Merge pull request #1 from galaxy-genome-annotation/3.0

python-tripal 3.0

.command-engine.yml

@@ -4,11 +4,10 @@ module:
     base_module: tripal
     instance_cls: "<class 'tripal.TripalInstance'>"
     instance_func: TripalInstance
-    instance_args: []
-    instance_kwargs:
-        tripal_url: "http://localhost/tripal/"
-        username: "admin"
-        password: "changeme"
+    instance_args:
+        - "http://localhost:8500/tripal/"
+        - "admin"
+        - "changeme"
 
     ignore:
         top_attrs:
@@ -17,6 +16,7 @@ module:
             - 'password'
             - 'auth_login'
             - 'auth_password'
+            - 'version'
         funcs:
             - get
             - post

.travis.yml

@@ -1,18 +1,88 @@
+sudo: required
 language: python
+
+services:
+  - docker
+
 python:
-- '2.7'
-- '3.5'
-script:
-- pip install -U pip setuptools
-- pip install -U flake8
-- flake8 tripal --ignore=E501 --exclude=scripts/
-- python setup.py install
-deploy:
-  provider: pypi
-  user: abretaud
-  password:
-    secure: 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
-  on:
-    tags: true
-    distributions: sdist bdist_wheel
-    repo: galaxy-genome-annotation/python-tripal
+  - '2.7'
+
+jobs:
+  include:
+    - stage: lint
+      install:
+        - pip install -U flake8 flake8-import-order
+      script:
+        - flake8 tripal test --ignore=E501 --exclude=scripts/
+    - stage: test  # Python 2.7 + tripal 2
+      env: TRIPAL_VERSION=2
+      python: '2.7'
+      install:
+        - pip install -U pip setuptools nose chado
+        - python setup.py install
+        - export TRIPAILLE_GLOBAL_CONFIG_PATH=`pwd`/test-data/tripal_v$TRIPAL_VERSION/tripaille.yml
+        - export CHAKIN_GLOBAL_CONFIG_PATH=`pwd`/test-data/tripal_v$TRIPAL_VERSION/chakin.yml
+        - sudo service postgresql stop
+        - cd test-data/tripal_v$TRIPAL_VERSION/
+        - docker-compose up -d
+        - cd ../../
+        - sleep 300 # Wait for the containers to be ready
+      script:
+        - python setup.py nosetests --tests test.tripal_v$TRIPAL_VERSION
+    - stage: test  # Python 3.5 + tripal 2
+      env: TRIPAL_VERSION=2
+      python: '3.5'
+      install:
+        - pip install -U pip setuptools nose chado
+        - python setup.py install
+        - export TRIPAILLE_GLOBAL_CONFIG_PATH=`pwd`/test-data/tripal_v$TRIPAL_VERSION/tripaille.yml
+        - export CHAKIN_GLOBAL_CONFIG_PATH=`pwd`/test-data/tripal_v$TRIPAL_VERSION/chakin.yml
+        - sudo service postgresql stop
+        - cd test-data/tripal_v$TRIPAL_VERSION/
+        - docker-compose up -d
+        - cd ../../
+        - sleep 300 # Wait for the container to be ready
+      script:
+        - python setup.py nosetests --tests test.tripal_v$TRIPAL_VERSION
+    - stage: test  # Python 2.7 + tripal 3
+      env: TRIPAL_VERSION=3
+      python: '2.7'
+      install:
+        - pip install -U pip setuptools nose chado
+        - python setup.py install
+        - export TRIPAILLE_GLOBAL_CONFIG_PATH=`pwd`/test-data/tripal_v$TRIPAL_VERSION/tripaille.yml
+        - export CHAKIN_GLOBAL_CONFIG_PATH=`pwd`/test-data/tripal_v$TRIPAL_VERSION/chakin.yml
+        - sudo service postgresql stop
+        - cd test-data/tripal_v$TRIPAL_VERSION/
+        - docker-compose up -d
+        - cd ../../
+        - sleep 300 # Wait for the containers to be ready
+      script:
+        - python setup.py nosetests --tests test.tripal_v$TRIPAL_VERSION
+    - stage: test  # Python 3.5 + tripal 3
+      env: TRIPAL_VERSION=3
+      python: '3.5'
+      install:
+        - pip install -U pip setuptools nose chado
+        - python setup.py install
+        - export TRIPAILLE_GLOBAL_CONFIG_PATH=`pwd`/test-data/tripal_v$TRIPAL_VERSION/tripaille.yml
+        - export CHAKIN_GLOBAL_CONFIG_PATH=`pwd`/test-data/tripal_v$TRIPAL_VERSION/chakin.yml
+        - sudo service postgresql stop
+        - cd test-data/tripal_v$TRIPAL_VERSION/
+        - docker-compose up -d
+        - cd ../../
+        - sleep 300 # Wait for the container to be ready
+      script:
+        - python setup.py nosetests --tests test.tripal_v$TRIPAL_VERSION
+    - stage: deploy
+      install: skip
+      script: echo "Deploying to Pypi"
+      deploy:
+        provider: pypi
+        user: abretaud
+        password:
+          secure: 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
+        on:
+          tags: true
+          distributions: sdist bdist_wheel
+          repo: galaxy-genome-annotation/python-tripal

