific for widget, list and user.
 If you are logged you can save your preference selecting the checkbox 'Save your preference'.

diff --git a/docs/get-started/amazon.rst b/docs/get-started/amazon.rst
@@ -1,11 +1,7 @@
 How to set up your InterMine environment on the Amazon Cloud
 ================================================================
 
-Where you should learn how to start your own MalariaMine web application
-on the Amazon Cloud.
-You could also use your InterMine Amazon instance to try building MalariaMine yourself (see http://intermine.readthedocs.org/en/latest/get-started/tutorial.html)
-or to build your own mine there.
-
+Where you should learn how to start your own MalariaMine web application on the Amazon Cloud. You could also use your InterMine Amazon instance to try building MalariaMine yourself or to build your own mine there.
 
 Pre-requisites
 ----------------------
@@ -15,10 +11,7 @@ You need an Amazon account: if you don't have one
 * click on ``Sign Up``
 * follow the instructions
 
-.. note::
- You will need to set up your key pair security mechanism (see for example step 7 below).
- Alternatively you will need your aws-access-key and your aws-secret-key
- to start your instance (not shown here).
+You will need to set up your key pair security mechanism (see for example step 7 below).  Alternatively you will need your aws-access-key and your aws-secret-key to start your instance (not shown here).
 
 
 Starting a new Instance
@@ -37,10 +30,8 @@ The image contains a ready deployed MalariaMine.
   you could set up also a few spare ones (20, 21, 8009).
 
   .. note::
-   You can do this also during step 7, but
-   **you cannot change the security group of an instance after starting it for the first time**
-   (unless you use a VPC instance, see http://docs.aws.amazon.com/AmazonVPC/latest/UserGuide/VPC_Introduction.html).
-  ..
+   You can do this also during step 7, but **you cannot change the security group of an instance after starting it for the first time**
+   (unless you use a VPC instance, see `User Guide <http://docs.aws.amazon.com/AmazonVPC/latest/UserGuide/VPC_Introduction.html>`_).
 
 4. go to the IMAGES/AMI console
 5. set the location on the top header (beside your username) to *US East (N. Virginia)*

diff --git a/docs/get-started/scheme.rst → docs/intermine/https.rst b/docs/get-started/scheme.rst → docs/intermine/https.rst
diff --git a/docs/intermine/index.rst b/docs/intermine/index.rst
@@ -9,4 +9,5 @@ InterMine
    roadmap
    intermine-versions
    get-involved
+   https
 
diff --git a/docs/support/index.rst b/docs/support/index.rst
@@ -7,6 +7,4 @@ Support
    mailing-list
    troubleshooting-tips
    /about/contact-us
-   upgrade
-   intermine-versions
 
diff --git a/docs/system-requirements/hardware/index.rst b/docs/system-requirements/hardware/index.rst
@@ -22,9 +22,11 @@ Suggestion for a large InterMine instance
 * 8 cores
 * 32 GB RAM
 * ~2TB usable storage (SAS disks are faster than SATA)
- * RAID 10 (4TB raw in RAID 10)
- * hardware RAID controller with a battery backed cache (gives faster write speeds)
- * it doesn't matter whether storage is in the same box or a separate disk array, if separate needs a Fibre Channel connection 
+
+    * RAID 10 (4TB raw in RAID 10)
+    * hardware RAID controller with a battery backed cache (gives faster write speeds)
+    * it doesn't matter whether storage is in the same box or a separate disk array, if separate needs a Fibre Channel connection 
+
 * Linux/Unix capable of running Java and PostgreSQL 
 
 .. note::

diff --git a/docs/system-requirements/software/gradle/FAQs.rst b/docs/system-requirements/software/gradle/FAQs.rst
@@ -27,7 +27,7 @@ I set `GRADLE_OPTS` properly and I still am getting an "out of memory" error mes
 Append `-Dorg.gradle.daemon=false` to prevent the use of Gradle daemons.
 
 I got ANOTHER error: "java.lang.ClassCastException: org.apache.xerces.parsers.XIncludeAwareParserConfiguration cannot be cast to org.apache.xerces.xni.parser.XMLParserConfiguration "
---------------------------------------------------------------------------------------------------------------------
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 
 Update your `GRADLE_OPTS` to disable deamons. 
 

diff --git a/docs/system-requirements/software/gradle/index.rst b/docs/system-requirements/software/gradle/index.rst
@@ -3,7 +3,7 @@ Gradle - Quick Start
 
 `Gradle <https://gradle.org>`_ is InterMine's build tool. In InterMine 2.0 Gradle replaced ant.
 
