-
Prep template
+
Prep template
EBI status: {{ebi_status}}
EBI study accession: {{ebi_study_accession}}
EBI submission accession: {{ebi_submission_accession}}
diff --git a/qiita_pet/templates/study_description_templates/raw_data_info.html b/qiita_pet/templates/study_description_templates/raw_data_info.html
new file mode 100644
index 000000000..163e3f179
--- /dev/null
+++ b/qiita_pet/templates/study_description_templates/raw_data_info.html
@@ -0,0 +1,56 @@
+
+
+
+
+
+
+ {% if raw_data_files %}
+
Files linked to this raw data:
+ {% for fname, ftype in raw_data_files %}
+
{{fname}}: {{ftype}}
+ {% end %}
+ {% if show_buttons %}
+
+
Unlink all files
+ {% end %}
+ {% else %}
+
There are no files currently linked to the raw data. Choose from the following list:
+
+
+ | File |
+ |
+ File type |
+
+ {% for f in files %}
+
+ | {{f}} |
+ |
+
+
+ |
+
+ {% end %}
+ {% if show_buttons %}
+ | |
+ | Link files |
+ {% end %}
+
+ {% end %}
+
{{link_msg}}
+
+
+
+
+
\ No newline at end of file
diff --git a/qiita_pet/templates/study_description_templates/raw_data_tab.html b/qiita_pet/templates/study_description_templates/raw_data_tab.html
deleted file mode 100644
index e8c6e3b3e..000000000
--- a/qiita_pet/templates/study_description_templates/raw_data_tab.html
+++ /dev/null
@@ -1,50 +0,0 @@
-
-
-
-
-
-
-
-
- What file type is your raw data?
-
- {% if other_studies_rd %}
-
- You could also select raw data from other studies that you have access to:
-
-
- {% end %}
-
-
Add raw data
-
-
-
- {% for _, _, rd, _ in available_raw_data %}
- {% module RawDataEditorTab(study, rd, full_access) %}
- {% end %}
-
-
-
-
diff --git a/qiita_pet/test/test_study_handlers.py b/qiita_pet/test/test_study_handlers.py
index d5a2bc4eb..b289d4287 100644
--- a/qiita_pet/test/test_study_handlers.py
+++ b/qiita_pet/test/test_study_handlers.py
@@ -56,7 +56,7 @@ def setUp(self):
'metadata_complete': True,
'study_title':
'Identification of the Microbiomes for Cannabis Soils',
- 'num_raw_data': 4,
+ 'num_raw_data': 1,
'number_samples_collected': 27,
'shared':
'
Shared',
@@ -201,31 +201,6 @@ def test_update_sample_template(self):
response = self.post('/study/description/1', post_args)
self.assertEqual(response.code, 200)
- def test_create_raw_data(self):
- # testing adding new raw data
- post_args = {
- 'filetype': '1',
- 'action': 'create_raw_data'
- }
- response = self.post('/study/description/1', post_args)
- self.assertEqual(response.code, 200)
-
- # testing an error due to previous raw data already added
- post_args = {
- 'previous_raw_data': '1',
- 'action': 'create_raw_data'
- }
- response = self.post('/study/description/1', post_args)
- self.assertEqual(response.code, 500)
-
- # testing an error due to previous_raw_data not existing
- post_args = {
- 'previous_raw_data': '5',
- 'action': 'create_raw_data'
- }
- response = self.post('/study/description/1', post_args)
- self.assertEqual(response.code, 500)
-
class TestStudyEditHandler(TestHandlerBase):
database = True
@@ -360,7 +335,7 @@ class TestSearchStudiesAJAX(TestHandlerBase):
'pmid': '
123456,
7891011',
- 'num_raw_data': 4,
+ 'num_raw_data': 1,
'proc_data_info': [{
'pid': 1,
'processed_date': '2012-10-01 09:30:27',
@@ -484,12 +459,13 @@ def test_delete_sample_template(self):
def test_delete_raw_data(self):
response = self.post('/study/description/1',
{'raw_data_id': 1,
+ 'prep_template_id': 1,
'action': 'delete_raw_data'})
self.assertEqual(response.code, 200)
