Merge branch 'master' into 'release'

Prepare for v1.1.0

See merge request !29

.gitlab-ci.yml

@@ -99,7 +99,7 @@ deploy-webserver-targetcentric:
     - cd ansible
     - whoami
     - ansible-playbook -vvv -i ./hosts_master deploy.yaml 
-      --extra-vars "deploy_user_name=ippidb repo_api_token=JZS-4cH7bWkFkHa2rAVf marvinjs_apikey=$MARVINJS_APIKEY_targetcentric galaxy_base_url=$GALAXY_BASE_URL_targetcentric galaxy_apikey=$GALAXY_APIKEY_targetcentric galaxy_compoundproperties_workflowid=$GALAXY_COMPOUNDPROPERTIES_WORKFLOWID_targetcentric secret_key=$SECRET_KEY_targetcentric dbname=$DBNAME_targetcentric dbuser=$DBUSER_targetcentric dbpassword=$DBPASSWORD_targetcentric dbhost=$DBHOST_targetcentric dbport=$DBPORT_targetcentric http_port=$HTTP_PORT_targetcentric branch=targetcentric"
+      --extra-vars "deploy_user_name=ippidb repo_api_token=JZS-4cH7bWkFkHa2rAVf marvinjs_apikey=$MARVINJS_APIKEY_targetcentric galaxy_base_url=$GALAXY_BASE_URL_targetcentric galaxy_apikey=$GALAXY_APIKEY_targetcentric galaxy_compoundproperties_workflowid=$GALAXY_COMPOUNDPROPERTIES_WORKFLOWID_targetcentric secret_key=$SECRET_KEY_targetcentric dbname=$DBNAME_targetcentric dbuser=$DBUSER_targetcentric dbpassword=$DBPASSWORD_targetcentric dbhost=$DBHOST_targetcentric dbport=$DBPORT_targetcentric http_port=$HTTP_PORT_targetcentric branch=$CI_COMMIT_REF_NAME gacode=$GACODE_targetcentric ippidb_media=$IPPIDB_MEDIA_targetcentric"
   only:
     - targetcentric
 
@@ -122,7 +122,7 @@ deploy-webserver-test:
     - cd ansible
     - whoami
     - ansible-playbook -vvv -i ./hosts_master deploy.yaml 
-      --extra-vars "deploy_user_name=ippidb repo_api_token=JZS-4cH7bWkFkHa2rAVf marvinjs_apikey=$MARVINJS_APIKEY_master galaxy_base_url=$GALAXY_BASE_URL_master galaxy_apikey=$GALAXY_APIKEY_master galaxy_compoundproperties_workflowid=$GALAXY_COMPOUNDPROPERTIES_WORKFLOWID_master secret_key=$SECRET_KEY_master dbname=$DBNAME_master dbuser=$DBUSER_master dbpassword=$DBPASSWORD_master dbhost=$DBHOST_master dbport=$DBPORT_master http_port=$HTTP_PORT_master branch=$CI_COMMIT_REF_NAME gacode=$GACODE_master"
+      --extra-vars "deploy_user_name=ippidb repo_api_token=JZS-4cH7bWkFkHa2rAVf marvinjs_apikey=$MARVINJS_APIKEY_master galaxy_base_url=$GALAXY_BASE_URL_master galaxy_apikey=$GALAXY_APIKEY_master galaxy_compoundproperties_workflowid=$GALAXY_COMPOUNDPROPERTIES_WORKFLOWID_master secret_key=$SECRET_KEY_master dbname=$DBNAME_master dbuser=$DBUSER_master dbpassword=$DBPASSWORD_master dbhost=$DBHOST_master dbport=$DBPORT_master http_port=$HTTP_PORT_master branch=$CI_COMMIT_REF_NAME gacode=$GACODE_master ippidb_media=$IPPIDB_MEDIA_master"
   only:
     - master
 