Makefile

@@ -1,3 +1,3 @@
 rebuild:
-	python scripts/autobuilder.py --galaxy
-	python scripts/commands_to_rst.py
+	python3 scripts/autobuilder.py --galaxy
+	python3 scripts/commands_to_rst.py

README.md

@@ -7,6 +7,18 @@ A Python library for interacting with [Tripal](http://tripal.info/)
 
 ## History
 
+ - 3.0
+    - Added some support for Tripal 3
+        - Add `job add_import_job` for generic Tripal 3 importer
+        - Add preliminary code for entity management (waiting for https://github.com/tripal/tripal/issues/202)
+        - sync and delete_orphans are not yet implemented (https://github.com/tripal/tripal/issues/337)
+    - GFF3: removed bugged 'refresh' and 'remove' loading mode (no more available in Tripal3)
+    - Renamed `organism get_organism_nodes` to `organism get_organisms_tripal`
+      and `analysis get_analysis_nodes` to `analysis get_analyses_tripal`.
+      Both now return Drupal Nodes for Tripal 2 or Entities for Tripal 3.
+    - Added `delete_orphans` methods for organisms and analyses
+    - Added tests
+
  - 2.0.4
     - Small bug fixes
 

docs/commands.rst

@@ -12,6 +12,8 @@ describes these commands.
 
    commands/analysis.rst
    commands/db.rst
+   commands/entity.rst
    commands/feature.rst
    commands/job.rst
-   commands/organism.rst
+   commands/organism.rst
+   commands/phylogeny.rst

docs/commands/analysis.rst

@@ -33,6 +33,31 @@ Create an analysis
       -h, --help            Show this message and exit.
     
 
+``delete_orphans`` command
+--------------------------
+
+**Usage**::
+
+    tripaille analysis delete_orphans [OPTIONS]
+
+**Help**
+
+Delete orphans Drupal analysis nodes
+
+
+**Output**
+
+
+    status
+
+**Options**::
+
+
+      --job_name TEXT  Name of the job
+      --no_wait        Return immediately without waiting for job completion
+      -h, --help       Show this message and exit.
+    
+
 ``get_analyses`` command
 ------------------------
 
@@ -65,28 +90,28 @@ Get analyses
       -h, --help             Show this message and exit.
     
 
-``get_analysis_nodes`` command
-------------------------------
+``get_analyses_tripal`` command
+-------------------------------
 
 **Usage**::
 
-    tripaille analysis get_analysis_nodes [OPTIONS]
+    tripaille analysis get_analyses_tripal [OPTIONS]
 
 **Help**
 
-Get analysis nodes
+Get analysis entities
 
 
 **Output**
 
 
-    Analysis node information
+    Analysis entity/node information
 
 **Options**::
 
 
-      --node INTEGER  filter on node id
-      -h, --help      Show this message and exit.
+      --analysis_id INTEGER  An analysis entity/node ID
+      -h, --help             Show this message and exit.
     