# checking that the action was sent
- self.assertIn("Raw data 1 has prep template(s) associated so it can't "
- "be erased", response.body)
+ self.assertIn("Couldn't remove raw data 1: Raw data (1) can't be "
+ "remove because it has linked files", response.body)
def test_delete_prep_template(self):
response = self.post('/study/description/1',
diff --git a/qiita_pet/uimodules/__init__.py b/qiita_pet/uimodules/__init__.py
index 88f893074..43fcf9724 100644
--- a/qiita_pet/uimodules/__init__.py
+++ b/qiita_pet/uimodules/__init__.py
@@ -7,12 +7,12 @@
# -----------------------------------------------------------------------------
from .study_information_tab import StudyInformationTab
-from .raw_data_tab import (RawDataTab, RawDataEditorTab, PrepTemplatePanel,
- EditInvestigationType)
+from .prep_template_tab import (PrepTemplateTab, PrepTemplateInfoTab,
+ RawDataInfoDiv, EditInvestigationType)
from .preprocessed_data_tab import PreprocessedDataTab, PreprocessedDataInfoTab
from .processed_data_tab import ProcessedDataTab, ProcessedDataInfoTab
-__all__ = ['StudyInformationTab', 'RawDataTab', 'RawDataEditorTab',
- 'PrepTemplatePanel', 'EditInvestigationType', 'PreprocessedDataTab',
+__all__ = ['StudyInformationTab', 'PrepTemplateTab', 'PrepTemplateInfoTab',
+ 'EditInvestigationType', 'RawDataInfoDiv', 'PreprocessedDataTab',
'PreprocessedDataInfoTab', 'ProcessedDataTab',
'ProcessedDataInfoTab']
diff --git a/qiita_pet/uimodules/prep_template_tab.py b/qiita_pet/uimodules/prep_template_tab.py
new file mode 100644
index 000000000..2686ed295
--- /dev/null
+++ b/qiita_pet/uimodules/prep_template_tab.py
@@ -0,0 +1,274 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
+from operator import itemgetter
+from os.path import basename
+from collections import defaultdict
+
+from future.utils import viewitems
+
+from qiita_db.util import (get_filetypes, get_files_from_uploads_folders,
+ get_data_types, convert_to_id, get_filepath_types)
+from qiita_db.study import Study
+from qiita_db.data import RawData
+from qiita_db.ontology import Ontology
+from qiita_db.metadata_template import (PrepTemplate, TARGET_GENE_DATA_TYPES,
+ PREP_TEMPLATE_COLUMNS_TARGET_GENE)
+from qiita_db.parameters import (Preprocessed454Params,
+ PreprocessedIlluminaParams)
+from qiita_pet.util import STATUS_STYLER
+from qiita_pet.handlers.util import download_link_or_path
+from .base_uimodule import BaseUIModule
+
+
+filepath_types = [k.split('_', 1)[1].replace('_', ' ')
+ for k in get_filepath_types()
+ if k.startswith('raw_')]
+fp_type_by_ft = defaultdict(
+ lambda: filepath_types, SFF=['sff'], FASTA=['fasta', 'qual'],
+ FASTQ=['barcodes', 'forward seqs', 'reverse seqs'])
+
+
+def _get_accessible_raw_data(user):
+ """Retrieves a tuple of raw_data_id and the last study title for that
+ raw_data
+ """
+ d = {}
+ for sid in user.user_studies:
+ for rdid in Study(sid).raw_data():
+ d[int(rdid)] = Study(RawData(rdid).studies[-1]).title
+ return d
+
+
+def _template_generator(study, full_access):
+ """Generates tuples of prep template information
+
+ Parameters
+ ----------
+ study : Study
+ The study to get all the prep templates
+ full_access : boolean
+ A boolean that indicates if the user has full access to the study
+
+ Returns
+ -------
+ Generator of tuples of (int, str, PrepTemplate, (str, str, str))
+ Each tuple contains the prep template id, the prep template data_type
