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Commit 65ee4b86 authored by Celine Noirot's avatar Celine Noirot
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Handle project spaces in pi1/project/run/analysis, add type check (projectid, ng6space)

parent 0eb5c7fe
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View file @ 65ee4b86
__pycache__
ui/nG6/res/smarty/*
src/ng6/analysis.py
View file @ 65ee4b86
......@@ -105,7 +105,7 @@ class Analysis (Component):
"""
# The directories structure into ng6
DIRECTORIES_STRUCTURE = "data/analyze/"
DIRECTORIES_STRUCTURE = "analyze/"
ANALYSIS_CONFIG_FILE_NAME = "analysis.cfg"
def __init__(self, name="", description="", software="",
......@@ -149,23 +149,14 @@ class Analysis (Component):
logging.getLogger("Analysis.__init__").debug("Connexion effectuée")
self.run = Run.get_from_id(self.__get_run_id())
from ng6.project import Project
self.project = Project.get_from_id(self.__get_project_id())
self.project = Project.get_from_run_id(self.__get_run_id())
self.space_id=self.project.space_id
self.directory = t3mysql.select_analysis_directory(id)
logging.getLogger("Analysis.__init__").debug("Building analysis with id=" + str(id) + " [" + str(self) + "]")
else :
self.version = self.get_version()
if isinstance(self.version, bytes):
self.version = self.version.decode()
directory_name = uuid.uuid4().hex[:9]
while True:
save_dir = os.path.join(ng6conf.get_save_directory(), ng6conf.get_space_directory(self.space_id), self.DIRECTORIES_STRUCTURE, directory_name)
logging.getLogger("Analysis.__init__").debug("Building analysis save_dir=" + save_dir)
work_dir = os.path.join(ng6conf.get_work_directory(), ng6conf.get_space_directory(self.space_id), self.DIRECTORIES_STRUCTURE, directory_name)
logging.getLogger("Analysis.__init__").debug("Building analysis work_dir=" + save_dir)
if not os.path.isdir(save_dir) and not os.path.isdir(work_dir):
break
directory_name = uuid.uuid4().hex[:9]
self.directory = os.path.join(ng6conf.get_space_directory(self.space_id), self.DIRECTORIES_STRUCTURE, directory_name)
logging.getLogger("Analysis.__init__").debug("Building brand new analysis [" + str(self) + "]")
def define_analysis(self):
......@@ -181,6 +172,19 @@ class Analysis (Component):
raise NotImplementedError
def execute(self):
ng6conf = NG6ConfigReader()
directory_name = uuid.uuid4().hex[:9]
while True:
save_dir = os.path.join(ng6conf.get_save_directory(), ng6conf.get_space_directory(self.space_id), self.DIRECTORIES_STRUCTURE, directory_name)
logging.getLogger("Analysis.__init__").debug("Building analysis save_dir=" + save_dir)
work_dir = os.path.join(ng6conf.get_work_directory(), ng6conf.get_space_directory(self.space_id), self.DIRECTORIES_STRUCTURE, directory_name)
logging.getLogger("Analysis.__init__").debug("Building analysis work_dir=" + save_dir)
if not os.path.isdir(save_dir) and not os.path.isdir(work_dir):
break
directory_name = uuid.uuid4().hex[:9]
self.directory = os.path.join(ng6conf.get_space_directory(self.space_id), self.DIRECTORIES_STRUCTURE, directory_name)
# first create the output directory
if not os.path.isdir(self.output_directory):
os.makedirs(self.output_directory, 0o751)
......@@ -215,7 +219,6 @@ class Analysis (Component):
inputs.append(self.parent.get_config_file_path())
# then run the component
self.process()
print (self)
# add the add_analysis command lines to the make
add = PythonFunction(add_analysis, cmd_format="{EXE} {ARG} {OUT} {IN}")
add(includes=wait_for_files, outputs=self.get_config_file_path(), inputs=inputs, arguments=parent_id)
......@@ -224,8 +227,9 @@ class Analysis (Component):
"""
Return a full description of the analysis
"""
return "name="+str(self.name)+";description="+str(self.description)+";software="+\
str(self.software)+";version="+str(self.version)+";options="+str(self.options)
return "id="+str(self.id)+";name="+str(self.name)+";description="+str(self.description)+";software="+\
str(self.software)+";version="+str(self.version)+";options="+str(self.options)+\
";space_id="+str(self.space_id)+";project="+str(self.project)+";run="+str(self.run)
def sync(self):
"""
......@@ -544,6 +548,7 @@ class Analysis (Component):
@param archive_name: the archive name if tar is requested
@param delete: delete files
"""
# First handle if only one file
if len(files) == 1 and mode == "tar.gz":
mode = "gz"
......
