working on docs

docs/api.md

@@ -0,0 +1,269 @@
+# API Methods and Commands
+
+# Commands 
+
+Pull API:
+
+    $ python manage.py api pull --help
+
+    optional arguments:
+      -h, --help     show this help message and exit
+      -r, --recipes  Pull recipes of --pid
+      --url URL      Site url.
+      --key KEY      API key. Required to access private projects.
+      --rid RID      Recipe uid to dump.
+      --pid PID      Project uid to dump.
+      --dir DIR      Directory to store in.
+
+    # Dump project from remote url (--url).
+    $ python manage.py api pull --pid tutorial --dir tmp/remote/projects/ --url URL
+
+    # Dump recipes from remote url ( --url) 
+    $ python manage.py api pull --pid tutorial --dir tmp/remote/recipes/ --url URL --recipes
+
+
+Push API:
+
+    $ python manage.py api push --help
+    optional arguments:
+      -h, --help           show this help message and exit
+      -u, --url_from_json  Extract url from conf file instead of --url.
+      --url URL            Site url.
+      --key KEY            API key. Required to access private projects.
+      --rid RID            Recipe uid to load.
+      --pid PID            Project uid to load.
+      --dir DIR            Directory with json files to load in bulk.
+      --json JSON          Project or recipe JSON file to load.
+
+
+     # Load project tutorial from json file. 
+     $ python manage.py api push --json ../biostar-recipes/projects/tutorial.hjson 
+
+     # Load recipe jsons in --dir to project --pid. Upload to remote host with -u flag.
+     $ python manage.py api push --pid tutorial --dir ../biostar-recipes/recipes/ -u --key API_KEY
+
+
+# Methods
+
+## Listing 
+    GET /api/list/
+
+List projects and recipes in a tab delimited fashion with columns: **Project ID** , **Project Name**, **Recipe ID**, **Recipe Name**, **Privacy**
+
+#### Example
+[/api/list/](https://www.bioinformatics.recipes/api/list/)
+
+    tutorial	Recipe Tutorials	environment	Environment Check	Public
+    tutorial	Recipe Tutorials	interface	Interface Elements	Public
+    tutorial	Recipe Tutorials	makefile	Makefile Example	Public
+    tutorial	Recipe Tutorials	rscript	R Script	Public
+    cookbook	Bioinformatics Cookbook	quality-check	Improve the quality of sequencing reads	Public
+    cookbook	Bioinformatics Cookbook	fastqc	Visualize FASTQ data quality	Public
+    cookbook	Bioinformatics Cookbook	pseudo-alignment	RNA-Seq Transcript Abundance Estimation	Public
+    cookbook	Bioinformatics Cookbook	augustus	Gene Prediction	Public
+
+
+## Project Information
+
+    GET /api/project/{id}/
+    PUT /api/project/{id}/
+
+#### Parameters
+* _id_: unique project ID
+
+#### Example
+[/api/project/tutorials/](https://www.bioinformatics.recipes/api/project/tutorials/)
+
+    {
+        settings:
+        {
+            uid: tutorial
+            name: Recipe Tutorials
+            image: tutorial.png
+            privacy: Public
+            help:
+                '''
+                This project contains simple analyses that demonstrate the process
+                of creating a **recipe**.
+
+                Follow the **instructions,** investigate the **data** and **recipe code**
+                to gain a deeper understanding of how recipes work.
+
+                Read the step by step instructions in the [How to write recipes](https://github.com/biostars/biostar-recipes/blob/master/docs/how-to-write-recipes.md).
+                '''
+            id: 2
+            project_uid: tutorial
+            url: http://localhost:8000
+        }
+        recipes:
+        [
+            empty
+            makefile
+            starter
+            interface
+            hello-world
+            environment
+            rscript
+        ]
+    }
+
+## Project Image
+
+    GET /api/project/image/{id}/
+    PUT /api/project/image/{id}/
+
+
+#### Parameters
+* _id_: unique project ID
+
+#### Example
+
+[/api/project/image/tutorials/](https://www.bioinformatics.recipes/api/project/image/tutorials/)