+ the PrepTemplate object and a tuple with 3 strings for the style of
+ the prep template status icons
+ """
+ for pt_id in study.prep_templates():
+ pt = PrepTemplate(pt_id)
+ if full_access or pt.status() == 'public':
+ yield (pt.id, pt.data_type(), pt, STATUS_STYLER[pt.status])
+
+
+class PrepTemplateTab(BaseUIModule):
+ def render(self, study, full_access):
+ files = [f for _, f in get_files_from_uploads_folders(str(study.id))]
+ data_types = sorted(viewitems(get_data_types()), key=itemgetter(1))
+ prep_templates_info = [
+ res for res in _template_generator(study, full_access)]
+ # Get all the ENA terms for the investigation type
+ ontology = Ontology(convert_to_id('ENA', 'ontology'))
+ # make "Other" show at the bottom of the drop down menu
+ ena_terms = []
+ for v in sorted(ontology.terms):
+ if v != 'Other':
+ ena_terms.append('
' % (v, v))
+ ena_terms.append('
')
+
+ # New Type is for users to add a new user-defined investigation type
+ user_defined_terms = ontology.user_defined_terms + ['New Type']
+
+ return self.render_string(
+ "study_description_templates/prep_template_tab.html",
+ files=files,
+ data_types=data_types,
+ available_prep_templates=prep_templates_info,
+ ena_terms=ena_terms,
+ user_defined_terms=user_defined_terms,
+ study=study,
+ full_access=full_access)
+
+
+class PrepTemplateInfoTab(BaseUIModule):
+ def render(self, study, prep_template, full_access, ena_terms,
+ user_defined_terms):
+ user = self.current_user
+ is_local_request = self._is_local()
+
+ template_fps = []
+ qiime_fps = []
+ # Unfortunately, both the prep template and the qiime mapping files
+ # have the sample type. The way to differentiate them is if we have
+ # the substring 'qiime' in the basename
+ for id_, fp in prep_template.get_filepaths():
+ if 'qiime' in basename(fp):
+ qiime_fps.append(
+ download_link_or_path(
+ is_local_request, fp, id_, 'Qiime mapping'))
+ else:
+ template_fps.append(
+ download_link_or_path(
+ is_local_request, fp, id_, 'Prep template'))
+
+ # Since get_filepaths returns the paths sorted from newest to oldest,
+ # the first in both list is the latest one
+ current_template_fp = template_fps[0]
+ current_qiime_fp = qiime_fps[0]
+
+ if len(template_fps) > 1:
+ show_old_templates = True
+ old_templates = template_fps[1:]
+ else:
+ show_old_templates = False
+ old_templates = None
+
+ if len(qiime_fps) > 1:
+ show_old_qiime_fps = True
+ old_qiime_fps = qiime_fps[1:]
+ else:
+ show_old_qiime_fps = False
+ old_qiime_fps = None
+
+ filetypes = sorted(
+ ((ft, ft_id, fp_type_by_ft[ft])
+ for ft, ft_id in viewitems(get_filetypes())),
+ key=itemgetter(1))
+ files = [f for _, f in get_files_from_uploads_folders(str(study.id))]
+
+ other_studies_rd = sorted(viewitems(
+ _get_accessible_raw_data(user)))
+
+ # A prep template can be modified if its status is sanbdox
+ is_editable = prep_template.status == 'sanbdox'
+
+ raw_data_id = prep_template.raw_data
+ preprocess_options = []
+ preprocessed_data = None
+ show_preprocess_btn = True
+ no_preprocess_msg = None
+ if raw_data_id:
+ rd = RawData(raw_data_id)
+ rd_ft = rd.filetype
+ # If the prep template has a raw data associated, it can be
+ # preprocessed. Retrieve the pre-processing parameters
+ if rd_ft in ('SFF', 'FASTA'):
+ param_iter = Preprocessed454Params.iter()
+ elif rd_ft == 'FASTQ':
+ param_iter = PreprocessedIlluminaParams.iter()
+ else:
+ raise NotImplementedError(
+ "Pre-processing of %s files currently not supported."
