Merge pull request #23 from wwPDB/DAOTHER-8398

Created link review section and table. Integration with mol*

wwpdb/apps/ann_tasks_v2/report/PdbxReport.py

@@ -20,12 +20,13 @@
 import sys
 import traceback
 
-from wwpdb.apps.ann_tasks_v2.report.styles.PdbxIo import PdbxReportIo, PdbxGeometryReportIo, PdbxXrayExpReportIo
+from wwpdb.apps.ann_tasks_v2.report.styles.PdbxIo import PdbxReportIo, PdbxGeometryReportIo, PdbxXrayExpReportIo, PdbxLinksReportIo
 from mmcif_utils.style.PdbxGeometryReportCategoryStyle import PdbxGeometryReportCategoryStyle
 
 from wwpdb.apps.ann_tasks_v2.report.PdbxReportDepictBootstrap import PdbxReportDepictBootstrap
 from wwpdb.apps.ann_tasks_v2.report.styles.DCCReport import PdbxXrayExpReportCategoryStyle
 from wwpdb.apps.ann_tasks_v2.report.styles.ModelReport import PdbxReportCategoryStyle
+from wwpdb.apps.ann_tasks_v2.report.styles.LinksReport import PdbxLinksReportCategoryStyle
 
 
 class PdbxReport(object):
@@ -109,6 +110,12 @@ def makeTabularReport(self, filePath=None, contentType=None, idCode=None, layout
                 dd = self.doReport(contentType)
                 rdd = PdbxReportDepictBootstrap(styleObject=PdbxGeometryReportCategoryStyle(), includePath=includePath, verbose=self.__verbose, log=self.__lfh)
                 oL = rdd.render(dd, style=layout, leadingHtmlL=leadingHtmlL, trailingHtmlL=trailingHtmlL)
+
+            if contentType in ["links-report"]:
+                self.setFilePath(filePath, fileFormat=fileFormat, idCode=idCode)
+                dd = self.doReport(contentType)
+                rdd = PdbxReportDepictBootstrap(styleObject=PdbxLinksReportCategoryStyle(), includePath=includePath, verbose=self.__verbose, log=self.__lfh)
+                oL = rdd.render(dd, style=layout, leadingHtmlL=leadingHtmlL, trailingHtmlL=trailingHtmlL)
 
             if self.__debug:
                 self.__lfh.write("+PdbxReport.makeTabularReport - generated HTML \n%s\n" % "\n".join(oL))
@@ -173,6 +180,8 @@ def doReport(self, contentType="model"):
                 pdbxR = PdbxGeometryReportIo(verbose=self.__verbose, log=self.__lfh)
             elif contentType == "dcc-report":
                 pdbxR = PdbxXrayExpReportIo(verbose=self.__verbose, log=self.__lfh)
+            elif contentType == "links-report":
+                pdbxR = PdbxLinksReportIo(verbose=self.__verbose, log=self.__lfh)
 
             pdbxR.setFilePath(localPath, idCode=None)
             pdbxR.get()

wwpdb/apps/ann_tasks_v2/report/PdbxReportDepictBootstrap.py

@@ -28,6 +28,7 @@ class PdbxReportDepictBootstrap(PdbxDepictBootstrapBase):
     This version uses Bootstrap CSS framework constructs.
 
     """
+    MAX_LINES = 12
 
     def __init__(self, styleObject=None, includePath=None, verbose=False, log=sys.stderr):
         """
@@ -96,7 +97,6 @@ def __setup(self):
                 # ('citation','Primary citation','column-wise'),
                 ("pdbx_validate_close_contact", "Close contacts", "row-wise"),
                 ("pdbx_validate_symm_contact", "Close symmetry contacts", "row-wise"),
-                ("struct_conn", "Links", "row-wise"),
                 # ('symmetry', 'Symmetry', 'row-wise'),
                 # ('cell', 'Cell constants', 'row-wise'),
                 # ('exptl_crystal_grow', 'Crystallization details', 'row-wise'),
@@ -132,6 +132,10 @@ def __setup(self):
                 ("pdbx_validate_polymer_linkage", "Polymer linkages", "row-wise"),
                 ("pdbx_validate_chiral", "Chirality exceptions", "row-wise"),
             ]
+        elif self.__st.getStyleId() in ["PDBX_LINKS_REPORT_V1"]:
+            self.__reportCategories = [
+                ("struct_conn", "", "row-wise"),
+            ]
 