src/ng6/run.py
View file @ 65ee4b86
......@@ -41,7 +41,7 @@ class Run(object):
"""
# The directories structure into ng6
DIRECTORIES_STRUCTURE = "data/run/"
DIRECTORIES_STRUCTURE = "run/"
SEQUENCERS = ["454", "454 GS FLX Titanium", "454 GS FLX+", "454 GS FLX XL+", "HiSeq 2000", "MiSeq"]
def __init__(self, name, date, species, data_nature, type, description, sequencer, space_id="default", id = None ):
......@@ -88,10 +88,7 @@ class Run(object):
break
directory_name = uuid.uuid4().hex[:9]
# Then make directories
print (ng6conf.get_work_directory())
work_dir = os.path.join(ng6conf.get_work_directory(), ng6conf.get_space_directory(self.space_id), self.DIRECTORIES_STRUCTURE, directory_name)
print (ng6conf.get_space_directory(self.space_id))
os.makedirs(work_dir, 0o751)
self.directory = os.path.join(ng6conf.get_space_directory(self.space_id), self.DIRECTORIES_STRUCTURE, directory_name)
......@@ -395,20 +392,21 @@ class Run(object):
Return a run object specified by its id
@param id : the run id
"""
my_run=None
try:
t3mysql = t3MySQLdb()
[name, date, species, data_nature, type, description, sequencer] = t3mysql.select_run(id)
my_run = Run(name, date, species, data_nature, type, description, sequencer, id)
my_run = Run(name, date, species, data_nature, type, description, sequencer, id=id)
# reload samples
try :
my_run.__samples = None
my_run.__samples = my_run.get_samples()
except :
logging.getLogger("Run.get_from_id").debug("Impossible to get samples for run id=" + str(id))
return my_run
except :
logging.getLogger("Run.get_from_id").debug("Impossible to build run id=" + str(id))
return None
try :
my_run.__samples = None
my_run.__samples = my_run.get_samples()
except :
logging.getLogger("Run.get_from_id").debug("Impossible to get samples for run id=" + str(id))
return my_run
@staticmethod
def get_from_config (config_file):
......
src/ng6/t3MySQLdb.py
View file @ 65ee4b86
......@@ -202,7 +202,6 @@ class t3MySQLdb(object):
VALUES ('%s','%s','%s','%s','%s','%s','%s','%s')" % (self.cfg_reader.get_pid(), crdate, crdate, admin_id,
self.esc_q(pdescription), self.esc_q(name), hidden, space_id)
qresult = self.execute(sql, commit = True)
#print ("t3MySQLdb.add_project QL "+sql)
project_id = qresult.lastrowid
self.execute("INSERT INTO fe_rights (fe_user_id, project_id, right_id) VALUES ('%s','%s','%s')" % (admin_id, project_id, right_level_id),
commit = True)
......@@ -938,7 +937,6 @@ class t3MySQLdb(object):
]
sql = " ".join(parts)
print ("select_purge_demand_directories",sql)
qresult = self.execute(sql, dictc = True)
# analysis directories
if qresult.rowcount >= 1:
......@@ -956,7 +954,6 @@ class t3MySQLdb(object):
'tx_nG6_analyze.uid IN (' + ','.join(analysis_ids) +')'
]
sql = " ".join(parts)
print ("select_purge_demand_directories",sql)
qresult = self.execute(sql, dictc = True)
for result in qresult.rows:
......@@ -972,7 +969,6 @@ class t3MySQLdb(object):
'WHERE',
'tx_nG6_run.uid IN (' + ','.join(run_ids) +')'
]
print ("select_purge_demand_directories",sql)
sql = " ".join(parts)
qresult = self.execute(sql, dictc = True)
......@@ -1001,7 +997,6 @@ class t3MySQLdb(object):
'WHERE',
table+'.uid IN (' + uids +')' ] )
sql = " ".join(parts)
print ('### ',sql)
qresult = self.execute(sql, dictc = True)
return(qresult)
......@@ -1017,7 +1012,6 @@ class t3MySQLdb(object):
'WHERE',
'tx_nG6_purge_demand.uid IN ('+str(demand_ids) +')' ]
sql = " ".join(parts)
print ("set_purge_demand_deleted",sql)
qresult = self.execute(sql, dictc = True)
if qresult.rowcount >= 1:
analysis_ids=[]
......