+ % rd_ft)
+
+ preprocess_options = []
+ for param in param_iter:
+ text = ("
%s: %s" % (k, v)
+ for k, v in viewitems(param.values))
+ preprocess_options.append((param.id,
+ param.name,
+ '
'.join(text)))
+ preprocessed_data = prep_template.preprocessed_data
+
+ # Check if the template have all the required columns for
+ # preprocessing
+ raw_data_files = rd.get_filepaths()
+ if len(raw_data_files) == 0:
+ show_preprocess_btn = False
+ no_preprocess_msg = (
+ "Preprocessing disabled because there are no files "
+ "linked with the Raw Data")
+ else:
+ if prep_template.data_type() in TARGET_GENE_DATA_TYPES:
+ key = ('demultiplex_multiple' if len(raw_data_files) > 2
+ else 'demultiplex')
+ missing_cols = prep_template.check_restrictions(
+ [PREP_TEMPLATE_COLUMNS_TARGET_GENE[key]])
+ show_preprocess_btn = len(missing_cols) == 0
+ if not show_preprocess_btn:
+ no_preprocess_msg = (
+ "Preprocessing disabled due to missing columns in "
+ "the prep template: %s" % ', '.join(missing_cols))
+ else:
+ no_preprocess_msg = None
+
+ preprocessing_status = prep_template.preprocessing_status
+
+ return self.render_string(
+ "study_description_templates/prep_template_info_tab.html",
+ pt_id=prep_template.id,
+ study_id=study.id,
+ raw_data=raw_data_id,
+ current_template_fp=current_template_fp,
+ current_qiime_fp=current_qiime_fp,
+ show_old_templates=show_old_templates,
+ old_templates=old_templates,
+ show_old_qiime_fps=show_old_qiime_fps,
+ old_qiime_fps=old_qiime_fps,
+ filetypes=filetypes,
+ files=files,
+ other_studies_rd=other_studies_rd,
+ prep_template=prep_template,
+ study=study,
+ ena_terms=ena_terms,
+ user_defined_terms=user_defined_terms,
+ investigation_type=prep_template.investigation_type,
+ is_editable=is_editable,
+ preprocess_options=preprocess_options,
+ preprocessed_data=preprocessed_data,
+ preprocessing_status=preprocessing_status,
+ show_preprocess_btn=show_preprocess_btn,
+ no_preprocess_msg=no_preprocess_msg)
+
+
+class RawDataInfoDiv(BaseUIModule):
+ def render(self, raw_data_id, prep_template, study, files):
+ rd = RawData(raw_data_id)
+ raw_data_files = [(basename(fp), fp_type[4:])
+ for _, fp, fp_type in rd.get_filepaths()]
+ filetype = rd.filetype
+ fp_types = fp_type_by_ft[filetype]
+ raw_data_link_status = rd.link_filepaths_status
+
+ show_buttons = rd.status(study) == 'sandbox'
+ link_msg = ""
+ if show_buttons:
+ # Define the message for the link status
+ if raw_data_link_status == 'linking':
+ link_msg = "Linking files..."
+ show_buttons = False
+ elif raw_data_link_status == 'unlinking':
+ link_msg = "Unlinking files..."
+ show_buttons = False
+ elif raw_data_link_status.startswith('failed'):
+ link_msg = "Error (un)linking files: %s" % raw_data_link_status
+
+ return self.render_string(
+ "study_description_templates/raw_data_info.html",
+ rd_id=raw_data_id,
+ rd_filetype=rd.filetype,
+ raw_data_files=raw_data_files,
+ prep_template_id=prep_template.id,
+ files=files,
+ filepath_types=fp_types,
+ filetype=filetype,
+ link_msg=link_msg,
+ show_buttons=show_buttons)
+
+
+class EditInvestigationType(BaseUIModule):
+ def render(self, ena_terms, user_defined_terms, prep_id, inv_type, ppd_id):
+ return self.render_string(
+ "study_description_templates/edit_investigation_type.html",
+ ena_terms=ena_terms,
+ user_defined_terms=user_defined_terms,
+ prep_id=prep_id,
+ investigation_type=inv_type,
+ ppd_id=ppd_id)
diff --git a/qiita_pet/uimodules/raw_data_tab.py b/qiita_pet/uimodules/raw_data_tab.py
deleted file mode 100644
index 495309bd3..000000000
--- a/qiita_pet/uimodules/raw_data_tab.py
+++ /dev/null
@@ -1,254 +0,0 @@
-# -----------------------------------------------------------------------------
-# Copyright (c) 2014--, The Qiita Development Team.