@@ -145,6 +145,6 @@ deploy-webserver-production:
     - cd ansible
     - whoami
     - ansible-playbook -vvv -i ./hosts_release deploy.yaml 
-      --extra-vars "deploy_user_name=ippidb repo_api_token=JZS-4cH7bWkFkHa2rAVf marvinjs_apikey=$MARVINJS_APIKEY_release galaxy_base_url=$GALAXY_BASE_URL_release galaxy_apikey=$GALAXY_APIKEY_release galaxy_compoundproperties_workflowid=$GALAXY_COMPOUNDPROPERTIES_WORKFLOWID_release secret_key=$SECRET_KEY_release dbname=$DBNAME_release dbuser=$DBUSER_release dbpassword=$DBPASSWORD_release dbhost=$DBHOST_release dbport=$DBPORT_release http_port=$HTTP_PORT_release branch=$CI_COMMIT_REF_NAME  gacode=$GACODE_release"
+      --extra-vars "deploy_user_name=ippidb repo_api_token=JZS-4cH7bWkFkHa2rAVf marvinjs_apikey=$MARVINJS_APIKEY_release galaxy_base_url=$GALAXY_BASE_URL_release galaxy_apikey=$GALAXY_APIKEY_release galaxy_compoundproperties_workflowid=$GALAXY_COMPOUNDPROPERTIES_WORKFLOWID_release secret_key=$SECRET_KEY_release dbname=$DBNAME_release dbuser=$DBUSER_release dbpassword=$DBPASSWORD_release dbhost=$DBHOST_release dbport=$DBPORT_release http_port=$HTTP_PORT_release branch=$CI_COMMIT_REF_NAME  gacode=$GACODE_release ippidb_media=$IPPIDB_MEDIA_release"
   only:
     - release

ansible/deploy.yaml

@@ -231,6 +231,12 @@
           GA_CODE = "{{ gacode }}"
         marker: "# {mark} ANSIBLE MANAGED GOOGLE ANALYTICS ID"
       when: gacode is defined
+    - name: Add media_url setting to iPPI-DB settings
+      blockinfile:
+        path: "{{ checkout_path }}/ippisite/ippisite/{{ ansible_hostname }}_settings.py"
+        block: |
+          MEDIA_URL = "{{ ippidb_media }}"
+        marker: "# {mark} ANSIBLE MEDIA_URL SETTINGS"
     - name: Add email/debug settings to iPPI-DB settings
       blockinfile:
         path: "{{ checkout_path }}/ippisite/ippisite/{{ ansible_hostname }}_settings.py"
@@ -326,6 +332,10 @@
       lineinfile: dest="{{ service_conf_path }}/httpd.conf" 
                   insertbefore=BOF
                   line="LimitRequestLine 32000"
+    - name: add httpd conf to set larger POST requests body
+      lineinfile: dest="{{ service_conf_path }}/httpd.conf" 
+                  regex='^LimitRequestBody'
+                  line="LimitRequestBody 104857600"
     - name: copy systemd service file for IPPIDB-web
       template: 
         src: "ippidb-web.service" 
@@ -339,13 +349,21 @@
       become: true
     - name: Enable firewalld
       service: name=firewalld state=started enabled=yes
-    - name: open http firewall port
+    - name: open http firewall service
       firewalld:
         service: http
         zone: public
         immediate: yes
         permanent: true
         state: enabled
+    - name: open http firewall port
+      firewalld:
+        port: "{{ http_port }}/tcp"
+        zone: public
+        permanent: true
+        immediate: yes
+        state: enabled
+        
     #
     # Start web server
     #

ansible/system.yaml

@@ -52,6 +52,6 @@
       become: true
     - name: Open firwall to port 80 81 traffic
       firewalld:
-        port: 80-81/tcp
+        port: "{{ http_port }}/tcp"
         permanent: true
         state: enabled

ippisite/docs/source/conf.py

@@ -19,24 +19,26 @@ import os
 import sys
 
 import matplotlib
+
 # avoid using tkinter with matplotlib
-matplotlib.use('agg')
+matplotlib.use("agg")
 