ui/nG6/pi1/analyzes/Adaptorcleaner.tpl
View file @ 65ee4b86
{*
Copyright (C) 2009 INRA
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
......@@ -43,9 +43,9 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</li>
{else}
{assign var="index" value=$params|@array_keys:"--adaptor"}
<li class="parameter">Adaptor used:
<br />
<div class="file-display">{$analyse_results["all"]["default"]["adaptor_file"]}</div>
<li class="parameter">Adaptor used:
<br />
<div class="file-display">{$analyse_results["all"]["default"]["adaptor_file"]}</div>
</li>
{/if}
</ul>
......@@ -89,7 +89,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</tbody>
</table>
</div>
<div class="tab-pane fade" id="adaptor">
{* First find out all adaptors used *}
{assign var="adaptors" value=array()}
......@@ -123,7 +123,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</tbody>
</table>
</div>
<div class="tab-pane fade" id="parameters">
{block name=params}
{block name=params_content}
......@@ -133,28 +133,28 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{/block}
{/block}
</div>
<div class="tab-pane fade" id="downloads">
{block name=download}
{if $nb_files != 0}
{if $nb_files != 0}
<p><ul>
{$dir=$data_folder|cat:$analyse.directory}
{$dir=$data_folder|cat:'/'|cat:$analyse.directory}
{assign var="nb_files" value=0}
{foreach $dir|scandir as $file}
{if $file != "." and $file != "" and $file != ".." and ($file|substr:-strlen(".png")) != ".png"}
{$link=(('fileadmin'|cat:$analyse.directory)|cat:'/')|cat:$file}
{$link=(('fileadmin'|cat:'/'|cat:$analyse.directory)|cat:'/')|cat:$file}
<li class="filelist"><a href="{$link}">{$file}</a> </li>
{$nb_files = $nb_files + 1}
{/if}
{/foreach}
</ul></p>
{else}
{else}
<div class="alert alert-info">
Results folder not synchronized yet...
</div>
{/if}
{/block}
</div>
</div>
{/block}
ui/nG6/pi1/analyzes/AnalysisTemplate.tpl
View file @ 65ee4b86
{*
Copyright (C) 2009 INRA
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
......@@ -40,38 +40,38 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<div class="sub-content sc-bottom">
{block name=content}
<ul id="myTab" class="nav nav-tabs">
{block name=nav_menu_results}
<li class="active"><a href="#results" data-toggle="tab">{block name=results_title} Results {/block}</a></li>
{/block}
{block name=nav_menu_params}
{if $analyse.params != ""}
<li><a href="#parameters" data-toggle="tab">{block name=params_title} Parameters {/block}</a></li>
{/if}
{/block}
{block name=nav_menu_downloads}
<li><a href="#downloads" data-toggle="tab">{block name=downloads_title} Downloads {/block}</a></li>
{/block}
{assign var="comment_tab" value="analysis_comments"}
<li><a href="#{$comment_tab}" data-toggle="tab">Comments</a></li>
{block name=nav_menu_update}{/block}
</ul>
<div id="myTabContent" class="tab-content">
{block name=tab_content_results}
<div class="tab-pane fade in active" id="results">
{block name=results}{/block}
</div>
{/block}
{block name=tab_content_params}
{if $analyse.params != ""}
<div class="tab-pane fade" id="parameters">
......@@ -84,7 +84,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{/foreach}
</ul>
{/block}
{block name=command_line_content}
{if $is_project_admin && $analyse.is_editable }
<br/>
......@@ -92,8 +92,8 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<div class="editable-block">
<span class="editable-block-head label label-info">Command</span>
<i>{$analyse.software}</i>
<span class="editable editable-block-content"
id="editable-command-line" data-pk="{$analyze_id}"
<span class="editable editable-block-content"
id="editable-command-line" data-pk="{$analyze_id}"
data-url="index.php?eID=tx_nG6&type=update_db_field&table=tx_nG6_analyze&field=params" data-type="textarea" >
{$analyse.params}
</span>
......@@ -104,26 +104,26 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</div>
{/if}
{/block}
{block name=tab_content_downloads}
<div class="tab-pane fade" id="downloads">
{block name=download}
{assign var="nb_files" value=0}
{$dir=$data_folder|cat:$analyse.directory}
{$dir=$data_folder|cat:'/'|cat:$analyse.directory}
{foreach $dir|scandir as $file}
{assign var="link" value=(('fileadmin'|cat:$analyse.directory)|cat:'/')|cat:$file}
{assign var="link" value=(('fileadmin'|cat:'/'|cat:$analyse.directory)|cat:'/')|cat:$file}
{if $file != "." and $file != "" and $file != ".." and ($file|substr:-strlen(".png")) != ".png" and !is_dir($link)}
{$nb_files = $nb_files + 1}
{/if}
{/foreach}
{if $nb_files == 0}
{if $nb_files == 0}
<div class="alert alert-info">
Results folder not synchronized yet...