-#
-# Distributed under the terms of the BSD 3-clause License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# -----------------------------------------------------------------------------
-
-from operator import itemgetter
-from os.path import basename
-
-from future.utils import viewitems
-
-from qiita_db.util import (get_filetypes, get_files_from_uploads_folders,
- get_data_types, convert_to_id, get_filepath_types)
-from qiita_db.study import Study
-from qiita_db.data import RawData
-from qiita_db.ontology import Ontology
-from qiita_db.metadata_template import (PrepTemplate, TARGET_GENE_DATA_TYPES,
- PREP_TEMPLATE_COLUMNS_TARGET_GENE)
-from qiita_db.parameters import (Preprocessed454Params,
- PreprocessedIlluminaParams)
-from qiita_pet.util import STATUS_STYLER
-from .base_uimodule import BaseUIModule
-
-
-def get_raw_data_from_other_studies(user, study):
- """Retrieves a tuple of raw_data_id and the last study title for that
- raw_data
- """
- d = {}
- for sid in user.user_studies:
- if sid == study.id:
- continue
- for rdid in Study(sid).raw_data():
- d[int(rdid)] = Study(RawData(rdid).studies[-1]).title
- return d
-
-
-def get_raw_data(rdis):
- """Get all raw data objects from a list of raw_data_ids"""
- return [RawData(rdi) for rdi in rdis]
-
-
-class RawDataTab(BaseUIModule):
- def render(self, study, full_access):
- user = self.current_user
-
- filetypes = sorted(viewitems(get_filetypes()), key=itemgetter(1))
- other_studies_rd = sorted(viewitems(
- get_raw_data_from_other_studies(user, study)))
-
- raw_data_info = [
- (rd.id, rd.filetype, rd, STATUS_STYLER[rd.status(study)])
- for rd in get_raw_data(study.raw_data())
- if full_access or rd.status(study) == 'public']
-
- return self.render_string(
- "study_description_templates/raw_data_tab.html",
- filetypes=filetypes,
- other_studies_rd=other_studies_rd,
- available_raw_data=raw_data_info,
- study=study,
- full_access=full_access)
-
-
-class RawDataEditorTab(BaseUIModule):
- def render(self, study, raw_data, full_access):
- user = self.current_user
- study_status = study.status
- user_level = user.level
- raw_data_id = raw_data.id
- files = [f for _, f in get_files_from_uploads_folders(str(study.id))]
-
- # Get the available prep template data types
- data_types = sorted(viewitems(get_data_types()), key=itemgetter(1))
-
- # Get all the ENA terms for the investigation type
- ontology = Ontology(convert_to_id('ENA', 'ontology'))
- # make "Other" show at the bottom of the drop down menu
- ena_terms = []
- for v in sorted(ontology.terms):
- if v != 'Other':
- ena_terms.append('
' % (v, v))
- ena_terms.append('
')
-
- # New Type is for users to add a new user-defined investigation type
- user_defined_terms = ontology.user_defined_terms + ['New Type']
-
- # Get all the information about the prep templates
- available_prep_templates = []
- for p in sorted(raw_data.prep_templates):
- if PrepTemplate.exists(p):
- pt = PrepTemplate(p)
- # if the prep template doesn't belong to this study, skip
- if (study.id == pt.study_id and
- (full_access or pt.status == 'public')):
- available_prep_templates.append(pt)
-
- # getting filepath_types
- if raw_data.filetype == 'SFF':
- fts = ['sff']
- elif raw_data.filetype == 'FASTA':
- fts = ['fasta', 'qual']
- elif raw_data.filetype == 'FASTQ':
- fts = ['barcodes', 'forward seqs', 'reverse seqs']
- else:
- fts = [k.split('_', 1)[1].replace('_', ' ')
- for k in get_filepath_types() if k.startswith('raw_')]
-
- # The raw data can be edited (e.i. adding prep templates and files)
- # only if the study is sandboxed or the current user is an admin
- is_editable = study_status == 'sandbox' or user_level == 'admin'
-
- # Get the files linked with the raw_data
- raw_data_files = raw_data.get_filepaths()
-
- # Get the status of the data linking
- raw_data_link_status = raw_data.link_filepaths_status
-
- # By default don't show the unlink button
- show_unlink_btn = False
- # By default disable the the link file button
- disable_link_btn = True
- # Define the message for the link status
- if raw_data_link_status == 'linking':
- link_msg = "Linking files..."