-sys.path.insert(0, os.path.abspath('../..'))
+sys.path.insert(0, os.path.abspath("../.."))
 import django
-os.environ['DJANGO_SETTINGS_MODULE'] = 'ippisite.settings'
+
+os.environ["DJANGO_SETTINGS_MODULE"] = "ippisite.settings"
 django.setup()
 
 # -- Project information -----------------------------------------------------
 
-project = 'iPPI-DB'
-copyright = '2018, Rachel Torchet, Alexandra Moine-Franel, Hélène Borges, Bryan Brancotte, Olivia Doppelt-Azeroual, Fabien Mareuil, Hervé Ménager, Olivier Sperandio'
-author = 'Rachel Torchet, Alexandra Moine-Franel, Hélène Borges, Bryan Brancotte, Olivia Doppelt-Azeroual, Fabien Mareuil, Hervé Ménager, Olivier Sperandio'
+project = "iPPI-DB"
+copyright = "2018, Rachel Torchet, Alexandra Moine-Franel, Hélène Borges, Bryan Brancotte, Olivia Doppelt-Azeroual, Fabien Mareuil, Hervé Ménager, Olivier Sperandio"
+author = "Rachel Torchet, Alexandra Moine-Franel, Hélène Borges, Bryan Brancotte, Olivia Doppelt-Azeroual, Fabien Mareuil, Hervé Ménager, Olivier Sperandio"
 
 # The short X.Y version
-version = ''
+version = ""
 # The full version, including alpha/beta/rc tags
-release = ''
+release = ""
 
 
 # -- General configuration ---------------------------------------------------
@@ -49,26 +51,26 @@ release = ''
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autosummary',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.coverage',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.graphviz',
-    'sphinxcontrib.bibtex'
+    "sphinx.ext.autosummary",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.coverage",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.graphviz",
+    "sphinxcontrib.bibtex",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -91,7 +93,7 @@ pygments_style = None
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 
 # Theme options are theme-specific and customize the look and feel of a theme
@@ -103,7 +105,7 @@ html_theme = 'sphinx_rtd_theme'
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -119,7 +121,7 @@ html_static_path = ['_static']
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'iPPI-DBdoc'
+htmlhelp_basename = "iPPI-DBdoc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -128,15 +130,12 @@ latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -146,8 +145,13 @@ latex_elements = {
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'iPPI-DB.tex', 'iPPI-DB Documentation',
-     'Rachel Torchet, Alexandra Moine-Franel, Hélène Borges, Bryan Brancotte, Olivia Doppelt-Azeroual, Fabien Mareuil, Hervé Ménager, Olivier Sperandio', 'manual'),
+    (
+        master_doc,
+        "iPPI-DB.tex",
+        "iPPI-DB Documentation",
+        "Rachel Torchet, Alexandra Moine-Franel, Hélène Borges, Bryan Brancotte, Olivia Doppelt-Azeroual, Fabien Mareuil, Hervé Ménager, Olivier Sperandio",
+        "manual",
+    ),
 ]
 
 
@@ -155,10 +159,7 @@ latex_documents = [
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'ippi-db', 'iPPI-DB Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "ippi-db", "iPPI-DB Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -167,9 +168,15 @@ man_pages = [
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'iPPI-DB', 'iPPI-DB Documentation',
-     author, 'iPPI-DB', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "iPPI-DB",
+        "iPPI-DB Documentation",
+        author,
+        "iPPI-DB",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 
@@ -188,7 +195,7 @@ epub_title = project
 # epub_uid = ''
 
 # A list of files that should not be packed into the epub file.
-epub_exclude_files = ['search.html']
+epub_exclude_files = ["search.html"]
 
 
 # -- Extension configuration -------------------------------------------------
@@ -196,16 +203,16 @@ epub_exclude_files = ['search.html']
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {"https://docs.python.org/": None}
 