     def render(self, eD, style="tabs", leadingHtmlL=None, trailingHtmlL=None):
         """ """
@@ -326,7 +330,11 @@ def __doRenderAccordion(self, eD):
                     oL.append('<a class="accordion-toggle" data-toggle="collapse" data-parent="#%s" href="#%s"><h4>%s</h4></a>' % (idTop, idSection, abbrev))
                 oL.append("</div>")
                 oL.append('<div id="%s" class="accordion-body collapse %s">' % (idSection, active))
-                oL.append('<div  class="accordion-inner">')
+
+                if len(cD[catName]) > PdbxReportDepictBootstrap.MAX_LINES:
+                    oL.append('<div  class="accordion-inner" style="max-height: 50vh; overflow-y: scroll;">')
+                else:
+                    oL.append('<div  class="accordion-inner">')
                 #
                 oL.append('<table class="table table-striped table-bordered table-condensed">')
                 if catStyle == "column-wise":
@@ -530,6 +538,15 @@ def __markupRow(self, catName, rD):
                         itemValue,
                         itemValue,
                     )
+
+        if catName == "struct_conn":
+            itemName = "_struct_conn.id"
+            if itemName in rD:
+                itemValue = rD[itemName]
+                rD[itemName] = '<a href="#" onclick="inspect(\'%s\'); return false;">%s</button>' % (
+                    itemValue.strip(),
+                    itemValue,
+                )
 
     def __attributePart(self, name):
         i = name.find(".")

wwpdb/apps/ann_tasks_v2/report/styles/LinksReport.py

@@ -0,0 +1,39 @@
+"""
+Report style details for PDBx struct_conn category.
+
+"""
+
+
+from mmcif_utils.style.PdbxCategoryStyleBase import PdbxCategoryStyleBase
+
+
+class PdbxLinksReportCategoryStyle(PdbxCategoryStyleBase):
+    _styleId = "PDBX_LINKS_REPORT_V1"
+    _categoryInfo = [
+        ("struct_conn", "table"),
+    ]
+    _cDict = {
+        "struct_conn": [
+            ('_struct_conn.id', '%s', 'str', ''),
+            ("_struct_conn.pdbx_leaving_atom_flag", "%s", "str", ""),
+            ("_struct_conn.ptnr1_auth_asym_id", "%s", "str", ""),
+            ("_struct_conn.ptnr1_auth_comp_id", "%s", "str", ""),
+            ("_struct_conn.ptnr1_auth_seq_id", "%s", "str", ""),
+            ("_struct_conn.ptnr1_symmetry", "%s", "str", ""),
+            ("_struct_conn.ptnr2_auth_asym_id", "%s", "str", ""),
+            ("_struct_conn.ptnr2_auth_comp_id", "%s", "str", ""),
+            ("_struct_conn.ptnr2_auth_seq_id", "%s", "str", ""),
+            ("_struct_conn.ptnr2_symmetry", "%s", "str", ""),
+            ("_struct_conn.pdbx_dist_value", "%s", "str", ""),
+        ],
+    }
+    _excludeList = []
+    _suppressList = []
+    #
+
+    def __init__(self):
+        super(PdbxLinksReportCategoryStyle, self).__init__(styleId=PdbxLinksReportCategoryStyle._styleId,
+                                                              catFormatL=PdbxLinksReportCategoryStyle._categoryInfo,
+                                                              catItemD=PdbxLinksReportCategoryStyle._cDict,
+                                                              excludeList=PdbxLinksReportCategoryStyle._excludeList,
+                                                              suppressList=PdbxLinksReportCategoryStyle._suppressList)