-Please see :doc:`Upgrade instructions </support/upgrade>` for details on how to migrate your system to use Gradle and :doc:`Gradle FAQs </system-requirements/software/gradle/FAQs>` for commonly asked questions about Gradle.
+Please see :doc:`Upgrade instructions </intermine/upgrade>` for details on how to migrate your system to use Gradle and :doc:`Gradle FAQs </system-requirements/software/gradle/FAQs>` for commonly asked questions about Gradle.
 
 Below are common commands you will use when building InterMine database and deploying webapps. See `docs.gradle.org <https://docs.gradle.org/current/userguide/command_line_interface.html>`_ for the full list.
 

diff --git a/docs/system-requirements/software/perl.rst b/docs/system-requirements/software/perl.rst
@@ -173,7 +173,7 @@ List of Perl Modules to Install
 .. index:: Perl installation
 
 How to install all the Perl Modules to Run the Data Downloader Script
----------------------------------------------
+----------------------------------------------------------------------
 
 In order to download all the Perl scripts required by the Data Downloader script, use the following cpan installation command:
 

diff --git a/docs/system-requirements/software/postgres/postgres.rst b/docs/system-requirements/software/postgres/postgres.rst
@@ -23,7 +23,7 @@ Mac
 Some of the recommended setting below may not apply to older versions of PostgreSQL.
 
 Configuration file
-------------------
+-------------------
 Most of the configurations below are made updating the file `postgresql.conf`, usually located in `/etc/postgres/version-nr/main`.
 
 Required Configurations
@@ -71,10 +71,9 @@ you can check the expected screenshot here [#screenshot]_ .
 Database Server Configuration
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-
-
 Kernel Memory setting
->>>>>>>>>>>>>>>>>>>>>
+""""""""""""""""""""""""""""
+
 Please check your server kernel setting
 
 .. code-block:: bash
@@ -104,7 +103,7 @@ and sourcing it
 
 
 PostgreSQL parameters
->>>>>>>>>>>>>>>>>>>
+""""""""""""""""""""""""""""
 
 
 For better performance. Read http://wiki.postgresql.org/wiki/Tuning_Your_PostgreSQL_Server for more information.
@@ -142,7 +141,7 @@ Note that most of the changes above require starting postgres.
 
 
 Client Authentication
->>>>>>>>>>>>>>>>>>>>>
+""""""""""""""""""""""""""""
 
 You should also add a line to the pg_hba.conf file to allow logging in via password:
 

diff --git a/docs/web-services/index.rst b/docs/web-services/index.rst
@@ -28,7 +28,7 @@ Look at some example code
     button). The generated code is meant to help get you started with the use of the
     client libraries.
 
-    There is also a :doc:`tutorial` for the Python API.
+    There is also a :doc:`/web-services/tutorial` for the Python API.
 
 Modify the code so it does what you want
     Working from the generated stub, you can edit the code to perform your intended task. You

diff --git a/docs/webapp/lists/list-upgrade.rst b/docs/webapp/lists/list-upgrade.rst
@@ -118,13 +118,20 @@ The list upgrade functionality uses a serialNumber that identifies the productio
 There are four cases:
 
 1. production serialNumber and userprofile serialNumber are both null ==> we don't need upgrade the list.
- * Scenario: I have released the webapp but I haven't re-build the production db.
+
+ Scenario: I have released the webapp but I haven't re-build the production db.
+
 2. production serialNumber is not null but userprofile serialNumber is null ==> we need upgrade the lists.
- * Scenario: I have run `build-db` in the production db and it's the first time that I release the webapp. On startup, the webapp sets `intermine_current` to false and the userprofile serialNumber value with the production serialNumber value.
+
+ Scenario: I have run `build-db` in the production db and it's the first time that I release the webapp. On startup, the webapp sets `intermine_current` to false and the userprofile serialNumber value with the production serialNumber value.
+
 3. production serialNumber = userprofile serialNumber ==> we don't need upgrade the lists.
- * Scenario: we have released the webapp but we haven't changed the production db.
+
+Scenario: we have released the webapp but we haven't changed the production db.
+
 4. production serialNumber != userprofile serialNumber ==> we need upgrade the lists.
- * Scenario: we have run `build-db` in the production and a new serialNumber has been generated.
+
+Scenario: we have run `build-db` in the production and a new serialNumber has been generated.
 