 # -- Extension configuration -------------------------------------------------i
 
 autoclass_content = "both"  # include both class docstring and __init__
 autodoc_default_flags = [
-        # Make sure that any autodoc declarations show the right members
-        "members",
-        "private-members",
-        "show-inheritance",
+    # Make sure that any autodoc declarations show the right members
+    "members",
+    "private-members",
+    "show-inheritance",
 ]
 autosummary_generate = True  # Make _autosummary files and include them
 napoleon_numpy_docstring = False  # Force consistency, leave only Google
@@ -213,11 +220,11 @@ napoleon_use_rtype = False  # More legible
 
 # The suffix of source filenames.
 autosummary_generate = True
-exclude_patterns = ['_build']
+exclude_patterns = ["_build"]
 
-#do not try to import tkinter for sphinx
-autodoc_mock_imports = ['_tkinter']
+# do not try to import tkinter for sphinx
+autodoc_mock_imports = ["_tkinter"]
 
 bibtex_bibfiles = [
-    'refs.bib',
+    "refs.bib",
 ]

ippisite/ippidb/admin.py

@@ -28,7 +28,16 @@ from .models import (
     Ppi,
     ProteinDomainComplex,
     Contribution,
+    Cavity,
+    Chain,
+    PDB,
+    Ligand,
+    InteractFile,
+    Partner,
+    Distance,
+    MetaInformation,
     Job,
+    Network,
 )
 from .tasks import launch_validate_contributions
 
@@ -62,6 +71,124 @@ class ViewOnSiteModelAdmin(admin.ModelAdmin):
     )
 
 
+@admin.register(Network)
+class NetworkAdmin(admin.ModelAdmin):
+    list_display = ("label", "number", "jsonfile", "default")
+    search_fields = ("label",)
+
+
+@admin.register(PDB)
+class PDBAdmin(admin.ModelAdmin):
+    list_display = ("code", "chains_info")
+    search_fields = ("code",)
+
+    def chains_info(self, obj):
+        return "\t".join(
+            [
+                "{}: {}".format(chain.pdb_chain_id, chain.protein.uniprot_id)
+                for chain in obj.chain_set.all()
+            ]
+        )
+
+
+@admin.register(Chain)
+class ChainAdmin(admin.ModelAdmin):
+    list_display = ("pdb_chain_id", "pdb_code", "protein")
+    search_fields = ("pdb_chain_id", "pdb__code", "protein__uniprot_id")
+    list_filter = ("pdb_chain_id", "protein__organism__name")
+    # if pdb is asked request never return
+    readonly_fields = ("pdb",)
+
+    def pdb_code(self, obj):
+        return obj.pdb.code
+
+
+@admin.register(InteractFile)
+class InteractFileAdmin(admin.ModelAdmin):
+    list_display = ("chain_info", "label")
+    list_filter = ("label",)
+    search_fields = ("chain__protein__uniprot_id",)
+    # if chain is asked request never return
+    readonly_fields = ("chain",)
+
+    def chain_info(self, obj):
+        return "{} {} {}".format(
+            obj.chain.pdb.code, obj.chain.pdb_chain_id, obj.chain.protein.uniprot_id
+        )
+
+
+@admin.register(Ligand)
+class LigandAdmin(admin.ModelAdmin):
+    list_display = (
+        "iupac_name",
+        "pdb_ligand_id",
+        "supplementary_id",
+        "pdb_code",
+    )
+    list_filter = ("pdb_ligand_id",)
+    search_fields = ("pdb_ligand_id", "supplementary_id", "pdb__code")
+    readonly_fields = ("pdb",)
+
+    def pdb_code(self, obj):
+        return obj.pdb.code
+
+
+@admin.register(Partner)
+class PartnerAdmin(admin.ModelAdmin):
+    list_display = ("partner",)
+    readonly_fields = ("chain", "ligand")
+
+    def partner(self, obj):
+        if obj.ligand:
+            return "Type: ligand, {}_{} {}".format(
+                obj.ligand.pdb_ligand_id,
+                obj.ligand.supplementary_id,
+                obj.ligand.pdb.code,
+            )
+        else:
+            return "Type: protein, {} {}".format(
+                obj.chain.protein.uniprot_id, obj.chain.pdb.code
+            )
+
+
+@admin.register(Cavity)
+class CavityAdmin(admin.ModelAdmin):
+    list_display = ("full_name", "info")
+    search_fields = ("full_name",)
+    list_filter = ("chain__protein__organism__name",)
+    readonly_fields = ("chain", "partner")
+
+    def info(self, obj):
+        if obj.partner.ligand:
+            return "Cavity {} from {} with {}_{} in {}".format(
+                obj.cavity_number,
+                obj.chain.protein.uniprot_id,
+                obj.partner.ligand.pdb_ligand_id,
+                obj.partner.ligand.supplementary_id,
+                obj.chain.pdb.code,
+            )
+        else:
+            return "Cavity {} from {} with {} in {}".format(
+                obj.cavity_number,
+                obj.chain.protein.uniprot_id,
+                obj.partner.chain.protein.uniprot_id,
+                obj.chain.pdb.code,
+            )
+
+
+@admin.register(Distance)
+class DistanceAdmin(admin.ModelAdmin):
+    list_display = ("similiarity_between", "distance")
+
+    def similiarity_between(self, obj):
+        return "{} and {}".format(obj.cavity1.full_name, obj.cavity2.full_name)
+
+
+@admin.register(MetaInformation)
+class MetaInformationAdmin(admin.ModelAdmin):
+    list_display = ("average", "std", "maximum", "minimum", "normalize_factor")
+
+
 @admin.register(Job)
 class JobModelAdmin(admin.ModelAdmin):
     date_hierarchy = "task_result__date_done"

