[WIP] EBI improvements

.travis.yml

@@ -14,22 +14,34 @@ before_install:
   - export PATH=/home/travis/miniconda3/bin:$PATH
   # Update conda itself
   - conda update --yes conda
+  # Downloading and setting up ascp for EBI testing
+  - wget ftp://ftp.microbio.me/pub/qiita/ascp-install-3.5.4.102989-linux-64-qiita.sh -O ascp-install-3.5.4.102989-linux-64-qiita.sh
+  - chmod +x ascp-install-3.5.4.102989-linux-64-qiita.sh
+  - ./ascp-install-3.5.4.102989-linux-64-qiita.sh
+  - if [ ${TRAVIS_PULL_REQUEST} == "false" ]; then openssl aes-256-cbc -K $encrypted_e698cf0e691c_key -iv $encrypted_e698cf0e691c_iv -in qiita_core/support_files/config_test_travis.cfg.enc -out qiita_core/support_files/config_test_travis.cfg -d; fi
 install:
   # install a few of the dependencies that pip would otherwise try to install
   # when intalling scikit-bio
-  - travis_retry conda create --yes -n env_name python=$PYTHON_VERSION pip nose flake8 pyzmq networkx pyparsing natsort mock 'pandas>=0.15' 'matplotlib>=1.1.0' 'scipy>0.13.0' 'numpy>= 1.7' 'h5py>=2.3.1' 'future==0.13.0'
+  - travis_retry conda create --yes -n env_name python=$PYTHON_VERSION pip nose flake8
+    pyzmq networkx pyparsing natsort mock 'pandas>=0.15' 'matplotlib>=1.1.0' 'scipy>0.13.0'
+    'numpy>= 1.7' 'h5py>=2.3.1' 'future==0.13.0'
   - source activate env_name
   - pip install sphinx sphinx-bootstrap-theme coveralls ipython[all]==2.4.1
   - travis_retry pip install .
 script:
   - export MOI_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg
+  - if [ ${TRAVIS_PULL_REQUEST} == "false" ]; then
+    export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test_travis.cfg;
+    export MOI_CONFIG_FP=`pwd`/qiita_core/support_files/config_test_travis.cfg;
+    fi
   - ipython profile create qiita-general --parallel
   - qiita-env start_cluster qiita-general
   - qiita-env make --no-load-ontologies
   - if [ ${TEST_ADD_STUDIES} == "True" ]; then test_data_studies/commands.sh ; fi
   - if [ ${TEST_ADD_STUDIES} == "False" ]; then qiita-test-install ; fi
-  - if [ ${TEST_ADD_STUDIES} == "False" ]; then nosetests --with-doctest --with-coverage ; fi
-  - if [ ${TEST_ADD_STUDIES} == "False" ]; then flake8 qiita_* setup.py scripts/qiita scripts/qiita-env scripts/qiita-test-install ; fi
+  - if [ ${TEST_ADD_STUDIES} == "False" ]; then nosetests --with-doctest --with-coverage; fi
+  - if [ ${TEST_ADD_STUDIES} == "False" ]; then flake8 qiita_* setup.py scripts/qiita
+    scripts/qiita-env scripts/qiita-test-install ; fi
   - ls -R /home/travis/miniconda3/envs/env_name/lib/python2.7/site-packages/qiita_pet/support_files/doc/
   - qiita pet webserver
 services:

CHANGELOG.md

@@ -5,6 +5,7 @@ Version 0.2.0-dev (Changes since version 0.2.0 go here)
 
 * Users can now change values and add samples and/or columns to sample and prep templates using the <kbd>Update</kbd> button (see the prep template and sample template tabs).
 * The raw files of a RawData can be now updated using the `qiita db update_raw_data` CLI command.
+* instrument_model is now a required prep template column for EBI submissions.
 