- elif raw_data_link_status == 'unlinking':
- link_msg = "Unlinking files..."
- else:
- # The link button is only disable if raw data link status is
- # linking or unlinking, so we can enable it here
- disable_link_btn = False
- # The unlink button is only shown if the study is editable, the raw
- # data linking status is not in linking or unlinking, and there are
- # files attached to the raw data. At this point, we are sure that
- # the raw data linking status is not in linking or unlinking so we
- # still need to check if it is editable or there are files attached
- show_unlink_btn = is_editable and raw_data_files
- if raw_data_link_status.startswith('failed'):
- link_msg = "Error (un)linking files: %s" % raw_data_link_status
- else:
- link_msg = ""
-
- # Get the raw_data filetype
- raw_data_filetype = raw_data.filetype
-
- return self.render_string(
- "study_description_templates/raw_data_editor_tab.html",
- study_id=study.id,
- study_status=study_status,
- user_level=user_level,
- raw_data_id=raw_data_id,
- files=files,
- data_types=data_types,
- ena_terms=ena_terms,
- user_defined_terms=user_defined_terms,
- available_prep_templates=available_prep_templates,
- filepath_types=fts,
- is_editable=is_editable,
- show_unlink_btn=show_unlink_btn,
- link_msg=link_msg,
- raw_data_files=raw_data_files,
- raw_data_filetype=raw_data_filetype,
- disable_link_btn=disable_link_btn)
-
-
-class PrepTemplatePanel(BaseUIModule):
- def render(self, prep, study_id, is_editable, ena_terms,
- study_status, user_defined_terms, raw_data_files):
- # Check if the request came from a local source
- is_local_request = self._is_local()
-
- prep_id = prep.id
- status_class1, status_class2, status_color = STATUS_STYLER[prep.status]
- data_type = prep.data_type()
- raw_data = RawData(prep.raw_data)
- filepaths = prep.get_filepaths()
- investigation_type = prep.investigation_type
- preprocessed_data = prep.preprocessed_data
- preprocessing_status = prep.preprocessing_status
-
- if raw_data.filetype in ('SFF', 'FASTA'):
- param_iter = Preprocessed454Params.iter()
- elif raw_data.filetype == 'FASTQ':
- param_iter = PreprocessedIlluminaParams.iter()
- else:
- raise ValueError("Don't know what to do but this exception will "
- "never actually get shown anywhere because why "
- "would you want to see tracebacks?")
-
- preprocess_options = []
- for param in param_iter:
- text = ("
%s: %s" % (k, v)
- for k, v in viewitems(param.values))
- preprocess_options.append((param.id,
- param.name,
- '
'.join(text)))
-
- # Unfortunately, both the prep template and the qiime mapping files
- # have the sample type. The way to differentiate them is if we have
- # the substring 'qiime' in the basename
- _fp_type = (lambda fp: "Qiime mapping"
- if 'qiime' in basename(fp) else "Prep template")
- filepaths = [(id_, fp, _fp_type(fp)) for id_, fp in filepaths]
-
- # Check if the template have all the required columns for preprocessing
- if prep.data_type() in TARGET_GENE_DATA_TYPES:
- key = ('demultiplex_multiple' if len(raw_data_files) > 2
- else 'demultiplex')
- missing_cols = prep.check_restrictions(
- [PREP_TEMPLATE_COLUMNS_TARGET_GENE[key]])
- show_preprocess_btn = len(missing_cols) == 0
- if not show_preprocess_btn:
- no_preprocess_msg = (
- "Preprocessing disabled due to missing columns in the "
- "prep template: %s" % ', '.join(missing_cols))
- else:
- no_preprocess_msg = None
- else:
- show_preprocess_btn = True
- no_preprocess_msg = None
-
- return self.render_string(
- "study_description_templates/prep_template_panel.html",
- prep_id=prep_id,
- status_class1=status_class1,
- status_class2=status_class2,
- status_color=status_color,