ippisite/ippidb/forms.py

@@ -551,7 +551,9 @@ TYPE_MOLECULE = (("smiles", "smiles"), ("iupac", "iupac"), ("sketch", "sketch"))
 
 class CompoundForm(forms.Form):
     compound_name = forms.CharField(
-        label=_("compound_name_label"), required=True, help_text=_(""),
+        label=_("compound_name_label"),
+        required=True,
+        help_text=_(""),
     )
     ligand_id = forms.CharField(
         label=_("PDB Ligand ID"),
@@ -805,7 +807,11 @@ class BaseInlineNestedFormSet(forms.BaseInlineFormSet):
 class CompoundActivityResultForm(ModelForm):
     compound_name = forms.ChoiceField(choices=(), required=True)
     activity_mol = forms.DecimalField(
-        label="Activity", required=True, max_digits=15, decimal_places=10, min_value=0,
+        label="Activity",
+        required=True,
+        max_digits=15,
+        decimal_places=10,
+        min_value=0,
     )
     activity_unit = forms.CharField(
         label="Activity unit",
@@ -1014,7 +1020,8 @@ CompoundActivityResultInlineFormset = inlineformset_factory(
 class TestActivityDescriptionForm(forms.ModelForm):
 
     test_name = CharFieldDataList(
-        data_class=models.TestActivityDescription, data_attr="test_name",
+        data_class=models.TestActivityDescription,
+        data_attr="test_name",
     )
 
     cell_line_name = CharFieldDataList(
@@ -1395,7 +1402,9 @@ class CompoundPKResultForm(ModelForm):
         super().__init__(*args, **kwargs)
         for f in self.fields.values():
             f.widget.attrs.update({"class": "col-3"})
-            if isinstance(f, forms.BooleanField) and not isinstance(f.widget, forms.Select):
+            if isinstance(f, forms.BooleanField) and not isinstance(
+                f.widget, forms.Select
+            ):
                 f.widget.attrs.update({"class": "col-3 mb-4"})
 
     def has_changed(self):