 
 ``load_blast`` command
@@ -127,6 +152,8 @@ Create a Blast analysis
       --is_concat              If the blast result file is simply a list of
                                concatenated blast results.
       --search_keywords        Extract keywords for Tripal search
+      --no_parsed TEXT         Maximum number of hits to parse per feature.
+                               Default=all  [default: all]
       --no_wait                Do not wait for job to complete
       --algorithm TEXT         analysis algorithm
       --sourceversion TEXT     analysis sourceversion
@@ -207,11 +234,8 @@ Load GFF3 file
       --analysis_id INTEGER         Analysis ID
       --import_mode TEXT            Import mode (add_only=existing features won't be
                                     touched, update=existing features will be
-                                    updated and obsolete attributes kept,
-                                    refresh=existing features will be updated and
-                                    obsolete attributes removed, remove=features
-                                    present in the db and in the GFF3 file will be
-                                    removed)')  [default: update]
+                                    updated and obsolete attributes kept)')
+                                    [default: update]
       --target_organism TEXT        In case of Target attribute in the GFF3, choose
                                     the organism abbreviation or common name to
                                     which target sequences belong. Select this only
@@ -286,22 +310,27 @@ Create a GO analysis
 **Options**::
 
 
-      --gaf_ext TEXT        If looking for files in a directory, extension of the
-                            GAF files
-      --query_type TEXT     The feature type (e.g. 'gene', 'mRNA', 'contig') of the
-                            query. It must be a valid Sequence Ontology term.
-      --query_uniquename    Use this if the --query-re regular expression matches
-                            unique names instead of names in the database.
-      --method TEXT         Import method ('add' or 'remove')  [default: add]
-      --re_name TEXT        Regular expression to extract the feature name from GAF
-                            file.
-      --no_wait             Do not wait for job to complete
-      --algorithm TEXT      analysis algorithm
-      --sourceversion TEXT  analysis sourceversion
-      --sourceuri TEXT      analysis sourceuri
-      --description TEXT    analysis description
-      --date_executed TEXT  analysis date_executed (yyyy-mm-dd)
-      -h, --help            Show this message and exit.
+      --organism TEXT        Organism common name or abbreviation
+      --organism_id INTEGER  Organism ID
+      --gaf_ext TEXT         If looking for files in a directory, extension of the
+                             GAF files
+      --query_type TEXT      The feature type (e.g. 'gene', 'mRNA', 'contig') of the
+                             query. It must be a valid Sequence Ontology term.
+      --query_matching TEXT  Method to match identifiers to features in the
+                             database. ('name', 'uniquename' or 'dbxref')  [default:
+                             uniquename]
+      --method TEXT          Import method ('add' or 'remove')  [default: add]
+      --name_column INTEGER  Column containing the feature identifiers (2, 3, 10 or
+                             11; default=2).  [default: 2]
+      --re_name TEXT         Regular expression to extract the feature name from GAF
+                             file.
+      --no_wait              Do not wait for job to complete
+      --algorithm TEXT       analysis algorithm
+      --sourceversion TEXT   analysis sourceversion
+      --sourceuri TEXT       analysis sourceuri
+      --description TEXT     analysis description
+      --date_executed TEXT   analysis date_executed (yyyy-mm-dd)
+      -h, --help             Show this message and exit.
     
 
 ``load_interpro`` command

docs/commands/entity.rst

@@ -0,0 +1,78 @@
+entity
+======
+
+This section is auto-generated from the help text for the tripaille command
+``entity``.
+
+
+``add_entity`` command
+----------------------
+
+**Usage**::
+
+    tripaille entity add_entity [OPTIONS] ENTITY
+
+**Help**
+
+Add a new entity to the database
+
+
+**Output**
+
+
+    Entity information
+
+**Options**::
+
+
+      --params TEXT  Values to populate the entity fields
+      -h, --help     Show this message and exit.
+    
+
+``get_entities`` command
+------------------------
+
+**Usage**::
+
+    tripaille entity get_entities [OPTIONS]
+
+**Help**
+
+Get entities
+
+
+**Output**
+
+
+    Entity information
+
+**Options**::
+
+
+      --entity TEXT        Name of the entity type (e.g. Organism)
+      --entity_id INTEGER  ID of an entity
+      -h, --help           Show this message and exit.
+    
+
+``get_fields`` command
+----------------------
+
+**Usage**::
+
+    tripaille entity get_fields [OPTIONS] ENTITY
+
+**Help**
+
+Get the list of available fields for an entity
+
+
+**Output**
+
+
+    Fields information
+
+**Options**::
+
+
+      -h, --help  Show this message and exit.
+