wwpdb/apps/ann_tasks_v2/report/styles/ModelReport.py

@@ -110,7 +110,6 @@ class PdbxReportCategoryStyle(PdbxCategoryStyleBase):
         ("struct_conf", "table"),
         ("struct_conf_type", "table"),
         ("pdbx_struct_mod_residue", "table"),
-        ("struct_conn", "table"),
         ("struct_conn_type", "table"),
         ("struct_ncs_oper", "table"),
         ("struct_sheet", "table"),
@@ -1027,43 +1026,6 @@ class PdbxReportCategoryStyle(PdbxCategoryStyleBase):
             ("_pdbx_struct_mod_residue.parent_comp_id", "%s", "str", ""),
             ("_pdbx_struct_mod_residue.details", "%s", "str", ""),
         ],
-        "struct_conn": [
-            # ('_struct_conn.id', '%s', 'str', ''),
-            ("_struct_conn.conn_type_id", "%s", "str", ""),
-            ("_struct_conn.pdbx_dist_value", "%s", "str", ""),
-            # ('_struct_conn.pdbx_PDB_id', '%s', 'str', ''),
-            # ('_struct_conn.pdbx_ptnr1_mod_name', '%s', 'str', ''),
-            # ('_struct_conn.pdbx_ptnr1_replaced_atom', '%s', 'str', ''),
-            ("_struct_conn.ptnr1_label_asym_id", "%s", "str", ""),
-            ("_struct_conn.ptnr1_label_comp_id", "%s", "str", ""),
-            # ('_struct_conn.ptnr1_label_seq_id', '%s', 'str', ''),
-            ("_struct_conn.ptnr1_auth_seq_id", "%s", "str", ""),
-            ("_struct_conn.ptnr1_label_atom_id", "%s", "str", ""),
-            # ('_struct_conn.pdbx_ptnr1_standard_comp_id', '%s', 'str', ''),
-            ("_struct_conn.ptnr1_symmetry", "%s", "str", ""),
-            ("_struct_conn.ptnr2_label_asym_id", "%s", "str", ""),
-            ("_struct_conn.ptnr2_label_comp_id", "%s", "str", ""),
-            ("_struct_conn.ptnr2_auth_seq_id", "%s", "str", ""),
-            # ('_struct_conn.ptnr2_label_seq_id', '%s', 'str', ''),
-            ("_struct_conn.ptnr2_label_atom_id", "%s", "str", ""),
-            ("_struct_conn.ptnr2_symmetry", "%s", "str", ""),
-            ("_struct_conn.pdbx_ptnr1_label_alt_loc", "%s", "str", ""),
-            ("_struct_conn.pdbx_ptnr1_label_ins_code", "%s", "str", ""),
-            ("_struct_conn.pdbx_ptnr2_label_alt_loc", "%s", "str", ""),
-            ("_struct_conn.pdbx_ptnr2_label_ins_code", "%s", "str", ""),
-            ("_struct_conn.ptnr1_auth_asym_id", "%s", "str", ""),
-            ("_struct_conn.ptnr1_auth_comp_id", "%s", "str", ""),
-            ("_struct_conn.ptnr2_auth_asym_id", "%s", "str", ""),
-            ("_struct_conn.ptnr2_auth_comp_id", "%s", "str", ""),
-            # ('_struct_conn.pdbx_ptnr3_label_atom_id', '%s', 'str', ''),
-            # ('_struct_conn.pdbx_ptnr3_label_seq_id', '%s', 'str', ''),
-            # ('_struct_conn.pdbx_ptnr3_label_comp_id', '%s', 'str', ''),
-            # ('_struct_conn.pdbx_ptnr3_label_asym_id', '%s', 'str', ''),
-            # ('_struct_conn.pdbx_ptnr3_label_alt_loc', '%s', 'str', ''),
-            # ('_struct_conn.pdbx_ptnr3_label_ins_code', '%s', 'str', ''),
-            ("_struct_conn.details", "%s", "str", ""),
-            ("_struct_conn.pdbx_value_order", "%s", "str", ""),
-        ],
         "struct_conn_type": [("_struct_conn_type.id", "%s", "str", ""), ("_struct_conn_type.criteria", "%s", "str", ""), ("_struct_conn_type.reference", "%s", "str", "")],
         "struct_ncs_oper": [
             ("_struct_ncs_oper.id", "%s", "str", ""),

wwpdb/apps/ann_tasks_v2/report/styles/PdbxIo.py

@@ -44,6 +44,7 @@
 
 # from mmcif_utils.style.PdbxReportCategoryStyle import PdbxReportCategoryStyle
 from wwpdb.apps.ann_tasks_v2.report.styles.ModelReport import PdbxReportCategoryStyle
+from wwpdb.apps.ann_tasks_v2.report.styles.LinksReport import PdbxLinksReportCategoryStyle
 
 logger = logging.getLogger()
 
@@ -133,6 +134,56 @@ def getContourLevelMap(self, mapId="primary map"):
             return ""
 