+
+Image in response:
+
+![20% center](tutorial.png)
+
+
+## Recipe Json
+
+    GET /api/recipe/json/{id}/
+    PUT /api/recipe/json/{id}/
+
+Recipe JSON used to generate interface
+
+#### Parameters
+* _id_: Unique recipe ID
+
+#### Fields in response 
+Fields associated with the recipe JSON
+
+#### Example
+[/api/recipe/json/starter/](https://www.bioinformatics.recipes/api/recipe/json/starter/)
+
+    {
+      readlen:
+      {
+        label: Read Length
+        display: INTEGER
+        value: 250
+        range:
+        [
+          70
+          100000
+        ]
+      }
+      instrument:
+      {
+        label: Select Instrument
+        display: DROPDOWN
+        choices:
+        [
+          [
+            hiseq
+            Illumina Hiseq
+          ]
+          [
+            pacbio
+            Pacific BioSciences Sequel
+          ]
+          [
+            minion
+            Oxford Nanopor Minion
+          ]
+        ]
+        value: pacbio
+      }
+      reference:
+      {
+        label: Reference Genome
+        display: DROPDOWN
+        type: FASTA
+        source: PROJECT
+        value: Genome.fa
+      }
+      settings:
+      {
+        name: Starter Recipe
+        image: starter.png
+        help:
+          '''
+          This recipe can be a starting point for other recipes.
+          # Help
+
+          Use this recipe to create new recipes.
+          '''
+        id: 12
+        uid: starter
+        project_uid: tutorial
+        url: http://localhost:8000
+      }
+    }
+
+## Recipe Template
+
+    GET /api/recipe/template/{id}/
+    PUT /api/recipe/template/{id}/
+
+Recipe template executed during analysis.
+
+#### Parameters
+* _id_: Unique recipe ID
+
+#### Example
+[/api/recipe/template/starter/](https://www.bioinformatics.recipes/api/recipe/template/starter/)
+
+    #
+    # A starter recipe with examples.
+    #
+
+    #
+    # You can fill in shell variables
+    #
+    READLEN=250
+
+    echo "Read length: $READLEN"
+
+    #
+    # Substitute into content
+    #
+    echo "Referene genome: Genome.fa"
+
+    #
+    # But you may also use Django Template constructs.
+    #
+
+
+    echo "Yes, it is Pacific Biosciences!"
+
+    #
+    # Generate a table of content with all files in the job directory.
+    #
+    find . -name '*' > files.txt
+
+    #
+    # Print the contents to the screen
+    #
+    echo "****** File List: files.txt ****"
+    cat files.txt
+    # Make a nested directory
+    mkdir -p foo/bar
+    find . -name '*' > foo/bar/all.txt
+
+
+## Recipe Image
+
+    GET /api/recipe/image/{id}/
+    PUT /api/recipe/image/{id}/
+
+
+#### Parameters
+* _id_: Unique recipe ID
+
+#### Example
+
+[api/recipe/image/starter/](https://www.bioinformatics.recipes/api/recipe/template/starter/)
+
+Image in response:
+
+![20%](starter.jpeg)

docs/index.rst

@@ -65,6 +65,7 @@ For more information see the documentation below:
 
    install
    recipes
+   api
    deploy
    customize
    about

docs/install.md

@@ -113,9 +113,7 @@ By default both the admin login name and the default admin password are set to
 
     admin@localhost
 
-The Django admin can be found at:
-
-* http://127.0.0.1:8000/accounts/admin/
+The Django admin can be found at http://127.0.0.1:8000/accounts/admin/.
 
 ## Customize Settings
 

docs/recipes.md

@@ -255,8 +255,35 @@ But the interface is still empty as the site does not yet know how to render a g
     }
 
 
-## Where can I see more code examples for interface and scripts?
+## Resources
 
 Visit the recipes website and see the various example recipes:
 
 * https://www.bioinformatics.recipes/
+
+
+The Makefile included with the engine contains additional commands.
+
+Test the software:
+
+    make test
+
+Re-initialize the database:
+
+    make reset
+
+Serve the current site:
+
+    make serve
+
+Initialize the example recipes from the `biostar-recipe` repository.
+
+    make recipes
+
+Run all tests:
+
+    make test
+
+Back up the data
+
+    make backup