</div>
{else}
<ul>
{foreach $dir|scandir as $file}
{assign var="link" value=(('fileadmin'|cat:$analyse.directory)|cat:'/')|cat:$file}
{assign var="link" value=(('fileadmin'|cat:'/'|cat:$analyse.directory)|cat:'/')|cat:$file}
{if $file != "." and $file != "" and $file != ".." and ($file|substr:-strlen(".png")) != ".png" and !is_dir($link)}
<li class="filelist"><a href="{$link}">{$file}</a> </li>
{/if}
......@@ -133,9 +133,9 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{/block}
</div>
{/block}
{include file='../comments.tpl' comments=$comments tab_id=$comment_tab add_new_comment=$is_project_admin user_id=$user_id}
{block name=tab_content_update}{/block}
</div>
{/block}
......
ui/nG6/pi1/analyzes/MothurOTU.tpl
View file @ 65ee4b86
{*
Copyright (C) 2009 INRA
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
......@@ -55,7 +55,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{/foreach}
{/foreach}
{assign var="beta_done" value=false}
{* Init tre values *}
{if $tree_avail}
{foreach $levels as $group}
......@@ -73,7 +73,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<li><a href="#parameters" data-toggle="tab">Parameters</a></li>
<li><a href="#downloads" data-toggle="tab">{block name=downloads_title} Downloads {/block}</a></li>
</ul>
<div id="myTabContent" class="tab-content">
<div class="tab-pane fade in active" id="alpha">
<table class="table table-striped table-bordered dataTable analysis-result-table">
......@@ -115,7 +115,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<input type="hidden" id="otus_{$i}_{$group|replace:".":"_"}" value="{$sample_results[$group].otus}"/>
{/if}
{/foreach}
</center></td>
</center></td>
{if $analyse_results|@count > 1 }
<td id="sample_id_{$i}">{$sample|get_description:$descriptions}</td>
{/if}
......@@ -153,13 +153,13 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</tfoot>
</table>
</div>
{if $tree_avail}
<div class="tab-pane fade" id="beta">
<div id="svgCanvas"></div>
</div>
{/if}
<div class="tab-pane fade" id="parameters">
{block name=params}
{block name=params_content}
......@@ -171,19 +171,19 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</div>
<div class="tab-pane fade" id="downloads">
{block name=download}
{if $nb_files != 0}
{if $nb_files != 0}
<p><ul>
{$dir=$data_folder|cat:$analyse.directory}
{$dir=$data_folder|cat:'/'|cat:$analyse.directory}
{assign var="nb_files" value=0}
{foreach $dir|scandir as $file}
{if $file != "." and $file != "" and $file != ".." and ($file|substr:-strlen(".png")) != ".png"}
{$link=(('fileadmin'|cat:$analyse.directory)|cat:'/')|cat:$file}
{$link=(('fileadmin'|cat:'/'|cat:$analyse.directory)|cat:'/')|cat:$file}
<li class="filelist"><a href="{$link}">{$file}</a> </li>
{$nb_files = $nb_files + 1}
{/if}
{/foreach}
</ul></p>
{else}
{else}
<div class="alert alert-info">
Results folder not synchronized yet...
</div>
......