ippisite/ippidb/management/commands/__init__.py

+from django.core.management.base import OutputWrapper
+
+
+class TaskOutWrapper(OutputWrapper):
+    """
+    OutWrapper with celery task object, allow to update
+    std_out and std_err in django database Job
+    """
+
+    def __init__(
+        self, out, style_func=None, ending="\n", task=None, std_out=None, std_err=None
+    ):
+        super(TaskOutWrapper, self).__init__(out, style_func=style_func, ending=ending)
+        self.task = task
+        self.std_out = std_out
+        self.std_err = std_err
+
+    def write(self, msg, style_func=None, ending=None):
+        super(TaskOutWrapper, self).write(msg, style_func=style_func, ending=ending)
+        if self.task:
+            if self.std_out:
+                self.task.write(std_out=msg, with_print=False)
+            else:
+                self.task.write(std_err=msg, with_print=False)

ippisite/ippidb/management/commands/clean_targetcentric.py

+from django.core.management.base import AppCommand
+from ippidb.models.targetcentric import (
+    Cavity,
+    Chain,
+    PDB,
+    Partner,
+)
+from ippidb.management.commands import TaskOutWrapper
+from celery import states
+import os
+import sys
+import pandas as pd
+
+"""
+Command to clean targetcentric databases from cavities to Protein
+"""
+
+
+def file_exist(string):
+    """
+    Test if a file exist
+    """
+    if os.path.exists(string):
+        return string
+    else:
+        raise FileNotFoundError(string)
+
+
+class Command(AppCommand):
+    """
+    Command to clean targetcentric databases from cavities to Protein
+    """
+
+    help = "Load Cavities from global csv file and delete all Cavities not present in the csv"
+
+    def __init__(
+        self, stdout=None, stderr=None, no_color=False, force_color=False, task=None,
+    ):
+        super(Command, self).__init__(
+            stdout=stdout, stderr=stderr, no_color=no_color, force_color=force_color
+        )
+        if task:
+            task.update_state(state=states.STARTED)
+            self.stdout = TaskOutWrapper(stdout or sys.stdout, task=task, std_out=True)
+            self.stderr = TaskOutWrapper(stderr or sys.stderr, task=task, std_err=True)
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "-c", "--csv", type=file_exist, help="cavities descriptors file, csv format"
+        )
+        parser.add_argument(
+            "-d",
+            "--delete",
+            dest="delete",
+            action="store_true",
+            help="If not flagged only list cavities present in the database and not present in the csv file",
+        )
+
+    def handle(self, *args, **options):
+        """
+        Perform the command's actions
+        """
+        database_cavities = Cavity.objects.all()
+        delete = options["delete"]
+        current_cavities = []
+        csv = pd.read_csv(options["csv"], sep=",")
+        clean = 0
+        for index, row in csv.iterrows():
+            current_cavities.append(row["Cavity"])
+        for cavity in database_cavities:
+            if cavity.full_name not in current_cavities:
+                clean = 1
+                self.stdout.write(
+                    self.style.WARNING(
+                        "WARNING {} doesn't exist in csv file".format(cavity.full_name)
+                    )
+                )
+                if delete:
+                    cavity.delete()
+        if not clean:
+            self.stdout.write(self.style.SUCCESS("No Cavity to remove"))
+
+        chains = Chain.objects.filter(cavity=None, partner=None)
+        clean = 0
+        for chain in chains:
+            try:
+                partner = Partner.objects.get(chain=chain.id)
+            except Partner.DoesNotExist:
+                partner = None
+            if not chain.cavity_set.count() and not partner:
+                clean = 1
+                self.stdout.write(
+                    self.style.WARNING(
+                        "WARNING {} {} is not implicated in a cavity".format(
+                            chain.pdb.code, chain.pdb_chain_id
+                        )
+                    )
+                )
+                if delete:
+                    chain.delete()
+        if not clean:
+            self.stdout.write(self.style.SUCCESS("No Chain to remove"))
+
+        pdbs = PDB.objects.filter(chain=None)
+        clean = 0
+        for pdb in pdbs:
+            if not pdb.chain_set.count():
+                clean = 1
+                self.stdout.write(
+                    self.style.WARNING(
+                        "WARNING {} has no linked chain".format(pdb.code)
+                    )
+                )
+                if delete:
+                    pdb.delete()