 Version 0.2.0 (2015-08-25)
 --------------------------

qiita_core/configuration_manager.py

@@ -78,16 +78,12 @@ class ConfigurationManager(object):
     smtp_email : str
         The email address that mail will be sent from when sending mail from
         the SMTP server
-    ebi_access_key : str
-        The access key issued by EBI for REST submissions
     ebi_seq_xfer_user : str
         The user to use when submitting to EBI
     ebi_seq_xfer_pass : str
         The password for the ebi_seq_xfer_user
     ebi_seq_xfer_url : str
         The URL of EBI's sequence portal site
-    ebi_skip_curl_cert : bool
-        Whether or not to skip the certificate check when curling the metadata
     ebi_center_name : str
         The name of the sequencing center to use when doing EBI submissions
     ebi_organization_prefix : str
@@ -213,14 +209,11 @@ def _get_smtp(self, config):
 
     def _get_ebi(self, config):
         sec_get = partial(config.get, 'ebi')
-        sec_getbool = partial(config.getboolean, 'ebi')
 
-        self.ebi_access_key = sec_get('EBI_ACCESS_KEY')
         self.ebi_seq_xfer_user = sec_get('EBI_SEQ_XFER_USER')
         self.ebi_seq_xfer_pass = sec_get('EBI_SEQ_XFER_PASS')
         self.ebi_seq_xfer_url = sec_get('EBI_SEQ_XFER_URL')
         self.ebi_dropbox_url = sec_get('EBI_DROPBOX_URL')
-        self.ebi_skip_curl_cert = sec_getbool('EBI_SKIP_CURL_CERT')
         self.ebi_center_name = sec_get('EBI_CENTER_NAME')
         self.ebi_organization_prefix = sec_get('EBI_ORGANIZATION_PREFIX')
 

qiita_core/support_files/config_test.cfg

@@ -99,30 +99,23 @@ ADMIN_PASSWORD =
 
 # ----------------------------- EBI settings -----------------------------
 [ebi]
-# The access key issued by EBI for REST submissions
-EBI_ACCESS_KEY =
-
 # The user to use when submitting to EBI
-EBI_SEQ_XFER_USER =
+EBI_SEQ_XFER_USER = Webin-41528
 
 # Password for the above user
 EBI_SEQ_XFER_PASS =
 
 # URL of EBI's FASP site
-EBI_SEQ_XFER_URL = fasp.sra.ebi.ac.uk
+EBI_SEQ_XFER_URL = webin.ebi.ac.uk
 
 # URL of EBI's HTTPS dropbox
 # live submission URL
 #EBI_DROPBOX_URL = https://www.ebi.ac.uk/ena/submit/drop-box/submit/
 # testing URL
 EBI_DROPBOX_URL = https://www-test.ebi.ac.uk/ena/submit/drop-box/submit/
 
-# Skip acertificate check when calling curl (necessary for using the EBI test
-# dropbox URL)
-EBI_SKIP_CURL_CERT = True
-
 # The name of the sequencing center to use when doing EBI submissions
-EBI_CENTER_NAME = CCME-COLORADO
+EBI_CENTER_NAME = qiita-test
 
 # This string (with an underscore) will be prefixed to your EBI submission and
 # study aliases

qiita_db/commands.py

@@ -102,42 +102,37 @@ def get_optional(name):
 
 
 def load_preprocessed_data_from_cmd(study_id, params_table, filedir,
-                                    filepathtype, params_id,
-                                    submitted_to_insdc_status,
+                                    filepath_type, params_id,
                                     prep_template_id, data_type):
     r"""Adds preprocessed data to the database
 
     Parameters
     ----------
     study_id : int
         The study id to which the preprocessed data belongs
+    params_table : str
+        The name of the table which contains the parameters of the
+        preprocessing
     filedir : str
         Directory path of the preprocessed data
-    filepathtype: str
+    filepath_type: str
         The filepath_type of the preprecessed data
-    params_table_name : str
-        The name of the table which contains the parameters of the
-        preprocessing
     params_id : int
         The id of parameters int the params_table
-    submitted_to_insdc_status : str, {'not submitted', 'submitting', \
-            'success', 'failed'}
-        INSDC submission status
     prep_template_id : int
         Prep template id associated with data
     data_type : str
         The data type of the template
     """
     with TRN:
         fp_types_dict = get_filepath_types()
-        fp_type = fp_types_dict[filepathtype]
+        fp_type = fp_types_dict[filepath_type]
         filepaths = [(join(filedir, fp), fp_type) for fp in listdir(filedir)]
         pt = (None if prep_template_id is None
               else PrepTemplate(prep_template_id))
         return PreprocessedData.create(
             Study(study_id), params_table, params_id, filepaths,
             prep_template=pt,
-            submitted_to_insdc_status=submitted_to_insdc_status,
             data_type=data_type)