 
+class PdbxLinksReportIo(PdbxStyleIoUtil):
+    """Methods for reading PDBx data files for reporting including style details. Specific to link information."""
+
+    def __init__(self, verbose=True, log=sys.stderr):
+        super(PdbxLinksReportIo, self).__init__(styleObject=PdbxLinksReportCategoryStyle(), verbose=verbose, log=log)
+        self.__lfh = log
+        self.__filePath = None
+        self.__idCode = None
+
+    def getCategory(self, catName="entity"):
+        return self.getItemDictList(catName)
+
+    def setFilePath(self, filePath, idCode=None):
+        """Specify the file path for the target and optionally provide an identifier
+        for the data section within the file.
+        """
+        self.__filePath = filePath
+        self.__idCode = idCode
+        if self.readFile(self.__filePath):
+            if self.__idCode is not None:
+                return self.setContainer(containerName=self.__idCode)
+            else:
+                return self.setContainer(containerIndex=0)
+        else:
+            return False
+
+    def get(self):
+        """
+        Check for a valid current data container.
+
+        Returns True for success or False otherwise.
+        """
+        return self.getCurrentContainerId() is not None
+
+    def complyStyle(self):
+        return self.testStyleComplete(self.__lfh)
+
+    def setBlock(self, blockId):
+        return self.setContainer(containerName=blockId)
+
+    def newBlock(self, blockId):
+        return self.newContainer(containerName=blockId)
+
+    def update(self, catName, attributeName, value, iRow=0):
+        return self.updateAttribute(catName, attributeName, value, iRow=iRow)
+
+    def write(self, filePath):
+        return self.writeFile(filePath)
+
+
 class PdbxGeometryReportIo(PdbxStyleIoUtil):
     """Methods for reading PDBx geometry data files for reporting applications including style details."""
 

wwpdb/apps/ann_tasks_v2/webapp/CommonTasksWebAppWorker.py

@@ -2104,6 +2104,7 @@ def _renderCheckReports(self, entryId, fileSource="archive", instance=None, cont
             "model",
             "dcc-report",
             "geometry-check-report",
+            "links-report",
             "misc-check-report",
             "format-check-report",
             "dict-check-report",
@@ -2185,6 +2186,15 @@ def _renderCheckReports(self, entryId, fileSource="archive", instance=None, cont
                 else:
                     # myD[cT] = self.__getMessageTextWithMarkup('No geometry issues.')
                     myD[cT] = self.__getMessageTextWithMarkup("")
+            elif cT == "links-report":
+                # Links report
+                ok = du.fetchId(entryId, contentType="model", formatType="pdbx", fileSource=fileSource, instance=instance, versionId=versionId)
+                if ok:
+                    downloadPath = du.getDownloadPath()
+                    aTagList.append(du.getAnchorTag())
+                    myD[cT] = "\n".join(pR.makeTabularReport(filePath=downloadPath, contentType="links-report", idCode=entryId, layout=layout))
+                else:
+                    myD[cT] = self.__getMessageTextWithMarkup("")
             elif cT == "misc-check-report":
                 # Misc check report
                 ok = du.fetchId(entryId, contentType="misc-check-report", formatType="txt", fileSource=fileSource, instance=instance)
@@ -2501,6 +2511,15 @@ def _makeCheckReports(self, entryIdList, fileSource="wf-archive", operationList=
                     rptPath = chk.getReportPath()
                     duL.copyToDownload(rptPath)
                     aTagList.append(duL.getAnchorTag())
+
+            if "read-links" in operationList:
+                reader = LinksReader(reqObj=self._reqObj, verbose=self._verbose, log=self._lfh)
+                reader.run(entryId=entryId, inpPath=modelFilePath)
+                hasDiags = chk.getReportSize() > 0
+                if hasDiags:
+                    rptPath = chk.getReportPath()
+                    duL.copyToDownload(rptPath)
+                    aTagList.append(duL.getAnchorTag())
 
             if "check-special-position" in operationList:
                 chk = SpecialPositionCalc(reqObj=self._reqObj, verbose=self._verbose, log=self._lfh)

wwpdb/apps/ann_tasks_v2/webapp/ReviewDataWebAppWorker.py

@@ -332,6 +332,7 @@ def _generateFullCheckReportHtml(self, idCode, fileSource="wf-archive", instance
             "dcc-report",
             "special-position-report",
             "geometry-check-report",
+            "links-report",
             "misc-check-report",
             "format-check-report",
             "dict-check-report",