From 0f8d6e42f0a0a2121feca0bc558b8e0133a9ae7d Mon Sep 17 00:00:00 2001 From: ubyndr Date: Mon, 20 May 2024 14:19:59 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20INCATool?= =?UTF-8?q?s/pandasaurus=5Fcxg@39c382483ec35f496ebbcce85a8d2fde5f1db811=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../graph_generator/graph_generator.html | 14 ++++++- .../graph_generator_utils.html | 35 ++++++++++++++++++ genindex.html | 2 + objects.inv | Bin 1031 -> 1052 bytes .../graph_generator_utils.html | 18 +++++++++ searchindex.js | 2 +- 6 files changed, 69 insertions(+), 2 deletions(-) diff --git a/_modules/pandasaurus_cxg/graph_generator/graph_generator.html b/_modules/pandasaurus_cxg/graph_generator/graph_generator.html index 58574fe..21f35ae 100644 --- a/_modules/pandasaurus_cxg/graph_generator/graph_generator.html +++ b/_modules/pandasaurus_cxg/graph_generator/graph_generator.html @@ -78,7 +78,6 @@

Source code for pandasaurus_cxg.graph_generator.graph_generator

import matplotlib.pyplot as plt import networkx as nx -import pandas as pd from pandasaurus.graph.graph_generator import GraphGenerator as graphgen from rdflib import OWL, RDF, RDFS, BNode, Graph, Literal, Namespace, URIRef from rdflib.plugins.sparql import prepareQuery @@ -92,9 +91,11 @@

Source code for pandasaurus_cxg.graph_generator.graph_generator

add_edge, add_node, add_outgoing_edges_to_subgraph, + citation_field_name, colour_mapping, find_and_rotate_center_layout, generate_subgraph, + parse_citation_field_into_dict, remove_special_characters, select_node_with_property, ) @@ -206,6 +207,17 @@

Source code for pandasaurus_cxg.graph_generator.graph_generator

for key, value in uns.items(): if not isinstance(value, str): continue + if key == citation_field_name: + citation_dict = parse_citation_field_into_dict(value) + for citation_key, citation_value in citation_dict.items(): + self.graph.add( + ( + dataset_class, + URIRef(self.ns[citation_key]), + Literal(citation_value), + ) + ) + self.graph.add((dataset_class, URIRef(self.ns[key]), Literal(value))) has_source = URIRef(HAS_SOURCE["iri"]) self.graph.add((has_source, RDFS.label, Literal(HAS_SOURCE["label"]))) diff --git a/_modules/pandasaurus_cxg/graph_generator/graph_generator_utils.html b/_modules/pandasaurus_cxg/graph_generator/graph_generator_utils.html index 5edb733..4509415 100644 --- a/_modules/pandasaurus_cxg/graph_generator/graph_generator_utils.html +++ b/_modules/pandasaurus_cxg/graph_generator/graph_generator_utils.html @@ -72,6 +72,7 @@

Source code for pandasaurus_cxg.graph_generator.graph_generator_utils

 import re
+from typing import Dict
 
 import networkx as nx
 from rdflib import OWL, RDF, RDFS, BNode, Graph, Literal, Namespace, URIRef
@@ -87,6 +88,8 @@ 
Source code for pandasaurus_cxg.graph_generator.graph_generator_utils
"http://purl.obolibrary.org/obo/PCL_0010001": "cyan",
 }
 
+citation_field_name = "citation"
+
 
 def add_edge(nx_graph: nx.Graph, subject, predicate, obj):
     edge_data = {
@@ -205,6 +208,38 @@ 
Source code for pandasaurus_cxg.graph_generator.graph_generator_utils
def remove_special_characters(input_string: str) -> str:
     return re.sub(r"[^a-zA-Z0-9_]", "", input_string.replace(" ", "_"))
+
+
+