 The following diagram shows the possible states. With the green, we identify the states that don't need a list upgrade, with the red those need a list upgrade.
 

diff --git a/docs/webapp/region-search/index.rst b/docs/webapp/region-search/index.rst
@@ -130,30 +130,41 @@ Search page
 
 GenomicRegionSearchService
   This class has the methods to:
+
     * generate data (JSON) for search page
     * parse search form and valid input
     * generate search queries (one region with one query)
     * generate results table and download/galaxy links
+
 This class can be basically replaced by webservices + html
 
 Update IQL query to pathquery
+
   Currently, region query is constructed by lQL (Intermine Query Language) due to lack of implementation on range constraint in pathquery at the time we developed it. Update IQL to pathqueries and send by webserive, the output will be a list of results tables or a single results table grouped by region.
-Ref https://github.com/intermine/intermine/blob/dev/bio/webapp/src/org/intermine/bio/web/logic/GenomicRegionSearchUtil.java#L270-497
+
+See `GenomicRegionSearchUtil.java#L270-497`
 
 Query fields:
+
   In the IQL
-      Ref https://github.com/intermine/intermine/blob/dev/bio/webapp/src/org/intermine/bio/web/logic/GenomicRegionSearchUtil.java#L318-323
+
+      See `GenomicRegionSearchUtil.java#L318-323`
+
   In ResultRow
-      Ref https://github.com/intermine/intermine/blob/dev/bio/webapp/src/org/intermine/bio/web/logic/GenomicRegionSearchQueryRunner.java#L186-212
+
+      See `GenomicRegionSearchQueryRunner.java#L186-212`
+
   In Results table
-      Ref https://github.com/intermine/intermine/blob/dev/bio/webapp/src/org/intermine/bio/web/logic/GenomicRegionSearchService.java#L1106-1112
+
+      See `GenomicRegionSearchService.java#L1106-1112`
 
 Polling
+
 	We create a synchronizedMap to hold all the query results and put it in an http request. On the results page, there is a checker (javascript) checking the size of the map, so a progress bar will be updating. The results table will be generated once 10 results return, the pager will be updated dynamically. he whole part will be replaced by InterMine results table.
-Ref https://github.com/intermine/intermine/blob/dev/bio/webapp/src/org/intermine/bio/web/logic/GenomicRegionSearchQueryRunner.java#L129-223
 
-Results table and download links
-	Replaced by InterMine results table. 
+See GenomicRegionSearchQueryRunner.java#L129-223
+
+Results table and download links. Replaced by InterMine results table. 
 
 .. index:: region search, genomic region search
 

diff --git a/docs/webapp/third-party-tools/galaxy.rst b/docs/webapp/third-party-tools/galaxy.rst
@@ -56,14 +56,6 @@ url.value        tool runner url                                   yes[3]_.
 welcomeMessage   displays on the homepage when coming from Galaxy  yes  
 ===============  ================================================  =========
 
-.. [1] when display is false  
-
-.. [2] default url is the main Galaxy server, but it can be replaced by any public/private server  
-
-.. [3] e.g. on main Galaxy server, the tool for flymine is `/tool_runner?tool_id=flymine`.  Customize this url to specific mines, learn how to create a tool from `Galaxy wiki <http://wiki.g2.bx.psu.edu/Admin/Tools/External%20Display%20Applications%20Tutorial?highlight=%28tool%29|%28runner%29>`_  
-
-
-
 .. code-block:: properties
 
 	# galaxy

diff --git a/docs/webapp/third-party-tools/heatmap.rst b/docs/webapp/third-party-tools/heatmap.rst
@@ -71,4 +71,4 @@ Further development
 
 A modern way of creating widget like heatmap would be using InterMine webservices framework to query and generate JSON strings and embed heatmap on any web page. To `learn more... <http://github.com/intermine/intermine-embedding-examples>`_
 
-An alternative library would be `D3.js <http://d3js.org/>`_, an example of heatmap can be found `here <http://www.larsko.org/v/mpte/>`_. In `ThaleMine <https://apps.araport.org/thalemine/begin.do>`_ there is a D3 implementation (see any gene list report page, for example `here <https://apps.araport.org/thalemine/bagDetails.do?scope=all&bagName=Demo+1+-+Sucrose+Transporters+List>`_, `code <https://github.com/intermine/CDN/blob/master/js/intermine/expression/1.0.3/expression.js>`_. However canvasXpress is particular designed to display genomics data, D3 is for a broader use. 
+An alternative library would be `D3.js <http://d3js.org/>`_, an example of heatmap can be found `here <http://www.larsko.org/v/mpte/>`_. In `ThaleMine <https://apps.araport.org/thalemine/begin.do>`_ there is a D3 implementation (see any gene list report page, `for example <https://apps.araport.org/thalemine/bagDetails.do?scope=all&bagName=Demo+1+-+Sucrose+Transporters+List>`_, `code <https://github.com/intermine/CDN/blob/master/js/intermine/expression/1.0.3/expression.js>`_. However canvasXpress is particular designed to display genomics data, D3 is for a broader use.