- data_type=data_type,
- filepaths=filepaths,
- investigation_type=investigation_type,
- preprocessed_data=preprocessed_data,
- preprocessing_status=preprocessing_status,
- study_id=study_id,
- is_local_request=is_local_request,
- is_editable=is_editable,
- ena_terms=ena_terms,
- study_status=study_status,
- user_defined_terms=user_defined_terms,
- preprocess_options=preprocess_options,
- show_preprocess_btn=show_preprocess_btn,
- no_preprocess_msg=no_preprocess_msg)
-
-
-class EditInvestigationType(BaseUIModule):
- def render(self, ena_terms, user_defined_terms, prep_id, inv_type, ppd_id):
- return self.render_string(
- "study_description_templates/edit_investigation_type.html",
- ena_terms=ena_terms,
- user_defined_terms=user_defined_terms,
- prep_id=prep_id,
- investigation_type=inv_type,
- ppd_id=ppd_id)
diff --git a/qiita_pet/webserver.py b/qiita_pet/webserver.py
index 9097fe1d5..324c31b86 100644
--- a/qiita_pet/webserver.py
+++ b/qiita_pet/webserver.py
@@ -28,7 +28,7 @@
from qiita_pet.handlers.logger_handlers import LogEntryViewerHandler
from qiita_pet.handlers.upload import UploadFileHandler, StudyUploadFileHandler
from qiita_pet.handlers.compute import (
- ComputeCompleteHandler, AddFilesToRawData, UnlinkAllFiles)
+ ComputeCompleteHandler, AddFilesToRawData, UnlinkAllFiles, CreateRawData)
from qiita_pet.handlers.preprocessing_handlers import PreprocessHandler
from qiita_pet.handlers.processing_handlers import ProcessHandler
from qiita_pet.handlers.stats import StatsHandler
@@ -81,6 +81,7 @@ def __init__(self):
(r"/study/list/socket/", SelectSamplesHandler),
(r"/study/search/(.*)", SearchStudiesAJAX),
(r"/study/add_files_to_raw_data", AddFilesToRawData),
+ (r"/study/create_raw_data", CreateRawData),
(r"/study/unlink_all_files", UnlinkAllFiles),
(r"/study/preprocess", PreprocessHandler),
(r"/study/process", ProcessHandler),
diff --git a/qiita_ware/dispatchable.py b/qiita_ware/dispatchable.py
index 7ff497bee..0c5883541 100644
--- a/qiita_ware/dispatchable.py
+++ b/qiita_ware/dispatchable.py
@@ -72,6 +72,14 @@ def run_analysis(analysis_id, commands, comm_opts=None,
return ar(analysis, commands, comm_opts, rarefaction_depth)
+def create_raw_data(filetype, prep_template, filepaths):
+ """Creates a new raw data
+
+ Needs to be dispachable because it moves large files
+ """
+ RawData.create(filetype, [prep_template], filepaths)
+
+
def add_files_to_raw_data(raw_data_id, filepaths):
"""Add files to raw data
diff --git a/test_data_studies/commands.sh b/test_data_studies/commands.sh
index 8cc709b54..779ac3e33 100755
--- a/test_data_studies/commands.sh
+++ b/test_data_studies/commands.sh
@@ -40,19 +40,19 @@ for i in ${studies[@]}; do
qiita db load_sample_template $sample_file --study $study_id
echo "Ok"
+ # Loading prep template
+ echo "\tloading prep template... "
+ output=`qiita db load_prep_template $prep_file --study $study_id --data_type "16S"`
+ pt_id=`echo -e "${output}" | cut -d " " -f 10`
+ echo "Ok"
+
# Loading raw data
echo "\tloading raw data... "
echo -e ">seq\nAAAA" > seqs.fna
- output="`qiita db load_raw --fp seqs.fna --fp_type raw_forward_seqs --filetype FASTQ --study $i`"
+ output="`qiita db load_raw --fp seqs.fna --fp_type raw_forward_seqs --filetype FASTQ --prep_template $pt_id`"
raw_id=`echo -e "${output}" | cut -d " " -f 10`
echo "Ok"
- # Loading prep template
- echo "\tloading prep template... "
- output=`qiita db load_prep_template $prep_file --raw_data $raw_id --study $study_id --data_type "16S"`
- pt_id=`echo -e "${output}" | cut -d " " -f 10`
- echo "Ok"
-
# Loading preprocessed data
echo "\tloading preprocessed data... "
echo -e ">seq\nAAAA" > temp/seqs.fna