+[docs]
+def parse_citation_field_into_dict(value: str) -> Dict[str, str]:
+    """
+    Parses a citation string into a dictionary by extracting key citation fields.
+
+    Args:
+        value: The string containing citation fields and values.
+
+    Returns:
+        A dictionary with keys such as 'Publication', 'Dataset Version', and 'Collection',
+          and corresponding values extracted from the input string.
+    """
+    # Split the input string on the key terms
+    parts = value.split(" ")
+    keys = ["Publication:", "Version:", "Collection:"]
+    key_indices = [parts.index(key) for key in keys if key in parts]
+    # Break down into key-value pairs
+    key_value_pairs = {}
+    for i, index in enumerate(key_indices):
+        current_value = " ".join(parts[index + 1 : index + 2])
+        key_value_pairs.update(
+            {
+                "download_link"
+                if parts[index][:-1].lower() == "version"
+                else parts[index][:-1].lower(): current_value
+            }
+        )
+    return key_value_pairs

+
diff --git a/genindex.html b/genindex.html index 32200c9..222d978 100644 --- a/genindex.html +++ b/genindex.html @@ -271,6 +271,8 @@

P

  • module
    • +
  • parse_citation_field_into_dict() (in module pandasaurus_cxg.graph_generator.graph_generator_utils) +
    • diff --git a/objects.inv b/objects.inv index 0d8c581db8cf6c596e120c2fc0f8f0c274d86247..3127eaa68959356067b20cffcc4e04f1f5efcdd5 100644 GIT binary patch delta 732 zcmV<20wev02%HFzvjfT`ZoT}OjNsEFJlit!~TT7uuh+y$@YA? zJCk1l8Gk71fTt{+4ct1o0oC+_I{fB#h!HV&2-K7x?eJqJSbRL+(_pHPI8ibIWirf} zo{s^G6MNqCoBl#Lqj})Dtv{g2wJE+JXr`Os`KLZj%zFzR2K7S)U_x4h>;0r$Miqt$ z8I5m?CM0!$0x~7Lp{adBE@M*tgmi`_-a$mxihm>#UV{Kdj8t#NH~ILc9JZyv9nIbG zp(rc~rP$g|oDU00p}qf{iml zF_WDHyBDTyabvH?-Zh*W#(lg=nsPv2heG=mJORJPVl)qz3S?^5GCwe&YtY!p{E}Mj z(0?iwVP1KM@6k5V@eEf?P@9D*R=$S|ZC17=n3K%%J_UjaQQFdCMT4?pz$s?JZew}1 zosMB~h($ZXC82fif9FPR^~PzR?Pz}hYne~t>RQ_xUt_Rg6GGzNOj_f|FI@?DM#}Eu z%Wt-k`)>QV2WhTlD(IC`zHnDEdkxw_?SBP#E8OkOC9G?yVqzx8da_;F1BqcepnImZ z%_)~f`}C+}2wG2$SGRtXBR&-`c|VB~7I`#~4R)L2V1u-w7p{P!#W^ZxogBK&{|2=f zm0>QlC9ws!uyFtW{ME=xrTJF4#PrFk8)c)wr=rFx^?V6e&jdDd-r<*Ii}HilxqtWJ z=$UrC8E?b)dS6CGqCsUxA9Oug^nqwRZ&VQFqe;-?TF{2F?-sEGqpe z76!SjgQ`9$7*(J?z+$Vy?Q%gs@=u+N-b6(&g?`p|uD!L^9eY+pWzDDy`qaHPfW39H z@*-b*gN}UDjnPa^=&I86k-Z0?b18?m#Qeg=sn+?UBe6VYwuKPQ{Gx%VFls9LIj{5N Ozdw>S1pfivN=3$j&2Mc0 delta 711 zcmV;&0yzDg2!{xevj>thd~eA4iIKXA9C4^n`ZoT}OjNsEFJlit!~TT7uuh+y$@YG^ zyOUo58GkD3fTt{+4ct1o0oC+_I{fB#h!HV&2-K7x?eb$LSbRL+(_pGaoG6)qG8yJf z&&PnpiM{XnO@ASr(LC_n(I3#{+7w?9G}BG+e5p?p^WH{>LH$qxn2^@sdOs8-Fc34a* zX0nrD_rkO-ZtV5gr-oC*xQ{nUQx53sP-wq{C*b#3jOO7|flSR><`)KZ4H_Gnf239? zw0}xPm{;E6XS7XpJi`?e)MjCdmG9v~o0V+|<|MPcrzKb%QBmx+2Z z9qkWbE%QlSeKfXu?-*>@gpjxwiB|9QTUWxJez?2&@|$gwzS}P8L7Hos3VNlKFN>AT zUW0Z}d%@ib_wD1-!L?K|F_U9G*`DWt#D6dy&^^=IM(kzLoIENSg4UDc)s5BUh)=~k z*-xT`MIH@ggWV<&*dT4_g)2{JagNGaCx>qHzdI_EZo08e>JjFX?_&$ zyX2EqH_AqVPeqMg>iH6`o(XK^yu&Za7UhE1x%c7dnRdO%Zo~I_y+uW$L1n)jbbmbv z^nqwR9#jzJlSI&?>25>W*Q4(Mxn94FlVD(hXv6Q*ARw1@P}PM5qYBgqSZr0eT`uTH zzSPO+O;q$!=x2TB-dlU!v1dh8){MHKPu*(+*jpznFY>iF=*TzS7|qm#t}0C**?Ryw tPiRZbZ(Q7Joj*Df%VTC+2+_Documentation +
    +pandasaurus_cxg.graph_generator.graph_generator_utils.parse_citation_field_into_dict(value: str) → Dict[str, str][source]
    +