ui/nG6/pi1/analyzes/MothurOTUAnalysis.tpl
View file @ 65ee4b86
{*
Copyright (C) 2009 INRA
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
......@@ -26,7 +26,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<ul>
{foreach from=$params item=param}
{assign var="args_cmd" value=","|explode:$param}
{if in_array("#make.shared(list=FILE.an.list", $args_cmd)}
{foreach from=$args_cmd item=arg_cmd}
{assign var="params_cmd" value="="|explode:$arg_cmd}
......@@ -39,7 +39,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<li class="parameter">{$param}</li>
</ul>
{/if}
{if in_array("#summary.single(shared=FILE.shared", $args_cmd)}
{foreach from=$args_cmd item=arg_cmd}
{assign var="params_cmd" value="="|explode:$arg_cmd}
......@@ -58,7 +58,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<li class="parameter">{$param}</li>
</ul>
{/if}
{if in_array("#rarefaction.single(shared=FILE.shared", $args_cmd)}
{foreach from=$args_cmd item=arg_cmd}
{assign var="params_cmd" value="="|explode:$arg_cmd}
......@@ -71,15 +71,15 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<li class="parameter">{$param}</li>
</ul>
{/if}
{if in_array("#tree.shared(shared=FILE.shared", $args_cmd)}
<li class="parameter">{$param}</li>
{/if}
{if in_array("#sub.sample(fasta=FILE.fasta", $args_cmd)}
<li class="parameter">{$param}</li>
{/if}
{if in_array("#classify.otu(list=FILE.list", $args_cmd)}
{foreach from=$args_cmd item=arg_cmd}
{assign var="params_cmd" value="="|explode:$arg_cmd}
......@@ -124,7 +124,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{/foreach}
{/foreach}
{assign var="beta_done" value=false}
{* Init tre values *}
{if $tree_avail}
{foreach $levels as $group}
......@@ -142,7 +142,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<li><a href="#parameters" data-toggle="tab">Parameters</a></li>
<li><a href="#downloads" data-toggle="tab">{block name=downloads_title} Downloads {/block}</a></li>
</ul>
<div id="myTabContent" class="tab-content">
<div class="tab-pane fade in active" id="alpha">
<table class="table table-striped table-bordered dataTable analysis-result-table">
......@@ -189,7 +189,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<input type="hidden" id="otus_{$i}_{$group|replace:".":"_"}" value="{$sample_results[$group].otus}"/>
{/if}
{/foreach}
</center></td>
</center></td>
{if $analyse_results|@count > 1 }
<td id="sample_id_{$i}">{$sample|get_description:$descriptions}</td>
{/if}
......@@ -230,13 +230,13 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</tfoot>
</table>
</div>
{if $tree_avail}
<div class="tab-pane fade" id="beta">
<div id="svgCanvas"></div>
</div>
{/if}
<div class="tab-pane fade" id="parameters">
{block name=params}
{block name=params_content}
......@@ -249,21 +249,21 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<div class="tab-pane fade" id="downloads">
{block name=download}
{assign var="nb_files" value=0}
{$dir=$data_folder|cat:$analyse.directory}
{$dir=$data_folder|cat:'/'|cat:$analyse.directory}
{foreach $dir|scandir as $file}
{assign var="link" value=(('fileadmin'|cat:$analyse.directory)|cat:'/')|cat:$file}
{assign var="link" value=(('fileadmin'|cat:'/'|cat:$analyse.directory)|cat:'/')|cat:$file}
{if $file != "." and $file != "" and $file != ".." and ($file|substr:-strlen(".png")) != ".png" and !is_dir($link)}
{$nb_files = $nb_files + 1}
{/if}
{/foreach}
{if $nb_files == 0}
{if $nb_files == 0}
<div class="alert alert-info">
Results folder not synchronized yet...
</div>
{else}
<ul>
{foreach $dir|scandir as $file}
{assign var="link" value=(('fileadmin'|cat:$analyse.directory)|cat:'/')|cat:$file}
{assign var="link" value=(('fileadmin'|cat:'/'|cat:$analyse.directory)|cat:'/')|cat:$file}
{if $file != "." and $file != "" and $file != ".." and ($file|substr:-strlen(".png")) != ".png" and !is_dir($link)}
<li class="filelist"><a href="{$link}">{$file}</a> </li>
{/if}
......@@ -274,4 +274,4 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</div>
</div>
{/block}
\ No newline at end of file
{/block}
ui/nG6/pi1/analyzes/RunAssembly.tpl
View file @ 65ee4b86
{*
Copyright (C) 2009 INRA
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
......@@ -33,10 +33,10 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<li><a href="#parameters" data-toggle="tab">{block name=params_title} Parameters {/block}</a></li>
<li><a href="#downloads" data-toggle="tab">{block name=downloads_title} Downloads {/block}</a></li>
</ul>
{assign var="analyse_results_sorted" value=$analyse_results|@ksort}
<div id="myTabContent" class="tab-content">
<div class="tab-pane fade in active" id="general">
{assign var="reads" value=0}
{assign var="bases" value=0}
......@@ -120,8 +120,8 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{/if}
</table>
</div>
{* If not a cdna assembly, display contigs info *}
{if !in_array("-cdna", $params)}
<div class="tab-pane fade" id="contigs">
......@@ -207,7 +207,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{* If it's a cdna assembly display isotigs and isogroups information *}
{else}