    Parses a citation string into a dictionary by extracting key citation fields.

    +
    +
    Parameters:
    +

    value – The string containing citation fields and values.

    +
    +
    Returns:
    +

    +
    A dictionary with keys such as ‘Publication’, ‘Dataset Version’, and ‘Collection’,

    and corresponding values extracted from the input string.

    +
    +
    +

    +
    +
    +
    + diff --git a/searchindex.js b/searchindex.js index adca3b8..1ffc12c 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"Anndata Analyzer": [[2, "anndata-analyzer"]], "Anndata Enricher": [[3, "anndata-enricher"]], "Anndata Enrichment Analysis": [[4, "anndata-enrichment-analysis"]], "Anndata Loader": [[9, "anndata-loader"]], "Contents:": [[0, null], [7, null], [8, null], [11, null]], "Documentation": [[2, "documentation"], [3, "documentation"], [4, "documentation"], [5, "documentation"], [6, "documentation"], [9, "documentation"], [10, "module-pandasaurus_cxg.utils.exceptions"]], "Exception Module": [[10, "exception-module"]], "Functions": [[6, "module-pandasaurus_cxg.graph_generator.graph_generator_utils"]], "Graph Generator": [[5, "graph-generator"], [7, "graph-generator"]], "Graph Generator Utils": [[6, "graph-generator-utils"]], "Indices and tables": [[0, "indices-and-tables"], [8, "indices-and-tables"]], "Installation": [[1, "installation"]], "Introduction": [[1, "introduction"]], "Library documentation": [[8, "library-documentation"]], "Roadmap": [[1, "roadmap"]], "Snippets": [[1, "id1"]], "Usage": [[1, "usage"]], "Using AnndataEnricher and AnndataAnalyzer Individually": [[1, "using-anndataenricher-and-anndataanalyzer-individually"]], "Using AnndataEnrichmentAnalyzer Wrapper": [[1, "using-anndataenrichmentanalyzer-wrapper"]], "Utils": [[11, "utils"]], "pandasaurus-cxg\u2019s documentation!": [[0, "pandasaurus-cxg-s-documentation"]]}, "docnames": ["index", "introduction", "pandasaurus_cxg/anndata_analyzer", "pandasaurus_cxg/anndata_enricher", "pandasaurus_cxg/enrichment_analysis", "pandasaurus_cxg/graph_generator/graph_generator", "pandasaurus_cxg/graph_generator/graph_generator_utils", "pandasaurus_cxg/graph_generator/index", "pandasaurus_cxg/index", "pandasaurus_cxg/utils/anndata_loader", "pandasaurus_cxg/utils/exception", "pandasaurus_cxg/utils/index"], "envversion": {"sphinx": 61, "sphinx.domains.c": 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